Development and deployment of versatile digital platforms for 'omics-based data sharing and analysis
Lead Research Organisation:
Earlham Institute
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
E-Infrastructure (and in particular, its high-performance computing (HPC) component) has become a primary platform underpinning modern, collaborative science. Following development of high-throughput ‘omics technologies, the community is challenging traditional HPC-heavy domains with their demand for resources, services and capability. Access to HPC resources has typically been limited to expert bioinformaticians and data scientists, with a steep learning curve for anyone outside these fields.
The National Capability in e-Infrastructure (NC3) encompasses the integration and interconnection of computational hardware and software technology, data resources and services, communications protocols and networks, as well as experienced teams and organisational structures required to support modern, internationally leading collaborative research.
EI significantly values the impact of empowering collaborative research via world-class high-performance computing (HPC) technology. As part of our core capability through our HPC Scientific Services for EI we deploy and maintain some of the largest HPC systems for Life Science research in Europe. By having this expertise in HPC, software development and network design we can enable and collaborate with others in the scientific community via the development and deployment of versatile digital platforms for 'omics-based data sharing and discovery.
NC3 will build upon the work in the current National Capability at EI where four e-Infrastructure platforms are being developed to support collaborative data analysis and sharing with national and international user bases:
? Large genome assembly including wheat and other cereals. The SGI UV systems at EI support the software assembly of genomes requiring up to 12 Terabytes of shared RAM in a single system
? CyVerse UK, the first federated node outside the US of the international CyVerse cyberinfrastructure project
? UK-SeeD, a Galaxy-based e-Infrastructure platform developed at EI for the advanced analysis of genotyping data in association with the international CIMMYT Seeds of Discovery project.
? SignaLink, a curated database of intertwined biological pathways integrated with regulatory networks, utilising novel modelling techniques to allow systems-level analysis of major intracellular signalling pathways in model species and human.
The National Capability in e-Infrastructure (NC3) encompasses the integration and interconnection of computational hardware and software technology, data resources and services, communications protocols and networks, as well as experienced teams and organisational structures required to support modern, internationally leading collaborative research.
EI significantly values the impact of empowering collaborative research via world-class high-performance computing (HPC) technology. As part of our core capability through our HPC Scientific Services for EI we deploy and maintain some of the largest HPC systems for Life Science research in Europe. By having this expertise in HPC, software development and network design we can enable and collaborate with others in the scientific community via the development and deployment of versatile digital platforms for 'omics-based data sharing and discovery.
NC3 will build upon the work in the current National Capability at EI where four e-Infrastructure platforms are being developed to support collaborative data analysis and sharing with national and international user bases:
? Large genome assembly including wheat and other cereals. The SGI UV systems at EI support the software assembly of genomes requiring up to 12 Terabytes of shared RAM in a single system
? CyVerse UK, the first federated node outside the US of the international CyVerse cyberinfrastructure project
? UK-SeeD, a Galaxy-based e-Infrastructure platform developed at EI for the advanced analysis of genotyping data in association with the international CIMMYT Seeds of Discovery project.
? SignaLink, a curated database of intertwined biological pathways integrated with regulatory networks, utilising novel modelling techniques to allow systems-level analysis of major intracellular signalling pathways in model species and human.
Planned Impact
unavailable
Organisations
- Earlham Institute (Lead Research Organisation)
- The Carpentries (Collaboration)
- Texas Advanced Computing Center (Collaboration)
- UNIVERSITY OF BRISTOL (Collaboration)
- University of California, Davis (Collaboration)
- Monogram Network (Collaboration)
- Johns Hopkins University (Collaboration)
- University of Leuven (Collaboration)
- French National Institute of Agricultural Research (Collaboration)
- U.S. Department of Agriculture USDA (Collaboration)
- EMBL European Bioinformatics Institute (EMBL - EBI) (Collaboration)
- John Innes Centre (Collaboration)
- Penn State University (Collaboration)
- Helmholtz Association of German Research Centres (Collaboration)
- UNIVERSITY OF ARIZONA (Collaboration)
- University of Graz (Collaboration)
- DivSeek International (Collaboration)
- ELIXIR (Collaboration)
- Albert Ludwig University of Freiburg (Collaboration)
- Curie Institute Paris (Institut Curie) (Collaboration)
- University of Luxembourg (Collaboration)
- University of Western Australia (Collaboration)
- Oregon Health and Science University (Collaboration)
- Oxford Nanopore Technologies (Collaboration)
- International Centre for Maize and Wheat Improvement (CIMMYT) (Collaboration)
- DIGITAL CATAPULT (Collaboration)
- International Livestock Research Institute (ILRI) (Collaboration)
- Rothamsted Research (Collaboration)
- Eagle Genomics Ltd (Collaboration)
- Cleveland Clinic (Collaboration)
- Cold Spring Harbor Laboratory (CSHL) (Collaboration)
People |
ORCID iD |
| Nicola Soranzo (Principal Investigator) |
Publications
Afgan E
(2018)
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.
in Nucleic acids research
Batut B
(2021)
RNA-Seq Data Analysis in Galaxy.
in Methods in molecular biology (Clifton, N.J.)
Batut B
(2018)
Community-Driven Data Analysis Training for Biology.
in Cell systems
Batut B
(2017)
Community-driven data analysis training for biology
Berger Gillam T
(2021)
Phase 2 of the Norwich COVID-19 testing initiative: an evaluation.
in Journal of public health (Oxford, England)
| Description | We have deployed and maintained since 2015 a Galaxy server, used by researchers at the Earlham Institute and at the Quadram Institute. Over 600 different tools are available, enabling various types of bioinformatics analysis such as phylogenetics, RNA-Seq, variant analysis, single-cell RNA-Seq, genome annotation, de novo assembly, metagenomics and computational chemistry. In 2020 the migration of the Galaxy backend source code from Python 2 to Python 3 was finally concluded, a project that we have been leading since 2016, and whose conclusion is now enabling the modernisation of the framework (asynchronous web server, OpenAPI support, type annotation). The CyVerse UK hardware and software has been deployed and made available to the public in 2016, allowing researchers to run bioinformatics applications registered on the platform. A dedicated storage system, federated with the parent CyVerse project, is also available for researchers to store their data and seamlessly share them with collaborators across geographic boundaries. In 2019 a public iRODS storage system federated with CyVerse US was made available. It provides storage of data that CyVerse users can share with collaborators or the public, as well as a Data Commons repository for curated DFW data. In 2018 the CyVerse UK cloud was used for the first time to provide virtual machines for a hands-on bioinformatics training in Kenya. Since then, we have expanded our training virtual infrastructure to support EI training courses that require trainees to work in an online virtual environment. The setup is such that both internal and external trainers can cooperate in the creation of a training image that can be used for multiple courses, storing data on the EI system, and trainees have access to a ready-to-use desktop-like environment with all relevant software and data pre-installed. This setup can support both training on site and virtual courses, and has been used for several computational courses run by EI over the following years. In 2021, to help with the switch to virtual training due to the pandemic, an Apache Guacamole server for training was established as a gateway to provide web-based access to remote desktop machines and command-line environments. This additional service has been used for the following EI training workshops: Genome Annotation 2021 (17 attendees), Nanopore Metagenomics 2022 (19), Genome annotation 2022 (20) and Single Cell RNAseq 2022 (19 attendees). Due to the flexibility of our CyVerse UK virtual cloud platform, in 2020 we were quickly able to set up the required infrastructure to manage the sending of Norwich Testing Initiative (NTI) COVID test result data to the University of East Anglia central database for pushing to those tested (https://doi.org/10.1093/pubmed/fdaa194). We are offering custom cloud resources to life science researchers, and have been receiving enquiries about complex services. Currently, we are hosting for external users 3 web services open to the community and have provided multiple virtual machines for development and research. Users who need a significant amount of resources for their analyses are given the possibility to submit jobs to the Cyverse UK HTCondor queue, to make the best use of available resources. The e-infrastructure also continues to host and support several web services developed by researchers at EI (COPO, CKAN, LotuS2, the KSGP database, SignaLink, Autophagy Regulatory Network, NRF2ome, TGAC Browser for wheat deletions and tilling, the Grassroots Infrastructure). The cloud is also hosting Sherlock, a data platform developed in the Korcsmaros group (EI CSP WP2) that helps researchers storing and converting databases to a common queryable format. In 2021 we temporarily hosted on CyVerse UK the online Bee Trail Game (https://www.earlham.ac.uk/the-bee-trail) for the Royal Society Summer Exhibition event (https://royalsociety.org/science-events-and-lectures/2021/summer-science-exhibition/). CyVerse UK has continued to support web hosting services and was able to provide requests for resources from researchers. Recently added web services are MARTi, a software package for performing real-time analysis of metagenomic samples using nanopore sequencing (https://marti.cyverseuk.org/), and readuntil, a web application that implements a predictive model of adaptive sampling, a method of software-controlled nanopore enrichment (https://readuntil.cyverseuk.org/). In collaboration with CyVerse US and CyVerse Austria, we created a Massively Open Online Course (MOOC, https://cyverse-learning-materials.github.io/cyverse_mooc/) for CyVerse, comprising a suite of short videos and training documents. Updates on the iRODs server's were successfully implemented, and gradually, we are building up our own Discovery Environment and another Apache Guacamole server as an access gateway for external collaborators. Since 2017, our work on Galaxy and related technologies have underpinned the publication of 12 peer-reviewed papers and a book chapter. In the last year, our group kept delivering several training workshops about Galaxy and basic computational skills: "Galaxy Admin Training 2023" (Gent, Belgium), "NRPDTP Student Elective: Artificial Intelligence and Advanced Digital Literacy" (EI), "Software Carpentry December 2023" (EI), "Data Carpentry 2024" (EI). We also led projects at the European Galaxy Days 2023 CoFest (University of Freiburg, Germany) and BioHackathon Europe 2023 (La Roca del Vallès, Spain). Since 2018, we have increased our involvement with ELIXIR (the intergovernmental organisation that brings together life science resources from across Europe) by attending several ELIXIR-sponsored events and with the appointment of Dr N. Soranzo as Technical Coordinator for the ELIXIR-UK Node. Since the end of 2020, Dr. Soranzo has also been one of the Co-Leads of the ELIXIR Galaxy Community. We participated in a workshop finalising the definition of an extended vocabulary to enable storing causal information (activation/inhibition) in the standard PSI-MI file format, to improve the application of the SignaLink data to more modelling problems. We recently published an updated version of SignaLink (SignaLink3) in which the users can download interactions based on tissue-specificity and also involving multiple non-coding RNAs (miRNAs, lncRNAs) (doi: 10.1093/nar/gkab909). These new features demonstrate an important connection to the EI CSP WP2 where the methodology to identify and analyse such interactions were partially developed. Using SignaLink as a basis, we set up two web resources on virtual machines inside CyVerse UK: the Autophagy Regulatory Network and NRF2ome - two gap filling resources targeting the autophagy and oxidative stress research communities, respectively. We have co-developed the new version of OmniPath, an integrated signalling network resource that provides one-stop-shop access to nearly 100 biological network and annotation resources via API, R, Python or Cytoscape. The new OmniPath contains cell-cell interaction data as well, enabling the functional analysis of single-cell sequence datasets of interaction cells (doi: 10.15252/msb.20209923). |
| Exploitation Route | The GeneSeqToFamily pipeline is now in use to investigate gene families in two large scale projects - DFW for the 14+ wheat varieties, and the 200+ mammal genomes through VGP and the Haerty group. In line with EI's strong commitment to Open Science, we have been contributing to several open-source projects, in particular Galaxy and its ecosystem (e.g. BioBlend, Bioconda). We have also contributed to the integration of several tools into Galaxy, the development of Galaxy training materials and provided support for external issues not relevant to our own Galaxy instances but those of the wider community. This benefits the whole Galaxy community, globally, so has a huge impact on the sustainability of the platform. A software library we maintain as part of the Galaxy ecosystem support, BioBlend, has been a fundamental building block of a COVID-19 genome surveillance project which regularly ran reproducible analysis workflows on the European Galaxy server to monitor the genome sequences published by the COVID-19 Genomics UK Consortium (COG-UK) for important data such as provenance and variants present. CyVerse UK gives users from a range of disciplines the ability to access a large and flexible cyberinfrastructure environment to carry out analysis, and to share data. The flexibility lends itself to the deployment of virtualised services also running within the same infrastructure, allowing EI and partners to deliver public web services to communities that are attached to HPC technology. SignaLink, ARN and NRF2ome provides a reusable database and interface for mining signalling and regulatory networks, freely accessible for international researchers. As CyVerse UK, we have collaborated with researchers at TU Graz (Austria) in the deployment of CyVerse as a standalone solution for their researchers. We teamed up with CyVerse US and CyVerse Austria to create a massive open online course (MOOC, https://cyverse-learning-materials.github.io/cyverse_mooc/) for self-guided students, covering the basics of data management and analysis in CyVerse. This is a perfect starting point for new users to get a basic understanding of how their computational workflows and data lifecycles can work in CyVerse. |
| Sectors | Agriculture Food and Drink Digital/Communication/Information Technologies (including Software) Education |
| URL | https://www.earlham.ac.uk/research-e-infrastructure |
| Description | The impact of this capability has been demonstrated in the dedicated support it has given to critical objectives within major UK research programmes. The CyVerse UK cyberinfrastructure is currently hosting projects that are vital to support major Institute and national projects, i.e. COPO for EI strategy and DTOL, ASG and ERGA, the Designing Future Wheat Grassroots infrastructure, the LotuS2 software, as well as genome browsers and GeneSeqToFamily services. We have been hosting 3 web servers on the CyVerse cloud platform for external users, thus multiplying the impact and allowing the community to be able to access resources such as CerealsDB, KnetMiner and AutoCloner. The cyberinfrastructure is also supporting the bioinformatics training of dozens of users every year thanks to the training offered at EI. The EI Galaxy server has more than 80 registered users from EI and QIB, which ran over 1,500,000 successful jobs in the last 3 years, thanks to the high-performance compute resources funded by EI's recent Core Capability Grant awarded by BBSRC. A large part of these computational jobs were for our published GeneSeqToFamily pipeline, a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline, which has been also used by researchers at EI and their external collaborators to analyse a set of 19 monocot and dicot plant genomes. Since 1 April 2018, the SignaLink website, which is also accessible from major web portals such as Uniprot, Flybase and Wormbase, has seen a consistent increase in use, with 9432 webpage visits and 1732 downloads in the period March 2022 - March 2023. This is also the case for the Autophagy Regulation Network (ARN) and SalmoNet websites, with 2228 visits and 285 downloads for ARN, and 821 visits and 137 downloads for Salmonet in the period March 2022 - March 2023. |
| First Year Of Impact | 2018 |
| Sector | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education |
| Impact Types | Cultural Economic Policy & public services |
| Description | BBSRC 20RM2 Committee |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Description | Covid-19 Agile Response Panel |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Description | Interview with Environment Adviser from the UK Parliamentary Office of Science and Technology |
| Geographic Reach | National |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| Impact | Contacted by UK Parliament to contribute to a POSTnote (short document to advise ministers on a given topic) on genebanks and Digital Sequence Information as a result of my recent election to the DivSeek Board of Directors. I was interviewed to provide information around current international policies on DSI and how future UK involvement might be shaped around open licencing/MTAs of DSI datasets. |
| URL | https://www.parliament.uk/postnotes |
| Description | MRC Data Platform Commissioning Group |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | UKRI Innovation Scholars: Data Science Training in Health & Bioscience Panel |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Description | Agri-Tech in China: Newton Network+ - Developing a novel aerial image analysis algorithm to enable the timing estimation of fertilisation and chemical applications for wheat in China. |
| Amount | £29,432 (GBP) |
| Funding ID | SM003 |
| Organisation | Department for Business, Energy & Industrial Strategy |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 06/2018 |
| Description | BBSRC 17ALERT Mid-range equipment initiative - Enabling UK wheat research with the CyVerse UK cyberinfrastructure |
| Amount | £283,383 (GBP) |
| Funding ID | BB/R000662/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2017 |
| End | 08/2018 |
| Description | Bayer Grants4Traits |
| Amount | £20,661 (GBP) |
| Organisation | Bayer |
| Department | Bayer CropScience Ltd |
| Sector | Private |
| Country | United Kingdom |
| Start | 01/2018 |
| End | 12/2018 |
| Description | BioFAIR - Digital Research Infrastructure |
| Amount | £34,000,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2024 |
| End | 07/2029 |
| Description | BioFAIR: A UK Institute delivering a Commons for data-driven bioscience |
| Amount | £300,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2020 |
| End | 05/2021 |
| Description | Building capacity in third-generation genomics and bioinformatics for agricultural biosciences in Africa |
| Amount | £99,952 (GBP) |
| Funding ID | BB/T017422/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2021 |
| End | 03/2022 |
| Description | ELIXIR Tools Platform (Commissioned Services 2024-28) |
| Amount | £18,462 (GBP) |
| Organisation | European Molecular Biology Laboratory |
| Sector | Academic/University |
| Country | Germany |
| Start | 01/2024 |
| End | 12/2027 |
| Description | ELIXIR-STEERS |
| Amount | £52,673 (GBP) |
| Funding ID | 10105345 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2024 |
| End | 01/2027 |
| Description | ELIXIR-UK: FAIR Data Stewardship training |
| Amount | £79,653 (GBP) |
| Funding ID | MR/V038966/1 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2021 |
| End | 03/2023 |
| Description | FTMA4 - Earlham Institute Flexible Talent Mobility Account |
| Amount | £107,000 (GBP) |
| Funding ID | BB/X017761/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2023 |
| End | 03/2023 |
| Description | GCRF Foundation Awards for Global Agriculture and Food Systems Research - Genetic improvement of rice seed vigour for dry direct-seeded conditions |
| Amount | £2,620 (GBP) |
| Funding ID | BB/P023428/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2017 |
| End | 04/2019 |
| Description | IPA Industrial Partnering Award - China Partnering Awards - Forge a long-term UK-China relationship in phenotyping, Agri-Tech innovation and crop research for Rice and Wheat |
| Amount | £30,429 (GBP) |
| Funding ID | BB/R021376/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 03/2021 |
| Description | IPA Industrial Partnering Award - Resistance: DNA methylation and the evolution of pesticide-resistance genes in aphids |
| Amount | £289,489 (GBP) |
| Funding ID | BB/R009481/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 03/2021 |
| Description | Integration of COPO and CGCore Schemas and Associated Repositories |
| Amount | £62,968 (GBP) |
| Funding ID | 2018X329.EI |
| Organisation | International Food Policy Research Institute (IFPRI) |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 08/2018 |
| End | 01/2019 |
| Description | NRP Science Links Seed Corn funding |
| Amount | £14,000 (GBP) |
| Funding ID | R205991 |
| Organisation | Norwich Research Park |
| Sector | Private |
| Country | United Kingdom |
| Start | 12/2017 |
| End | 11/2018 |
| Description | NRP Seed fund - A GPU-accelerated machine-learning based agricultural vehicle navigation system for crop monitoring and trait analysis |
| Amount | £2,500 (GBP) |
| Funding ID | SLSF 74 |
| Organisation | Norwich Research Park |
| Sector | Private |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 08/2018 |
| Description | NRP Seed fund - Deconstructing somites using advanced genomics approaches |
| Amount | £7,000 (GBP) |
| Funding ID | SLSF 66 |
| Organisation | Norwich Research Park |
| Sector | Private |
| Country | United Kingdom |
| Start | 12/2017 |
| End | 11/2018 |
| Description | Open - Brain-enriched voltage-gated calcium channel isoforms: novel, genetically informed, therapeutic targets for psychiatric disorders |
| Amount | £167,504 (GBP) |
| Funding ID | MR/P026028/1 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2017 |
| End | 05/2019 |
| Description | Open call - Mapping for Conservation of Native Tilapia Resources in East Africa |
| Amount | £12,461 (GBP) |
| Organisation | JRS Biodiversity Foundation |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 09/2017 |
| End | 09/2020 |
| Description | Responsive Mode - Ribosomal DNA variation in multi-locus systems |
| Amount | £28,268 (GBP) |
| Funding ID | BB/P022030/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2017 |
| End | 02/2020 |
| Description | UK-2021-Galaxy |
| Amount | € 27,425 (EUR) |
| Organisation | ELIXIR |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 05/2021 |
| End | 05/2023 |
| Title | Host-Microbe interaction workflow |
| Description | Integrated Computational workflow to infer the effect of bacterial proteins on host processes |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | Targeted interplay between bacterial pathogens and host autophagy. Sudhakar P, Claire-Jacomin A, Hautefort I, Samavedam S, Fatemian K, Ari E, Gul L, Demeter A, Jones E, Korcsmaros T and Nezis I. Autophagy 2019. (In Press). Host-Microbe interaction pipeline based on protein-protein interactions - applicable to single species and community wide microbial proteomic data. Sudhakar P, Andrighetti T, Gul L, Fazekas D, Korcsmaros T. (in preparation - to be submitted April 2019) |
| Title | Improvements to the COPO system |
| Description | COPO is a computational system that attempts to address the challenges of making data FAIR by enabling scientists to describe their research objects (raw or processed data, publications, samples, images, etc.) using community-sanctioned metadata sets and vocabularies, and then use public or institutional repositories to share it with the wider scientific community. COPO encourages data generators to adhere to appropriate metadata standards when publishing research objects, using semantic terms to add meaning to them and specify relationships between them. This allows data consumers, be they people or machines, to find, aggregate, and analyse data which would otherwise be private or invisible. Building upon existing standards to push the state of the art in scientific data dissemination whilst minimising the burden of data publication and sharing. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Improvements to the COPO user interfaces and underlying code which have resulted in more data being submitted to public repositories through the system. The CGIAR CGCore v2 implementation is complete and undergoing testing to document and provide improvements. The Darwin Tree of Life project has chosen to use COPO as its main sample metadata submission route. |
| URL | https://github.com/collaborative-open-plant-omics/COPO |
| Title | Systems biology of gut organoids |
| Description | Since its first publication in 2009, the in vitro organoid model has been recognized as a major technological breakthrough tool in many basic biology and clinical applications. Organoids are near-physiological 3D model systems that facilitate studying a range of in vivo biological processes including cell differentiation, antimicrobial peptide production, host-microbe interactions and cell-cell communications. Organoids can also used to examine the effect of certain mutations by generating organoids from transgenic mice strains. The key aim of this joint project is to perform 'omics analyses of the generated organoids, examine the differences between cell-types and disease conditions using computational approaches, as well as generate and validate testable hypotheses regarding the affect of the identified functional differences. |
| Type Of Material | Model of mechanisms or symptoms - in vitro |
| Year Produced | 2017 |
| Provided To Others? | No |
| Impact | In the last 12 months we 1) performed proteomics analysis of the organoids that allowed to identify biomedically relevant and scientifically interesting differences ; 2) tested and established a protocol/pipeline to perform RNAseq and microRNA profiling at Earlham Institute. ; 3) Our in silico analysis of the proteomic datasets also confirmed the differentiated organoids do express proteins expected for the given cell types (e.g., enzymes important in peptide synthesis in Paneth cell differentiated organoids). By analysing interaction data we interestingly pointed out that autophagy (cellular self-eating) could degrade many of the cell-specific key proteins. ATG16L1 is an autophagy protein involved in selecting proteins for autophagy-driven degradation, and it also contributes to the general autophagy process.; 4) In a second series of experiments we have generated organoids from the intestine of mice generated at UEA that lack expression of Atg16L1 specifically in intestinal epithelial cells (Atg16L1 dIEC). The proteomic profiles of these autophagy deficient Paneth cell and goblet cell organoids were also carried out at the University of Liverpool. Strikingly, when we analysed the proteins whose protein levels differed in the autophagy deficient background, we found several of them are known or predicted to be degraded through autophagy. In Paneth cell organoids, the functional analysis of those proteins whose level was significantly higher in the ATG16L1 knock-out background (potentially as they have not been degraded properly) pointed out their importance in 'acute inflammatory response', 'immune response', 'negative regulation of gene expression', and 'protein processing'. This list indicates that autophagy malfunction negatively affects protein (antimicrobial peptide) production as well as deregulates inflammatory responses. Failure of these process are well known for Paneth cells in Crohn's disease but so far they have not been connected directly with autophagy malfunction. We found similar results for the mucosa producing goblet cells. To confirm these findings, we will directly examine some affected key functions using organoids. Reference: Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy. Emily Jones*, Zoe Matthews*, Lejla Gul*, Padhmanand Sudhakar, Agatha Treveil, Devina Divekar, Jasmine Buck, Tomasz Wrzesinski, Matthew Jefferson, Stuart Armstrong, Lindsay Hall, Alastair Watson, Simon Carding, Wilfried Haerty, Federica Di Palma, Ulrike Mayer, Penny Powell, Isabelle Hautefort, Tom Wileman, Tamas Korcsmaros. Disease Models and Mechanisms 2019. http://dmm.biologists.org/content/early/2019/02/26/dmm.037069. (* joint first authors) |
| Title | Additional file 1 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| Description | Additional file 1: Supplementary Table 1. Assembly statistics. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Chromosome-level_genome_se... |
| Title | Additional file 1 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| Description | Additional file 1: Supplementary Table 1. Assembly statistics. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Chromosome-level_genome_se... |
| Title | Additional file 1 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis |
| Description | Additional file 1: Supplementary Table S1. Read counts and number of OTUs/ASVs in the OTU/ASV matrix of each pipeline. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_LotuS2_an_ultrafast_and_hi... |
| Title | Additional file 2 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis |
| Description | Additional file 2: Supplementary Table S2. Significance of differences between each pipeline in the reproducibility of beta diversity between the technical replicates. Significance of differences in Bray-Curtis distance between the pipelines were calculated based on the Tukey's HSD test. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_2_of_LotuS2_an_ultrafast_and_hi... |
| Title | Additional file 3 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| Description | Additional file 3: Supplementary Table 2. Genomics regions in GIFT with evidence of O. mossambicus introgression. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Chromosome-level_genome_se... |
| Title | Additional file 3 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| Description | Additional file 3: Supplementary Table 2. Genomics regions in GIFT with evidence of O. mossambicus introgression. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Chromosome-level_genome_se... |
| Title | Additional file 3 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis |
| Description | Additional file 3: Supplementary Table S3. Correlation and beta distance between the mock community and re-constructed mock community by each pipeline. A-B) Spearman and Pearson correlation between the expected abundances in the mock community and the observed abundances by each pipeline. C) Bray-Curtis dissimilarity between the known mock community and re-constructed mock community composition by each pipeline. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_of_LotuS2_an_ultrafast_and_hi... |
| Title | Additional file 4 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis |
| Description | Additional file 4: Supplementary Table S4. Accuracy of each pipeline in re-constructing the mock community at genus level. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_4_of_LotuS2_an_ultrafast_and_hi... |
| Title | Additional file 5 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis |
| Description | Additional file 5: Supplementary Figure S1. Galaxy web interface of LotuS2. Raw reads can be uploaded into the LotuS2 via the Galaxy web interface and analysed (accessible on https://usegalaxy.eu/ ). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_5_of_LotuS2_an_ultrafast_and_hi... |
| Title | Additional file 6 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| Description | Additional file 6: Supplementary Table 3. Genes identified within O. mossambicus introgressed regions including corresponding orthologs in medaka. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_6_of_Chromosome-level_genome_se... |
| Title | Additional file 6 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| Description | Additional file 6: Supplementary Table 3. Genes identified within O. mossambicus introgressed regions including corresponding orthologs in medaka. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_6_of_Chromosome-level_genome_se... |
| Title | Additional file 8 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| Description | Additional file 8: Supplementary Table 4. Ontology terms significantly enriched among genes identified within O. mossambicus introgressed regions. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_8_of_Chromosome-level_genome_se... |
| Title | Additional file 8 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus |
| Description | Additional file 8: Supplementary Table 4. Ontology terms significantly enriched among genes identified within O. mossambicus introgressed regions. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_8_of_Chromosome-level_genome_se... |
| Title | Autophagy Regulatory Network |
| Description | A manually curated dataset of autophagy components and their interactions. Integrated resource with known protein regulators of autophagy. Contains possible transcriptional and post-transcriptional regulators (ie., transcription factors and miRNA) of autophagy and its protein regulators. Links all autophagy component and regulators to major signaling pathways. Predict novel regulators and interactions. Can be downloaded in a user-specified content and format. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2015 |
| Provided To Others? | Yes |
| Impact | Autophagy Regulatory Network - a systems-level bioinformatics resource for studying autophagy components and their regulation (2015). Türei D, Földvári-Nagy L, Fazekas D, Módos D, Kubisch J, Kadlecsik T, Demeter A, Lenti K, Csermely P, Vellai T, Korcsmáros T. Autophagy, 11(1):155-165. - 26 citations |
| URL | http://autophagyregulation.org |
| Title | GAFA database |
| Description | GAFA database is generated by Gene Align and Family Aggregator (GAFA) tool as part of final stages of GeneSeqToFAmily workflow. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | GAFA database is usable by Galaxy, in which Aequatus plugin for Galaxy reads data from GAFA database and visualises gene families. |
| URL | https://github.com/TGAC/earlham-galaxytools/tree/master/tools/GAFA/schema |
| Title | NRF2ome |
| Description | A manually curated dataset of regulatory connections of NRF2 Integrated resource with known protein regulators of NRF2 Contains possible transcriptional and post-transcriptional regulators (ie., transcription factors and miRNA) of NRF2 and its protein regulators. Links NRF2 and regulators to major signaling pathways. Predict novel regulators and interactions. Can be downloaded in a user-specified content and format. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2013 |
| Provided To Others? | Yes |
| Impact | NRF2-ome, an integrated web resource to discover protein interaction and regulatory networks of NRF2. Türei D, Papp D, Fazekas D, Földvári-Nagy L, Módos D, Lenti K, Csermely P, Korcsmáros T. (2013) - Oxidative Medicine and Cellular Longevity, 2013:737591 - 18 citations The NRF2-related interactome and regulome contain multifunctional proteins and fine-tuned autoregulatory loops. (2012) Papp D, Lenti K, Módos D, Fazekas D, Dúl Z, Türei D, Földvári-Nagy L, Nussinov R, Csermely P, Korcsmáros T. FEBS Letters 586, 13, 1795-1802. - 54 citations |
| URL | http://nrf2.elte.hu/ |
| Title | SalmoNet2.0 |
| Description | An integrated network resource containing regulatory, metabolic and protein-protein interactions For multiple Salmonella strains classified as gastro-intestinal or extra-intestinal pathogens An interaction resource with manually curated, high-throughput and predicted interactions Provides a strain specific and consensus networks Can be downloaded in a user-specified content and format |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation Métris A., Sudhakar P., Fazekas D., Demeter A., Ari E., Branchu P, Kingsley R.A., Baranyi J., Korcsmáros T. npj Systems Biology and Applications 3, Article number: 31 (2017) doi:10.1038/s41540-017-0034-z |
| URL | http://salmonet.org/ |
| Title | Sherlock - big data analytics platform for bioinformatics data |
| Description | The Sherlock tool is utilizing standard, open source big data technologies (like S3, Presto and docker) in order to execute simple analytical SQL queries on top of the integrated bioinformatics data organized into an S3-based data lake. |
| Type Of Material | Data analysis technique |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | The method will help to increase the productivity of data heavy bioinformatics projects, easing the data cleaning, filtering and integration related tasks which are usually the first steps in each complex bioinformatics pipeline. Github link : https://github.com/NetBiol/sherlock |
| Title | SignaLink 2 |
| Description | A multi-layered network structure allows the selection of user-specific details Manually curated dataset of major signaling pathways Extends pathways with integrated regulatory resources Contains pathway-specific transcription factors, miRNA, scaffolds and post translational modifying enzymes Multi-pathway proteins: proteins can belong to more than one pathway Proteins are classified by pathway position (core/non-core) and section (ligand, receptor, mediator, etc.) Signaling interactions are directed and labeled with PubMed IDs of experimental evidence Browse signaling pathways, cross-talks and multi-pathway proteins Select transcriptional, post- transcriptional and post translational regulators of a signaling pathway Download species- and pathway-specific information in several formats Design genetic/biochemical experiments to verify predicted pathway member proteins Model tissue- or disease-specific signaling processes by merging SignaLink with expression data Discover novel signaling drug target candidates |
| Type Of Material | Database/Collection of data |
| Year Produced | 2013 |
| Provided To Others? | Yes |
| Impact | Downloaded >2,000 times from 400 institutes in 79 countries. > 78,000 signalling protein data pages upon 18,000 visits The visitors have spent altogether 73 days using the SignaLink website 78 citations |
| URL | http://signalink.org/ |
| Title | The DFW CKAN Digital Repository |
| Description | The CKAN digital repository has been set up as part of WP4 of Designing Future Wheat to hold all DFW publications alongside any supplementary datasets and information. This gives the public and researchers immediate access to DFW funded research through open access routes where available. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | We have buit scripts to find and make available open access versions of all DFW published research, either as preprints or as journal articles. We also supply any supplementary information as appropriate to aid information dissemination. The DFW CKAN runs within Earlham Institute's CyVerse UK National Capability. |
| URL | https://ckan.grassroots.tools |
| Title | The Earlham Institute CKAN Digital Repository |
| Description | The CKAN digital repository has been set up as part of WP3 of Earlham Institute's CSP to hold all EI strategic publications alongside any supplementary datasets and information. This gives the public and researchers immediate access to EI's BBSRC funded research through open access routes where available. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | We have buit scripts to find and make available open access versions of all EII published research, either as preprints or as journal articles. We also supply any supplementary information as appropriate to aid information dissemination. The EI CKAN runs within Earlham Institute's CyVerse UK National Capability. |
| URL | https://ckan.earlham.ac.uk |
| Title | The Grassroots DFW Data Portal |
| Description | Continually updated large datasaet repository for the DFW project. Houses a variety of key wheat and associated datasets that are either under the Toronto licence or others as apprpriate for the level of open access. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | To date, we house 24TB of wheat datasets that have been accessed by over 4000 researchers from 64 countries. |
| URL | https://grassroots.tools/dfw |
| Description | A meeting between CIMMYT and DFW funded by BMGF to discuss collaboration projects |
| Organisation | International Centre for Maize and Wheat Improvement (CIMMYT) |
| Country | Mexico |
| Sector | Charity/Non Profit |
| PI Contribution | I organised a meeting funded by Bill and Melinda Gates Foundation brought together members of the BBSRC's coordinated wheat programme (Designing Future Wheat) with members of CIMMYT (who breed wheat for the resource poor in the developing world), discuss potential opportunities for interaction. These opportunities are taken forward by writing proposals for Newton , GCRF or IWYP funding calls |
| Collaborator Contribution | See above |
| Impact | This interaction is still ongoing between members of BBSRC's coordinated wheat programme (Designing Future Wheat) and researchers within CIMMYT with proposals being written for IWYP and Newton calls |
| Start Year | 2018 |
| Description | ACACIA Bioinformatics Community of Practice (BixCoP) |
| Organisation | International Livestock Research Institute (ILRI) |
| Country | Kenya |
| Sector | Charity/Non Profit |
| PI Contribution | Members of EI delivered training throughout the year for the BixCoP fellowship programme. |
| Collaborator Contribution | The GCRF STARS project was led by JIC and hosted at BeCA-Hub ILRI in Nairobi. |
| Impact | The training programme trsulted in a group of Fellows ready to take their skills back into their home countries and communities, with some undertaking Carpentries instructor training so that they can lead their own training courses in those communities. |
| Start Year | 2018 |
| Description | ACACIA Bioinformatics Community of Practice (BixCoP) |
| Organisation | John Innes Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Members of EI delivered training throughout the year for the BixCoP fellowship programme. |
| Collaborator Contribution | The GCRF STARS project was led by JIC and hosted at BeCA-Hub ILRI in Nairobi. |
| Impact | The training programme trsulted in a group of Fellows ready to take their skills back into their home countries and communities, with some undertaking Carpentries instructor training so that they can lead their own training courses in those communities. |
| Start Year | 2018 |
| Description | COVID Disease Map Consortia |
| Organisation | University of Luxembourg |
| Department | Luxembourg Centre for Systems Biomedicine |
| Country | Luxembourg |
| Sector | Academic/University |
| PI Contribution | We provide resourcs (SignaLink, OmniPath and VIralLink) to the curators of the project. And we participate in a weekly TC among 150 scientists from all around the world. |
| Collaborator Contribution | They provided domain expertise to optimise our tool development, and feedback on our study design. |
| Impact | Ostaszewski et al, bioRXiv, 2021; doi: 10.1101/2020.10.26.356014 |
| Start Year | 2020 |
| Description | Collaboration with Oxford Nanopore Technologies |
| Organisation | Oxford Nanopore Technologies |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | As part of the upcoming EI strategic programme we will be producing novel protocols for single cell long read RNA and DNA sequencing as well as novel approaches to detect DNA replication through base modification |
| Collaborator Contribution | ONT will contribute through providing expertise in machine learning models applications (base modification), technology solutions and protocols developments for single cell RNA / DNA seq |
| Impact | Engagement with ONT on March 7th to develop the collaboration as part of the upcoming ISPs |
| Start Year | 2022 |
| Description | CyVerse UK MOOC development partnership |
| Organisation | University of Arizona |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We have been working with the CyVerse US staff at the University of Arizona to develop a series of online courses to help users with using the platforms in the US, UK and Austria |
| Collaborator Contribution | Development of course materials |
| Impact | A set of reusable and open course materials for use in CyVerse training events |
| Start Year | 2021 |
| Description | CyVerse UK MOOC development partnership |
| Organisation | University of Graz |
| Country | Austria |
| Sector | Academic/University |
| PI Contribution | We have been working with the CyVerse US staff at the University of Arizona to develop a series of online courses to help users with using the platforms in the US, UK and Austria |
| Collaborator Contribution | Development of course materials |
| Impact | A set of reusable and open course materials for use in CyVerse training events |
| Start Year | 2021 |
| Description | DivSeek Partnership |
| Organisation | DivSeek International |
| Sector | Learned Society |
| PI Contribution | I bring infrastructure expertise to this partnership, influencing and impacting policy to provide computational and training capacity to other DivSeek partners. I promote the range of infrastructure projects that are developed in my group at EI, but also solutions developed at other centres that can contribute to the DivSeek consortium. Partners are exposed to EI projects such as COPO, Grassroots (Wheat Information System, CerealsDB, marker design), CyVerse UK and Galaxy, through working group communications and meetings at international conferences such as PAG and RDA. I lead the Data Standards for Interoperable Tools working group, and we aim to collate community-suggested standards and tools, and advise the partnership and their stakeholders in best practice for delivery of sustainable and interoperable infrastructure. |
| Collaborator Contribution | The DivSeek consortium contributes expertise and knowledge exchange in advances in crop diversity, improving our networking and understanding of challenges and potential solutions to social, structural, and biological problems. With over 66 global partners including EI, this is a powerful and highly respected group of research institutes that are working together to enable a step change in efficiency of interactions, leading to improved crop diversity research and data sharing. |
| Impact | EI is a founding partner of DivSeek, and Dr Davey leads one of the new working groups, "Data Standards for Interoperable Tools" (http://www.divseek.org/standards/) |
| Start Year | 2015 |
| Description | ELIXIR Biodiversity Working Group |
| Organisation | ELIXIR |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Drs Davey and Shaw attended the first ELIXIR Biodiversity working group meeting in Milan 2020. Davey gave a talk on UK efforts to track biodiversity data, for example with the COPO platform. |
| Collaborator Contribution | ELIXIR initiated this working group and invited member ELIXIR nodes to attend. |
| Impact | Main outcome is building the community with a view to submitting an implementation study around biodiversity data. |
| Start Year | 2020 |
| Description | Galaxy Project |
| Organisation | Albert Ludwig University of Freiburg |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. The Galaxy Committers team, established in 2015 as an extension of the original Galaxy Team, leads the development, testing and support of the Galaxy platform and of various Galaxy servers and related infrastructure. Dr. N. Soranzo is a member of the Galaxy Committers since it was formed. |
| Collaborator Contribution | All members of the Galaxy Committers team contribute to the development, testing and support of the Galaxy platform and of various Galaxy servers and related infrastructure. |
| Impact | Multiple Galaxy releases: 15.07, 15.10, 16.01, 16.04, 16.10, 17.01, 17.05, 17.09, 18.01, 18.05, 18.09 and 19.01 . Ongoing support of users and deployers of Galaxy servers across various channels, like mailing lists, chat systems, issue trackers. Production and update of freely training materials, hosted at https://training.galaxyproject.org/ This collaboration is multi-disciplinary in scope, involving biology, bioinformatics and medicine. |
| Start Year | 2015 |
| Description | Galaxy Project |
| Organisation | Cleveland Clinic |
| Department | Lerner Research Institute |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. The Galaxy Committers team, established in 2015 as an extension of the original Galaxy Team, leads the development, testing and support of the Galaxy platform and of various Galaxy servers and related infrastructure. Dr. N. Soranzo is a member of the Galaxy Committers since it was formed. |
| Collaborator Contribution | All members of the Galaxy Committers team contribute to the development, testing and support of the Galaxy platform and of various Galaxy servers and related infrastructure. |
| Impact | Multiple Galaxy releases: 15.07, 15.10, 16.01, 16.04, 16.10, 17.01, 17.05, 17.09, 18.01, 18.05, 18.09 and 19.01 . Ongoing support of users and deployers of Galaxy servers across various channels, like mailing lists, chat systems, issue trackers. Production and update of freely training materials, hosted at https://training.galaxyproject.org/ This collaboration is multi-disciplinary in scope, involving biology, bioinformatics and medicine. |
| Start Year | 2015 |
| Description | Galaxy Project |
| Organisation | Curie Institute Paris (Institut Curie) |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. The Galaxy Committers team, established in 2015 as an extension of the original Galaxy Team, leads the development, testing and support of the Galaxy platform and of various Galaxy servers and related infrastructure. Dr. N. Soranzo is a member of the Galaxy Committers since it was formed. |
| Collaborator Contribution | All members of the Galaxy Committers team contribute to the development, testing and support of the Galaxy platform and of various Galaxy servers and related infrastructure. |
| Impact | Multiple Galaxy releases: 15.07, 15.10, 16.01, 16.04, 16.10, 17.01, 17.05, 17.09, 18.01, 18.05, 18.09 and 19.01 . Ongoing support of users and deployers of Galaxy servers across various channels, like mailing lists, chat systems, issue trackers. Production and update of freely training materials, hosted at https://training.galaxyproject.org/ This collaboration is multi-disciplinary in scope, involving biology, bioinformatics and medicine. |
| Start Year | 2015 |
| Description | Galaxy Project |
| Organisation | Johns Hopkins University |
| Department | Department of Biology |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. The Galaxy Committers team, established in 2015 as an extension of the original Galaxy Team, leads the development, testing and support of the Galaxy platform and of various Galaxy servers and related infrastructure. Dr. N. Soranzo is a member of the Galaxy Committers since it was formed. |
| Collaborator Contribution | All members of the Galaxy Committers team contribute to the development, testing and support of the Galaxy platform and of various Galaxy servers and related infrastructure. |
| Impact | Multiple Galaxy releases: 15.07, 15.10, 16.01, 16.04, 16.10, 17.01, 17.05, 17.09, 18.01, 18.05, 18.09 and 19.01 . Ongoing support of users and deployers of Galaxy servers across various channels, like mailing lists, chat systems, issue trackers. Production and update of freely training materials, hosted at https://training.galaxyproject.org/ This collaboration is multi-disciplinary in scope, involving biology, bioinformatics and medicine. |
| Start Year | 2015 |
| Description | Galaxy Project |
| Organisation | Oregon Health and Science University |
| Department | School of Medicine |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. The Galaxy Committers team, established in 2015 as an extension of the original Galaxy Team, leads the development, testing and support of the Galaxy platform and of various Galaxy servers and related infrastructure. Dr. N. Soranzo is a member of the Galaxy Committers since it was formed. |
| Collaborator Contribution | All members of the Galaxy Committers team contribute to the development, testing and support of the Galaxy platform and of various Galaxy servers and related infrastructure. |
| Impact | Multiple Galaxy releases: 15.07, 15.10, 16.01, 16.04, 16.10, 17.01, 17.05, 17.09, 18.01, 18.05, 18.09 and 19.01 . Ongoing support of users and deployers of Galaxy servers across various channels, like mailing lists, chat systems, issue trackers. Production and update of freely training materials, hosted at https://training.galaxyproject.org/ This collaboration is multi-disciplinary in scope, involving biology, bioinformatics and medicine. |
| Start Year | 2015 |
| Description | Galaxy Project |
| Organisation | Penn State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. The Galaxy Committers team, established in 2015 as an extension of the original Galaxy Team, leads the development, testing and support of the Galaxy platform and of various Galaxy servers and related infrastructure. Dr. N. Soranzo is a member of the Galaxy Committers since it was formed. |
| Collaborator Contribution | All members of the Galaxy Committers team contribute to the development, testing and support of the Galaxy platform and of various Galaxy servers and related infrastructure. |
| Impact | Multiple Galaxy releases: 15.07, 15.10, 16.01, 16.04, 16.10, 17.01, 17.05, 17.09, 18.01, 18.05, 18.09 and 19.01 . Ongoing support of users and deployers of Galaxy servers across various channels, like mailing lists, chat systems, issue trackers. Production and update of freely training materials, hosted at https://training.galaxyproject.org/ This collaboration is multi-disciplinary in scope, involving biology, bioinformatics and medicine. |
| Start Year | 2015 |
| Description | IBD Multi-omics, Prof. Severine Vermeire, KU Leuven |
| Organisation | University of Leuven |
| Country | Belgium |
| Sector | Academic/University |
| PI Contribution | Stemming from our strategic collaboration with the IBD unit headed by Prof. Séverine Vermeire at KU Leuven, we have access to patient -omic datasets (such as genotyping, tissue and immune cell transcriptomics, blood proteomics, gut microbiome etc). We use data integration approaches aided by systems biology and machine learning to disentangle the complexity of IBD by exploiting the benefits delivered by the cumulative insights rendered by multiple -omic layers. |
| Collaborator Contribution | Clinical datasets including -omic and phenotypic trait data. Scientific advice on grants |
| Impact | The project is multi-disciplinary involving concepts from systems biology, statistics, microbiology, mathematics, computational biology (software resources etc) and experimental validation where appropriate and necessary. Outcomes Machine Learning and Big Data integration in the clinical research of Inflammatory Bowel Disease. Seyed-Tabib N, Madgwick M, Sudhakar P, Verstockt B, Korcsmaros T, Vermeire S. (under review) Systems genomics of ulcerative colitis: combining GWAS and signalling networks for patient stratification and individualised drug targeting in ulcerative colitis. J. Brooks*, D. Modos*, P. Sudhakar*, D. Fazekas, A. Zoufir, A. Watson, M. Tremelling, B. Verstockt, S. Vermeire, A. Bender, S. Carding, T. Korcsmaros. (in preparation - to be submitted March 2019) (*joint first authors) |
| Start Year | 2018 |
| Description | Machine Intelligence Garage - Digital Catapult |
| Organisation | Digital Catapult |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | EI will be contributing to this programme by supporting SMEs in the life sciences sector with expertise in how to enable the most efficient way to process large and complex data, provide repository platforms for data and software distribution, publication, and large-scale data visualisation. |
| Collaborator Contribution | Machine Intelligence Garage programme provides support to SMEs who are seeking access to expertise and computational power to accelerate their growth (develop new products and services). |
| Impact | EI signed an MoU with Digital Catapult Machine Intelligence Garage https://www.migarage.ai/about-mi-garage/ to support their programme. |
| Start Year | 2020 |
| Description | Strategic partnership on future ISPs with Eagle Genomics |
| Organisation | Eagle Genomics Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Provided technical expertise and input on how Eagle Genomics could help DECODE ISP and CELLGEN ISP to realise impact through scaling up newly developed bioinformatic pipelines, making the pipelines and data accessible and deployable for users to develop real world products and services. |
| Collaborator Contribution | Exploring the onboarding and scaling of Earlham tools on Eagle Platform E-Data scientist. |
| Impact | Further funding to the Earlham Institute as part of the DECODE ISP and CELLGEN ISP. |
| Start Year | 2022 |
| Description | The Carpentries |
| Organisation | The Carpentries |
| Country | United States |
| Sector | Charity/Non Profit |
| PI Contribution | With five members of EI faculty trained as Carpentries trainers, we host at least one Software Carpentry and one Data Carpentry workshop per year. The trainers are able to contribute to the community-developed training materials, which are hosted on the Carpentries website. |
| Collaborator Contribution | The Carpentries website hosts the community-developed training materials, which are under development and improvement based on feedback from users. The Carpentries are also able to list upcoming courses on their website, as well as provide templates for the workshop programme pages and, as part of this, generates links to standardised pre and post-workshop surveys to which we are provided reports. |
| Impact | Software Carpentry and Data Carpentry workshops held and offered to the community, developing researcher skills in data management and programming. |
| Start Year | 2013 |
| Description | Wheat Information System (WheatIS) |
| Organisation | Cold Spring Harbor Laboratory (CSHL) |
| Country | United States |
| Sector | Charity/Non Profit |
| PI Contribution | The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative. |
| Collaborator Contribution | All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project. |
| Impact | This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/ |
| Start Year | 2011 |
| Description | Wheat Information System (WheatIS) |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative. |
| Collaborator Contribution | All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project. |
| Impact | This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/ |
| Start Year | 2011 |
| Description | Wheat Information System (WheatIS) |
| Organisation | French National Institute of Agricultural Research |
| Department | INRA Versailles |
| Country | France |
| Sector | Academic/University |
| PI Contribution | The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative. |
| Collaborator Contribution | All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project. |
| Impact | This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/ |
| Start Year | 2011 |
| Description | Wheat Information System (WheatIS) |
| Organisation | Helmholtz Association of German Research Centres |
| Department | Helmholtz Zentrum Munchen |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative. |
| Collaborator Contribution | All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project. |
| Impact | This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/ |
| Start Year | 2011 |
| Description | Wheat Information System (WheatIS) |
| Organisation | International Centre for Maize and Wheat Improvement (CIMMYT) |
| Country | Mexico |
| Sector | Charity/Non Profit |
| PI Contribution | The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative. |
| Collaborator Contribution | All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project. |
| Impact | This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/ |
| Start Year | 2011 |
| Description | Wheat Information System (WheatIS) |
| Organisation | Monogram Network |
| Sector | Academic/University |
| PI Contribution | The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative. |
| Collaborator Contribution | All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project. |
| Impact | This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/ |
| Start Year | 2011 |
| Description | Wheat Information System (WheatIS) |
| Organisation | Rothamsted Research |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative. |
| Collaborator Contribution | All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project. |
| Impact | This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/ |
| Start Year | 2011 |
| Description | Wheat Information System (WheatIS) |
| Organisation | U.S. Department of Agriculture USDA |
| Department | Agricultural Research Service |
| Country | United States |
| Sector | Public |
| PI Contribution | The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative. |
| Collaborator Contribution | All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project. |
| Impact | This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/ |
| Start Year | 2011 |
| Description | Wheat Information System (WheatIS) |
| Organisation | University of Bristol |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative. |
| Collaborator Contribution | All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project. |
| Impact | This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/ |
| Start Year | 2011 |
| Description | Wheat Information System (WheatIS) |
| Organisation | University of California, Davis |
| Department | UC Davis College of Biological Sciences |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative. |
| Collaborator Contribution | All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project. |
| Impact | This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/ |
| Start Year | 2011 |
| Description | Wheat Information System (WheatIS) |
| Organisation | University of Western Australia |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | The Grassroots infrastructure (https://grassroots.tools) developed at EI is being used to consolidate data and analyses, facilitating consistent approaches to generating, processing and disseminating public wheat datasets. The Grassroots infrastructure comprises: a data management layer to provide structure to unstructured filesystems; interfaces to interact with local or cloud-based analysis platforms; a search layer to provide multi-faceted metadata and literature querying; a web server layer to deliver content and provide access to public programmatic interfaces. EI has an extensive National Capability to provide scientific computing hardware to the UK research community and is therefore perfectly positioned to build a point-of-access to previously disparate resources to serve wheat breeders, biologists and bioinformaticians. Coupling the Grassroots project with BBSRC-funded efforts to bring Galaxy and CyVerse UK to UK researchers provides community standardised methodologies for data integration, interpretation and discovery in wheat. These resources are designed to be queried programmatically, and we are integrating them with other WheatIS resources (such as CerealsDB) accordingly via open source and freely available infrastructure. By doing so we will be promoting and facilitating an inclusive and collaborative community of experts to provide access to an interconnected network of wheat data to a scale that was simply not available previously. EI also has representation on the WheatIS Expert Working Group, meeting yearly at PAG to discuss strategy and policy for the Wheat Initiative. |
| Collaborator Contribution | All WheatIS partners contribute to the global effort in harmonising, standardising, and sharing wheat data in a way that is technically sensible and user focused, thus minimising cost across a multi-faceted and independently funded project. |
| Impact | This collaboration is multi-disciplinary in scope, undertaken by biologists, bioinformaticians, and breeders. Wheat Data Interoperability Guidelines - https://ist.blogs.inra.fr/wdi/ |
| Start Year | 2011 |
| Description | collaboration to federate US and UK CyVerse execution systems |
| Organisation | Texas Advanced Computing Center |
| Country | United States |
| Sector | Private |
| PI Contribution | We are working in set up the UK side of a system that will allow flocking jobs from the submission point in the US to our execution system in the UK. |
| Collaborator Contribution | Collaborators are working in setting up the US side of a system that will allow flocking from their infrastructure to our in the UK. |
| Impact | Once the federation is completed it will allow UK/EU users to run their jobs in a more favourable location (the UK), while keeping submitting their jobs in the Discovery Environment, which will be maintained by the US team. |
| Start Year | 2017 |
| Description | collaboration to federate US and UK CyVerse execution systems |
| Organisation | University of Arizona |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We are working in set up the UK side of a system that will allow flocking jobs from the submission point in the US to our execution system in the UK. |
| Collaborator Contribution | Collaborators are working in setting up the US side of a system that will allow flocking from their infrastructure to our in the UK. |
| Impact | Once the federation is completed it will allow UK/EU users to run their jobs in a more favourable location (the UK), while keeping submitting their jobs in the Discovery Environment, which will be maintained by the US team. |
| Start Year | 2017 |
| Description | collaboration to federate US and UK CyVerse storage systems |
| Organisation | Texas Advanced Computing Center |
| Country | United States |
| Sector | Private |
| PI Contribution | We are working together with the US team to enable storage federation of CyVerse UK and CyVerse US trough iRODS. |
| Collaborator Contribution | We are working together with the US team to enable storage federation of CyVerse UK and CyVerse US trough iRODS. |
| Impact | It is now possible to interact with the UK storage system with the same command line tool as the US systems. Data files can be easily and quickly moved between the two location, which is virtually hidden from the end user. |
| Start Year | 2017 |
| Description | collaboration to federate US and UK CyVerse storage systems |
| Organisation | University of Arizona |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We are working together with the US team to enable storage federation of CyVerse UK and CyVerse US trough iRODS. |
| Collaborator Contribution | We are working together with the US team to enable storage federation of CyVerse UK and CyVerse US trough iRODS. |
| Impact | It is now possible to interact with the UK storage system with the same command line tool as the US systems. Data files can be easily and quickly moved between the two location, which is virtually hidden from the end user. |
| Start Year | 2017 |
| Title | APoc Galaxy wrapper |
| Description | Galaxy wrapper for APoc, a tool for large-scale structural comparison of protein pockets. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Since the upload to the Galaxy ToolShed, this tool has been cloned / installed 9 times. |
| URL | https://toolshed.g2.bx.psu.edu/view/earlhaminst/apoc |
| Title | Adaptive Sequencing Enrichment model - hosting on the CyVerse UK e-infrastructure |
| Description | A shiny web application that provides an interactive implementation of a nanopore adaptive sequencing model. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | Enables users to plan their own adaptive sequencing experiments. |
| URL | https://readuntil.cyverseuk.org |
| Title | Aequatus |
| Description | Aequatus Browser is an open-source web-based tool developed at EI to visualise homologous gene structures among differing species or subtypes of a common species. Aequatus uses the Ensembl Compara and Core database schemas to store comparative information between organisms. Aequatus uses precalculated gene family information and genomic alignments data in the form of CIGAR strings, from Ensembl Compara or the GeneSeqToFamily pipeline, and cross-references these sequences to Ensembl Core databases for each species to gather genomic feature information via stable_ids. Aequatus then processes the comparative and feature data to provide a visual representation of the phylogenetic and structural relationships among the set of chosen species. The ultimate goal of the Aequatus Browser is to provide a unique and informative way to render and explore complex relationships between genes from various species at a level that has so far been unrealised. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | New developments to Aequatus have been..... |
| URL | http://aequatus.earlham.ac.uk/ |
| Title | Aequatus.js plugin for Galaxy |
| Description | Aequatus.js is an open-source JavaScript library to visualise homologous gene structures among differing species or subtypes of a common species. It is developed as part of Aequatus project. Here by, it is configured to be used into Galaxy as a visualisation plugin |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | This development of Aequatus.js into Galaxy will allow anyone using GeneSeqToFamily workflow to visualise gene family within Galaxy. |
| URL | https://github.com/TGAC/earlham-galaxytools/tree/master/visualisations/aequatus |
| Title | BAM to Fastq application |
| Description | Application allow user to convert BAM files to Fastq. It includes a wrapper of the software and a Docker image of it. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Users can now run jobs requiring this application in the UK. |
| URL | https://de.cyverse.org/de/?type=apps&app-id=BAM_to_Fastq_2.25.0-0.0.0u1&system-id=agave |
| Title | Beast 2.4.3 application |
| Description | CyVerse application to run Beast 2 software. It includes a wrapper to run it on the CyVerse system and a Docker image for the software. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Users are now able to run the software from an easy to use interface in the UK. |
| URL | https://de.cyverse.org/de/?type=apps&app-id=beast2.4.3-1.0.0u1&system-id=agave |
| Title | Blastn application |
| Description | Application to run Blastn. It includes a wrapper to run it in CyVerse and a Docker image for the software. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Users are now able to run Blastn trough an easy to use web interface in the UK execution system. |
| URL | https://de.cyverse.org/de/?type=apps&app-id=blastn_2.2.31-0.0.0u1&system-id=agave |
| Title | Blastp application |
| Description | Application to run Blastp in CyVerse, it includes a wrapper and a Docker image for the software. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Users are now able to run Blastp from an easy to use web interface in the UK execution system. |
| URL | https://de.cyverse.org/de/?type=apps&app-id=blastp_2.2.31-0.0.0u1&system-id=agave |
| Title | Bowtie 2 application |
| Description | Application to run Bowtie 2 in CyVerse, it includes a wrapper and a Docker image of the software. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Users are now able to run Bowtie 2 from an easy to use web interface in the UK execution system. |
| URL | https://de.cyverse.org/de/?type=apps&app-id=Bowtie2-2.2.6u1&system-id=agave |
| Title | Btrim application |
| Description | Application to run Btrim in CyVerse, it includes a wrapper and a Docker image of the software. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Users are now able to run Btrim from an easy to use web interface in the UK execution system. |
| URL | https://de.cyverse.org/de/?type=apps&app-id=btrim-0.0.0u1&system-id=agave |
| Title | Collaborative Open Plant Omics (COPO) |
| Description | COPO streamlines the process of data deposition to public repositories by hiding much of the complexity of metadata capture and data management from the end-user. The ISA infrastructure (www.isa-tools.org) is leveraged to provide the interoperability between metadata formats required for seamless deposition to repositories. COPO facilitates the links to data analysis platforms such as CyVerse UK and Galaxy. Logical groupings of artefacts (e.g. PDFs, raw data, contextual supplementary information) relating to a body of work are stored in COPO collections and represented by common standards, which are publicly searchable. Bundles of multiple data objects themselves can then be deposited directly into public repositories through COPO interfaces. This improvement output represents the beta release of the COPO platform in 2017. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | COPO has been added to the ELIXIR-UK roadmap for ELIXIR core data services, and is currently being used by EI and JIC researchers to deposit real, large scale sequencing datasets into the European Nucleotide Archive. COPO is also being investigated as a potential data entry tool for the CGIAR Big Data project, and this will be explored in a joint EAGER submission with CIMMYT. COPO has also been selected to act as one of the data ingestion pipelines for data arising from the Designing Future Wheat programme, depositing open data into the Grassroots repository. COPO is also being included in grant submissions to assist vertebrate and wheat communities in effective metadata management. COPO runs within the CyVerse UK National Capability infrastructure. |
| URL | https://copo-project.org |
| Title | Cufflinks application |
| Description | application to run Cufflinks in CyVerse, it includes a wrapper and a Docker image for the software. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Users are now able to run cufflinks in the UK execution system through an easy to use web interface. |
| URL | https://de.cyverse.org/de/?type=apps&app-id=cufflinks-0.0.0u1&system-id=agave |
| Title | Cuffmerge application |
| Description | Application to run cuffmerge on CyVerse, it includes a wrapper and a Docker image for the related Cufflinks software. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Users are now able, with an easy to use web interface, to run jobs in the UK execution system. |
| URL | https://de.cyverse.org/de/?type=apps&app-id=cuffmerge-0.0.0u1&system-id=agave |
| Title | Cutadapt SE application |
| Description | Application to use cutadapt for single reads on CyVerse. It includes a wrapper and a Docker image for the software. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Users can now run cutadapt jobs for single end reads in the CyVerse UK execution system, using a user-friendly web interface. |
| URL | https://de.cyverse.org/de/?type=apps&app-id=cutadapt_SE-1.13.0u1&system-id=agave |
| Title | CyVerse UK web application |
| Description | Website to use CyVerse UK applications taking advantage of the EI storage system. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | UK users have now a graphical interface to run jobs in the UK, and, requesting access to it, can archive their jobs on site without the need for command line tools. |
| URL | https://cyverseuk.herokuapp.com/ |
| Title | DFW cloud HPC resources |
| Description | Designing Future Wheat researchers are able to request virtual machines within CyVerse UK to undertake bioinformatics analysis. |
| Type Of Technology | Grid Application |
| Year Produced | 2019 |
| Impact | We have produced a robust and secure cloud framework within CyVerse UK to allow DFW researchers to access DFW and public data to analyse, as well as upload their own. We have already completed two successful pilot projects with external collaborators, and are now making the services available to all DFW researchers. |
| URL | http://cyverseuk.org/about/collaborations/designing-future-wheat/ |
| Title | Gene Align and Family Aggregator |
| Description | Gene Align and Family Aggregator (GAFA) generates an SQLite database that can be visualised with Aequatus, an open-source homology browser developed with novel rendering approaches to visualise homologous, orthologous and paralogous gene structures. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Since the upload to the Galaxy ToolShed, this tool has been cloned / installed 31 times |
| URL | https://toolshed.g2.bx.psu.edu/view/earlhaminst/gafa/ |
| Title | GeneSeqToFamily |
| Description | GeneSeqToFamily represents the Ensembl Compara pipeline as a set of interconnected Galaxy tools, so they can be run interactively within the Galaxy's user-friendly workflow environment while still providing the flexibility to tailor the analysis by changing configurations and tools if necessary. Additional tools allow users to subsequently visualise the gene families produced by the workflow, using the Aequatus.js interactive tool, which has been developed as part of the Aequatus software project. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | This new workflow has been used for a number of research projects at the Earlham Institute, including the investigation of gene families for the koala genome, in collaboration with Kathy Belov, Wilfried Haerty, Will Nash and Federica di Palma. The workflow was published as a preprint on bioRxiv in 2017 and subsequently accepted into the GigaScience journal in 2018. |
| Title | LotuS2 Galaxy wrapper |
| Description | Galaxy wrappers for LotuS2, a complete amplicon pipeline and quality filter to cluster sequences into operational taxonomic units (OTUs). |
| Type Of Technology | Software |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | This Galaxy tool was used as part of the "Analysis of 16S rRNA metagenomic experiments" training course, held virtually 14-15/06/2021 with 19 attendees. |
| URL | https://toolshed.g2.bx.psu.edu/view/earlhaminst/lotus2/ |
| Title | MARTi demonstration server - hosting on the CyVerse UK e-infrastructure |
| Description | MARTi is software for real-time analysis of metagenomic sequence data. Cyverse UK hosts two instances of MARTi - one is a demonstration server for potential users to try out, one is a development server for sharing analysis with key collaborators. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | Requests for access to the software. |
| URL | http://marti.cyverseuk.org |
| Title | Pocket Nebula |
| Description | Pocket Nebula provides an instant isolated environment for OpenNebula operations (host and guest config and management). Comprises of the code to create a Dev Container preconfigured with the OpenNebula CLI, and the Ansible orchestration tool. - OpenNebula is an Open Source Cloud & Edge Computing Platform. - A development container allows you to use a container as an isolated, full-featured development environment. |
| Type Of Technology | Software |
| Year Produced | 2025 |
| Open Source License? | Yes |
| Impact | Pocket Nebula allows all NBI institutes using OpenNebula to have an instant administration environment, and enabling quick repeatable researcher support. |
| URL | https://github.com/aioue/pocket-nebula |
| Title | SMART Domains |
| Description | Search domains in protein sequences using SMART |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Since developed this tool has been cloned / installed for 7 times, we are expecting more usage once its become part of GeneSeqToFamily workflow. |
| URL | https://toolshed.g2.bx.psu.edu/view/earlhaminst/smart_domains/ |
| Title | Suite Ensembl REST |
| Description | A suite of Galaxy tools designed to work with Ensembl REST API. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Since developed this tool has been cloned / installed for 44 times. |
| URL | https://toolshed.g2.bx.psu.edu/view/earlhaminst/suite_ensembl_rest/ |
| Title | The Grassroots Infrastructure |
| Description | The Grassroots software is an open source "as-a-Service" stack that powers a number of data dissemination and analysis activities at EI, and other sites such as CerealsDB at the University of Bristol. We have continued to develop the functionality within the software stack to share crop-related datasets. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Grassroots has previously been used to host the Field Pathogenomics project website and Yellow Rust map, the EI wheat BLAST service, the CerealsDB federation project, and the multi-scale improvements to the Polymarker marker design software. Recently, Grassroots has been put forward as the main data repository and metadata catalogue for the Designing Future Wheat project, and has started to host data from this project, the Open Wild Wheat Consortium, and 5 new wheat genomes from EI. The Grassroots service runs within the CyVerse UK National Capability infrastructure. |
| URL | https://grassroots.tools/ |
| Title | TreeBeST best |
| Description | Developed Galaxy wrapper for TreeBeST 'best'. TreeBeST is a tool to generate a phylogenetic tree using CDS alignment and species tree. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Since developed this tool has been cloned / installed for 31times. |
| URL | https://toolshed.g2.bx.psu.edu/view/earlhaminst/treebest_best/ |
| Title | application to concatenate multiple files |
| Description | Application that allows concatenating multiple files in the CyVerse UK execution system, it includes a wrapper. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Users can now concatenate multiple files in the UK execution system, without need to download and reupload their data for further analysis. |
| URL | https://cyverseuk.herokuapp.com/submission/concatenate_files-0.0.0u1 |
| Title | application to create blast databases |
| Description | Application to create a blast database in CyVerse, it includes a wrapper and a Docker image for the related software. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Users are now able to create a blast database in the UK execution system, using a user-friendly web interface. |
| URL | https://de.cyverse.org/de/?type=apps&app-id=create_blast_db_2.2.31-0.0.0u1&system-id=agave |
| Title | coveragebed application |
| Description | Application to run "coveragebed" in CyVerse, it includes a wrapper and a Docker image for the related software. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Users are now able to run coveragebed in the UK execution system, from an easy to use web interface. |
| URL | https://de.cyverse.org/de/?type=apps&app-id=coverageBED_2.25.0-0.0.0u1&system-id=agave |
| Title | cuffdiff application |
| Description | Application to run Cuffdiff in CyVerse, it includes a wrapper and a Docker image for Cufflinks. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Users are now able to use cuffdiff, with as much as 16 conditions, in the UK execution system, accessing a user-friendly web interface. |
| URL | https://de.cyverse.org/de/?type=apps&app-id=Cuffdiff-0.0.0u1&system-id=agave |
| Title | ete |
| Description | Analyse phylogenetic trees using the ETE Toolkit |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Since developed this tool has been cloned / installed for 33 times. |
| URL | https://toolshed.g2.bx.psu.edu/view/earlhaminst/ete/ |
| Title | file processing application to cut columns |
| Description | Application to process files filtering columns in CyVerse. It includes a wrapper to use the official ubuntu:16.04 Docker image. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Users are now able to process their files filtering data by columns without the need to download and re-upload them again to the CyVerse UK execution system. They can also do so through an easy to use web interface. |
| URL | https://de.cyverse.org/de/?type=apps&app-id=cut_columns-test-0.0.0&system-id=agave |
| Title | gblocks Galaxy wrapper |
| Description | Galaxy wrapper for gblocks, a tool to select conserved blocks from multiple sequence alignments. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Since the upload to the Galaxy ToolShed, this tool has been cloned / installed 18 times. |
| URL | https://toolshed.g2.bx.psu.edu/view/earlhaminst/gblocks |
| Title | hcluster_sg |
| Description | Developed Galaxy wrapper for hcluster_sg, a hierarchically clustering on a sparse graph |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Impact | Since developed it's been downloaded/cloned for 70 times. |
| URL | https://toolshed.g2.bx.psu.edu/view/earlhaminst/hcluster_sg/ |
| Title | hcluster_sg_parser |
| Description | Converts hcluster_sg output into separate list of ids |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Since tool is available on Galaxy ToolShed, its been cloned / installed 48 times. |
| URL | https://toolshed.g2.bx.psu.edu/view/earlhaminst/hcluster_sg_parser/ |
| Title | iRODS server open to the public |
| Description | data store federated with CyVerse for users to store and share datasets with collaborators. It also hosts a data commons for DFW project |
| Type Of Technology | Systems, Materials & Instrumental Engineering |
| Year Produced | 2019 |
| Impact | Users can now store a considerable amount of data in a UK repository, while being able to run jobs using such data as input. They can also easily share data with collaborators relying on fast data transfer. They can also make data public changing permissions or submit them with metadata to public folders |
| Title | minia Galaxy wrapper |
| Description | Galaxy wrappers for minia, a short-read assembler based on a de Bruijn graph. |
| Type Of Technology | Software |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | This tool was developed as part of the "Pangenome tools in Galaxy" project during the "COVID-19 Biohackathon", virtual, 05-11/04/2020, to enable the study of variation of SARS-CoV-2 genomes using the Galaxy bioinformatics web platform. |
| URL | https://toolshed.g2.bx.psu.edu/view/iuc/minia/ |
| Title | rDock Galaxy wrapper |
| Description | Galaxy wrapper for rDock, a fast, versatile and Open Source program for docking ligands to proteins and nucleic acids. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | Since the upload to the Galaxy ToolShed, this tool has been cloned / installed 14 times. |
| URL | https://toolshed.g2.bx.psu.edu/view/earlhaminst/rdock |
| Title | rfparser |
| Description | rfparser parses publications retrieved from ResearchFish via its API and produces the files needed to automatically update the profile pages for researchers and groups on the Earlham Institute's website. |
| Type Of Technology | Software |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | rfparser helps the Earlham Institute in fulfilling its obligations under the UK Research and Innovation open access policy. |
| URL | https://github.com/TGAC/rfparser/ |
| Title | scater Galaxy wrapper |
| Description | Galaxy wrappers for scater, a Bioconductor package to facilitate rigorous pre-processing, quality control, normalization and visualization of scRNA-seq data. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | These Galaxy tools were used as part of a "Single-Cell RNAseq Training Course" at the Earlham Institute to teach how to perform pre-processing, quality control, normalization and visualization of scRNA-seq data. |
| URL | https://toolshed.g2.bx.psu.edu/view/iuc/suite_scater/ |
| Title | smina Galaxy wrapper |
| Description | Galaxy wrapper for smina, a fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Since the upload to the Galaxy ToolShed, this tool has been cloned / installed 12 times. |
| URL | https://toolshed.g2.bx.psu.edu/view/earlhaminst/smina |
| Title | web hosting for research service - lotus2 |
| Description | we provided web hosting service and support for lotus2, which is now available to the research community |
| Type Of Technology | Systems, Materials & Instrumental Engineering |
| Year Produced | 2020 |
| Impact | the software is now available to everyone who may wish to use it on its own website |
| Title | web server hosting on the CyVerse UK e-infrastructure |
| Description | CyVerseUK is hosting a 3 web servers for external researchers free of charge for a total of 5 hosts. |
| Type Of Technology | Systems, Materials & Instrumental Engineering |
| Year Produced | 2019 |
| Impact | Researchers have the possibility to host their work free of charge for the community to take advantage of. they don't have to rely on commercial vendors and can take advantage of EI support in case of issues. |
| Title | wheelforge |
| Description | Recipes and continuous integration (CI) to build wheels for Python packages that don't provide them on PyPI. |
| Type Of Technology | Software |
| Year Produced | 2022 |
| Open Source License? | Yes |
| Impact | Since its introduction, this tool has been adopted by the Galaxy Project, which has used it to build Python wheels for more than 10 backend dependencies that were not provided on PyPI. |
| URL | https://github.com/galaxyproject/wheelforge/ |
| Description | "Support Python 3.13 and NumPy 2" project at the 2024 Galaxy Community Conference (GCC2024) CollaborationFest |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Nicola Soranzo led the "Support Python 3.13 and NumPy 2" project at the CollaborationFest community gathering, part of the 2024 Galaxy Community Conference (GCC2024). The project aimed at enabling support for the new versions of Python and NumPy in the Galaxy project ( https://galaxyproject.org/ ) backend code. Slides for all the CollaborationFest projects and their outcomes: https://docs.google.com/presentation/d/1uAgjha2Tqz0esolcu46xP89Jv43k3Edg4r4n4SBfHfE/edit#slide=id.g2e8d05ba6e2_0_94 |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://galaxyproject.org/events/gcc2024/cofest/ |
| Description | "Where is the dark matter? The Galaxy Community shedding light on activities, connections, scope and unaddressed shortcomings" workshop at the ELIXIR All Hands 2024 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo, together with Björn Grüning, led the workshop "Where is the dark matter? The Galaxy Community shedding light on activities, connections, scope and unaddressed shortcomings" at the ELIXIR All Hands 2024 meeting, 10-12/06/2024, Uppsala, Sweden. The workshop was organised by the ELIXIR Galaxy Community in order to raise awareness and foster interdisciplinary exchange, with members of the Community presenting their particular activities and underlying technical highlights in a world café setup. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://docs.google.com/document/d/1i5coxz4ubcMdMr5E4v6OVPqbHs2S7ujOVnkRj6I33Cg/edit?usp=sharing |
| Description | 17-21 July 2017_2nd Interdisciplinary Signaling Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | In this interdisciplinary workshop advanced science was combined with informal summer activities to solve multi-disciplinary scientific questions, by bringing early career scientists together with more established researchers in a relaxing and beautiful location. Invited speakers presented talks on the topics of cell regulation, network modelling, genomics, systems biology, bioinformatics, structural biology, biochemistry, and cheminformatics. Then, selected talks from other participants will be followed by multi-disciplinary teamwork sessions in the afternoon, followed by cultural and social activities, such as medieval team building and handicraft activities in the Visegrad Castle. Poster sessions and plenty of informal opportunities allowed the participants to discuss complex and exciting questions as well as develop new collaborations. The renaissance surroundings of the venue nicely matched with the interdisciplinary nature of the workshop. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://signalingworkshop.org/ |
| Description | 1st ELIXIR-UK Hackathon |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo and Ms Catherine Hunter (together with Gabriella Rustici from the University of Cambridge) organised this hackathon at the University of Cambridge, Cambridge, UK, 11-13/09/2019. The hackathon was attended by 11 participants from across Great Britain, which worked on the integration of various ELIXIR-supported resources, like Bioschemas, FAIRDOM SEEK, FAIRsharing, Galaxy, InterMine, and TeSS. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://docs.google.com/document/d/1xyW0F7LxnDnmwli_Ftvwjo6rXcsEY2gkEksCFNnBbmM/edit?usp=sharing |
| Description | 2020 Galaxy Admin Training |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo was one of the 5 trainers at this workshop at the Barcelona Supercomputing Centre, Barcelona, Spain, 2-6/3/2020. Over the course of 5 intense days, 31 attendees from 4 Continents learned how to install and manage a production-level Galaxy server and related services. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://galaxyproject.org/events/2020-03-admin/ |
| Description | 2021 Galaxy Community Conference (GCC2021) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The 2021 Galaxy Community Conference (GCC2021), online, 28/06-09/07/2021, brought together almost 400 of faculty, clinicians, researchers, and students interested in the Galaxy platform, all working in and supporting data intensive science that is accessible, sharable and reproducible. Dr. Nicola Soranzo helped at the Developer track during the week of training that preceded the conference. Dr. Soranzo also led the "Galaxy Workflow formats and exporting" project at the CollaborationFest that closed the event. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.vibconferences.be/events/gcc2021-virtual-edition |
| Description | 2022 Galaxy Community Conference (GCC2022) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The 2022 Galaxy Community Conference (GCC2022), University of Minnesota, USA, 17-23/07/2022, brought together hundreds of researchers, trainers, tool developers, software engineers, and computational infrastructure providers interested in the Galaxy platform, all working in and supporting data intensive science that is accessible, sharable and reproducible. Dr. Nicola Soranzo led the "At the edge of the Galaxy, the lonely life of a (small scale) local Galaxy server admin" Birds of a Feather (BOF) session. Dr. Soranzo also led the "Add type annotations to BioBlend API" project at the CollaborationFest that closed the event. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://galaxyproject.org/events/gcc2022/ |
| Description | 24-25 April 2017_Multiscale analysis of host-microbe interactions in plants, animals and humans |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | The aim of this workshop was to bring together key experts and early-stage scientists working on host-microbe interactions, including pathogen infections, commensals and microbiome level studies, to share novel scientific ideas on the multiscale investigation of host-microbe interactions and to provide an exciting opportunity to establish and improve cross-disciplinary and UK-wide collaborations. After kick off with three keynote speakers on current challenges, the program provides structured study groups to discuss 1) novel methodological approaches; 2) potential future projects requiring participants from different disciplines; 3) the best ways to get funding for such multi-disciplinary projects. We facilitated these goals with short presentations and brainstorming opportunities in coordinated team works, and with panel discussion with representatives of key relevant funding agencies and charities. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.multiscalebiology.org.uk/events/event/multiscale-analysis-of-host-microbe-interactions/ |
| Description | 5 ways EI is improving global food security |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | 5 ways EI is improving global food security |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/5-ways-earlham-institute-improving-global-food-security |
| Description | 600k machine learning collaboration to supercharge data driven science |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | 600k machine learning collaboration to supercharge data driven science |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/newsroom/%C2%A3600k-machine-learning-collaboration-supercharge-data-driven... |
| Description | A PhD, is it worth it? Just ask our students |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | A PhD, is it worth it? Just ask our students |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/phd-it-worth-it-just-ask-our-students |
| Description | AI for Wheat workshop 2020 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Attended the DFW AI for Wheat workshop at the Alan Turing Institute, where we discussed and planned the submission of proposals for collaborative Data Study Groups around the use of machine learning for wheat data analysis. |
| Year(s) Of Engagement Activity | 2020 |
| Description | ARN2: Uncovering the multi-layered regulation of autophagy From Functional Genomics to Systems Biology |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | ARN2: Uncovering the multi-layered regulation of autophagy From Functional Genomics to Systems Biology |
| Year(s) Of Engagement Activity | 2019 |
| Description | Aequatus and the Galaxy workflow (GeneSeqToFamily) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Organised a workshop as a part of 3rd Annual BiVi Conference, and introduced Aequatus and GeneSeqToFamily workflow |
| Year(s) Of Engagement Activity | 2017 |
| Description | Analysing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions Scientific Advisory Board Meeting Earlham Institute |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Analysing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions Scientific Advisory Board Meeting Earlham Institute |
| Year(s) Of Engagement Activity | 2019 |
| Description | Analysis of 16S rRNA metagenomic experiments |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo was one of the trainers at this online training course organised by VIB, 14-16/06/2021. Participants learned how about the processing and statistical analysis of 16S rRNA metagenomic experiments using the LotuS2 pipeline and R, both on the Galaxy platform and the command line. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://training.vib.be/all-trainings/analysis-16s-rrna-metagenomic-experiments-online |
| Description | Analysis of 16S rRNA metagenomic experiments 2022 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo was one of the trainers at this online training course organised by VIB, 21-23/11/2022. Participants learned how about the processing and statistical analysis of 16S rRNA metagenomic experiments using the LotuS2 pipeline and R, both on the Galaxy platform and the command line. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://training.vib.be/all-trainings/analysis-16s-rrna-metagenomic-experiments-online-0 |
| Description | Analyzing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions SYSBIO 2018 - Advanced Lecture Course on Systems Biology |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Analyzing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions SYSBIO 2018 - Advanced Lecture Course on Systems Biology |
| Year(s) Of Engagement Activity | 2019 |
| Description | Article - How are we related? A Compara-bly easy workflow to find gene families |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Press release to introduce GeneSeqToFamily, an open-source Galaxy workflow that helps scientists to find gene families. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Attendance at ELIXIR Node Coordinators Triangle Meeting: Nicola Soranzo, Krzysztof Poterlowicz and Catherine Knox |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | ELIXIR Node Coordinators Triangle Meeting 4-6 March 2024, Hybrid (Prague and Virtual), this meeting is for all Node Coordinators - Technical, Training and Node from each Node to get together to share knowledge and Best Pratices between Nodes. Nicola Soranzo - Technical Coordinator (virtual), Krzysztof Poterlowicz - Training Coordinator (in person) and Catehrine Knox - Node Coordinator (virtual) |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://elixir-europe.org/events/training-platform-and-coordinators-triangle-co-located-event |
| Description | Attendance at the Biodiversity Genomics 2020 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Rob Davey attended Biodiversity Genomics 2020 which brought together researchers across the world to celebrate the achievements in genome sequencing across the eukaryotic tree of life, explored current challenges and their likely solutions, and looked forward to the coming decade of the application of genomics across the globe. With major projects starting to deliver data at scale, new tools for sequencing and assembling genomes becoming available, and increased awareness of the power of whole genome data in understanding organismal biology and ecosystem processes, Biodiversity Genomics 2020 promised to be a milestone in the effort to "sequence life for the future of life". Continuing the tradition of ambitious, collaborative science Biodiversity Genomics 2020 continues the tradition of previous meetings of Genomes 10k, the Vertebrate Genomes Project, the Global Invertebrate Genomics Alliance, and the Earth BioGenome Project. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.sanger.ac.uk/science/biodiversity-genomics-2020/ |
| Description | Attendance at the ELIXIR All Hands 2020 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Attendance at the ELIXIR All Hands representing COPO and possible future collaborations |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://elixir-europe.org/events/elixir-all-hands-2020 |
| Description | Attendance at the ELIXIR-UK All Hands 2020 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Rob Davey attended the ELIXIR-UK All Hands 2020 to take part in discussions about ongoing and possible future collaborations |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/elixir-uk-all-hands-2020 |
| Description | Attendance at the UK-Conference of Bioinformatics and Computational Biology 2020 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Attendance at the UK-Conference of Bioinformatics and Computational Biology 2020 The UK-CBCB conference is designed to bring together biologists, bioinformaticians, computer scientists, software engineers and data scientists across the life sciences to share innovations, applications and best practice in their fields. Rob Davey, Nicola Soranzo, Alice Minotto attended to participate in discussions and to add impact to the ongoing work in bioinformatics |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/uk-conference-bioinformatics-and-computational-biology-2020#About- |
| Description | Attended and Presented a talk at the DFW All Hands 2020 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Rob Davey attended the DFW All Hands 2020 (DFW Annual Meeting) and presented a talk on the work being carried out in WP4 |
| Year(s) Of Engagement Activity | 2020 |
| Description | BIKE data management |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | We gave an overview of good practice for data management to post graduate students working in research park as part of the bioinformatics knowledge exchange series of lesson they organise. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Big Data Science Training for EDESIA Year 1 Cohort 27-28 January 2021 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | An introductory workshop for the first cohort of EDESIA PhD students. This workshop was spread over two days (10:00-15:00), delivered via Zoom and covered the following topics: Research Data Life Cycle; an Introduction to Galaxy including Hands-on session; an Introduction to machine learning; Data Brokering and FAIR data (including demonstration of COPO (Collaborative OPen Omics platform); and an Introduction to Network Biology using Cytoscape, including hands-on exercises. All presentations and hands-on sessions were recorded and shared with the students after the workshop had concluded. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Big Data Science Workshop for DTP and EDESIA students 16 February 2023 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | As part of the Norwich DTP and EDESIA Year 1 Cohort of students (~40) workshop in Big Data Science, breakout discussion groups were facilitated to allow students to share with their peers their awareness of online training resources providing valuable bioinformatics skills. Presentations were given by training leads at each of John Innes Centre, University of East Anglia and Earlham Institute to provide signposting to further, free-to-access training materials online, which will be valuable to their skills development over the course of their PhDs. |
| Year(s) Of Engagement Activity | 2023 |
| Description | BioCompute Objects: Tools for Communicating Next Generation Sequencing Data and Analysis |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The workshop engages various stakeholders in both the public and private sectors in creating and using the BioCompute standard for NGS and other bioinformatics data analysis communications with the FDA. Specifically, the workshop had two components: use case examples, and hands on & demonstrations of new tools that leverage BioCompute. A new Precision FDA-BioCompute Challenge was also launched at the event. Dr. Nicola Soranzo presented a demo of the Galaxy web-based platform for accessible, reproducible, and transparent computational research. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.biocomputeobject.org/2019-workshop.html |
| Description | BioHackathon Europe 2022 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo participated to this European hackathon in Seine Port, France, 07-11/11/2022. During this week of intense hacking and collaboration, Dr. Soranzo contributed to the "Support for the Common Workflow Language standard version 1.2 in Galaxy" project ( https://github.com/elixir-europe/biohackathon-projects-2022/tree/main/28 ). A slide with the outcomes of this hacking project is available at https://docs.google.com/presentation/d/1AuLhyI1V1QNRJFl3jn3uxZSo1G-UaqRlDAiuJW7JYjY/edit#slide=id.p29 |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://2022.biohackathon-europe.org/ |
| Description | Biohackathon Europe 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo participated to this hackathon in Seine-Port, France, 18-22/11/2019. During this week of intense hacking and collaboration, Dr. Soranzo contributed to various Galaxy-related projects, in particular to one called "Updating the Galaksio workflow management interface for Galaxy and migrating it to Vue.js" ( https://github.com/elixir-europe/BioHackathon-projects-2019/tree/master/projects/19 ). |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://2019.biohackathon-europe.org/ |
| Description | Biohackathon Europe 2020 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo participated to this virtual hackathon, 09-13/11/2020. During this week of intense hacking and collaboration, Dr. Soranzo led the "Improve the support of Common Workflow Language in Galaxy" project ( https://github.com/elixir-europe/BioHackathon-projects-2020/tree/master/projects/17 ). A short presentation with the outcomes of this hacking project is available at https://docs.google.com/presentation/d/1CFnYT_kf13qMXGgRSmqlIej1jNL6fmYvKHRyRhL5ocA/edit?usp=sharing |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://2020.biohackathon-europe.org/ |
| Description | Biohackathon Europe 2021 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo participated to this European hackathon in Terrassa, Barcelona, Spain, 08-12/11/2021. During this week of intense hacking and collaboration, Dr. Soranzo led the "Support for the Common Workflow Language version 1.2 in Galaxy" project ( https://github.com/elixir-europe/bioHackathon-projects-2021/tree/main/projects/37 ). A slide with the outcomes of this hacking project is available at https://docs.google.com/presentation/d/1SqFs22-XN5U69r1Y65nmc3MdblvXiQWFhl-MA-HkxHY/edit#slide=id.g10110a35a6e_0_2506 |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://2021.biohackathon-europe.org/ |
| Description | Build, empower and amplify: bioinformatics for agri-research in Africa - 16/07/2018 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. Collectively, our international reach as of March 2019 has extended across the globe, with highlight pieces in the Guardian, the BBC World Service, the Washington Post and more, as well as local TV and radio. In 2018, the estimated readership of news stories we shared was well in excess of 1 million. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://acaciaafrica.org/build-empower-amplify-bioinformatics-agri-research-africa/ |
| Description | COPO: A Data Stewardship Platform for Plant Scientists - Computer Demo session (PAG XXV) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | We present Collaborative Open Plant Omics (COPO), a brokering service between plant scientists and public repositories, which enables management, aggregation and publication of research outputs described and integrated using linked data. COPO provides consolidated access to services and disparate information sources via a web interface and Application Programming Interfaces. Users create profiles which represent a logical span of research, such as a grant funding round or PhD project. 'Research objects' comprising a broad spectrum of potential outputs (such as sequence data, images, manuscripts, source code, posters) can be uploaded into the profile. Annotation of these objects with community-supported standards is facilitated using simple user-interface wizards which aim to reduce the complexity of this task, supported by ISA components (http://isa-tools.org/) for metadata interoperability and automated metadata format conversion. COPO uses the Ontology Lookup Service (http://www.ebi.ac.uk/ols) to provide the crucial contextual metadata required for standardised data description. Currently, deposition of both data and metadata to the European Nucleotide Archive for sequence data, and Figshare for data types such as images, posters, and presentations is supported. In the future, we will support more public repositories for multi-omic data submission, and users will be able to search for and pull such data into analysis environments such as CyVerse and Galaxy. We will subsequently track the outputs and associated metadata in COPO, thus creating a provenance trail from data to publication. http://copo-project.org/ https://github.com/collaborative-open-plant-omics/COPO |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://pag.confex.com/pag/xxv/meetingapp.cgi/Paper/23791 |
| Description | COVID-19 Biohackathon 2020 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo participated to this virtual hackathon, 05-11/04/2020. During this week of intense hacking and collaboration, Dr. Soranzo participated to the "Pangenome tools in Galaxy" project ( https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome#pangenome-tools-in-galaxy ). The goal of this project was to add the missing tools (and conda dependencies) to enable the creation of a Galaxy workflow for pangenome analysis, in order to allow the study of variation of SARS-CoV-2 genomes using the Galaxy bioinformatics web platform. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://github.com/virtual-biohackathons/covid-19-bh20 |
| Description | Chair of a Workshop at the ELIXIR All Hands 2023: Nicola Soranzo, Day Two: Workshop: Scaling user support: Galaxy from a service perspective |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Nicola Soranzo co Chaired a workshop on scaling user support: Galaxy from a servcie perspective |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://docs.google.com/document/d/1kTot1V-t7xJx5ftQJiWiht5e3ix3nAq3MkFKhU4_4lA/edit?usp=sharing |
| Description | Challenges and Opportunities in Plant Science Data Management (Workshop, PAG 2019) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Davey organised the PAG 2019 workshop Challenges and Opportunities in Plant Science Data Management alongside Carolyn Lawrence-Dill from Iowa State University, USA. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.intlpag.org/2019/ |
| Description | CollaborationFest of the Bioinformatics Community Conference 2020 (BCC2020) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo was one of the organisers of the CollaborationFest, part of the Bioinformatics Community Conference 2020 (BCC2020), virtual, 17-25/07/2020. Participants from the BOSC and Galaxy communities gathered together online to contribute code, documentation, training materials, and challenging analysis problems and use cases. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://bcc2020.github.io/cofest/ |
| Description | Conference Poster Presentation: Discovery and visualisation of homologous genes and gene families using Galaxy |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The poster presented at the International Plant and Animal Genomes Conference (San Diego, USA) conference was selected on abstract submission. The poster was presented in front of industry participants, donors, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Anil Thanki, Nicola Soranzo, Wilfried Haerty, Robert Davey and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Conference Talk - Aequatus : An open-source homology browser (ICG-13) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | More than 300 people attended conference and had a good discussion after the talk about new features, which could be useful |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.icg-13.org |
| Description | CyVerse UK workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | About 40 researchers attended the workshop, where it was given a wide presentation of CyVerse and CyVerse UK, including the resources available to scientists. It was also showed how to use some of the applications developed or hosted on CyVerse. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.eventbrite.co.uk/e/cyverseuk-workshop-tickets-29982258743# |
| Description | CyVerse for Brassica: Performing Associative Transcriptomics by Integrating with Sequence and Phenotype Repositories |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | As part of the "CyVerse - Software, Tools, and Services for Data-Driven Discovery" workshop, Annemarie Eckes in the Davey group at EI spoke about Associative Transcriptomics (AT). AT is a method that links a physical genome, via the transcriptome, to quantitative phenotypic information. For complex polyploid crops such as Brassica napus, AT can be used to facilitate the identification of SNP markers. However, there are certain problems in performing AT for the Brassica Community: 1) this process is often data-intensive, as it commonly relies on large-scale genotypic and phenotypic raw data, and not all research groups have the computational capacity to do such analysis; 2) many groups are still dependent on the expertise of a small number of researchers who are able to generate AT data. With the help of CyVerse UK (http://cyverseuk.org), we are developing a reproducible workflow to make AT analysis available to the UK Brassica Community and beyond. The aim is to integrate phenotyping data stored in the Brassica Information Portal (BIP) (https://bip.earlham.ac.uk/) and sequence data from sequence repositories to establish an AT analysis framework, powered by tools and resources available within CyVerse. A Brassica researcher would first submit their genotypic and phenotypic raw data to the BIP and respective public repositories (e.g. the SRA/ENA sequence read archives). This ensures that their data will be stored in standardised formats and marked up with required metadata to enable reuse and subsequent comparison. With the data in place, the researcher will then be able to run AT analyses on CyVerse. We will present the current state of the project to the CyVerse user and Brassica communities in order to receive additional input and feedback. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://pag.confex.com/pag/xxv/meetingapp.cgi/Paper/25485 |
| Description | Cyberinfrastructure and the Carpentries - Workshop in Bogota, Colombia 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | We delivered a Carpentries instructor training in Bogota, Colombia, as part of the GROW Colombia project. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://froggleston.github.io/2019-10-22-ttt-colombia/ |
| Description | Data Brokering for Plant Scientists (DivSeek partner's meeting, PAG 2018, San Diego) |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Delivered a lightning talk to promote the COPO data brokering platform at the annual DivSeek partner's meeting at PAG. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Data Carpentry 1-4 March 2021 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | This workshop is designed to teach fundamental data skills and included sessions on: data organisation in spreadsheets, data cleaning with OpenRefine, SQL for data management, R for data analysis and visualisation. This workshop was converted from a 2-day face-to-face event into four, shorter days (10:00-15:00), which are better suited for virtual learning and maintaining concentration. Around 50% of attendees were PhD students, in line with our target audience and 100% of those providing feedback rated the workshop overall as 'Very Good' or 'Excellent', rated the trainers as 'Very Good' or 'Excellent' and would recommend the workshop. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/data-carpentry-virtual-workshop-2021 |
| Description | Data Carpentry 13 - 16 Mar 2023 (In-person) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | During two days of the Data Carpentry workshop (14th and 15th of March, 2023), I supported the lead instructor in teaching R for data analysis and visualization. My role was to field questions, provide clarifications, and assist participants as they navigated the complexities of R. I helped ensure that the concepts were clearly understood and effectively applied, furthering the aim of this workshop to enhance productivity through fundamental computing skills. My efforts played a crucial role in making R an integral part of the participants' research processes. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/events/data-carpentry-workshop-2023 |
| Description | Data Carpentry 28 Feb-3 Mar 2022 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | This workshop is designed to teach fundamental data skills and included sessions on: data organisation in spreadsheets, data cleaning with OpenRefine, SQL for data management, R for data analysis and visualisation. This workshop is usually run as a 2-day face-to-face event, but was delivered as four, shorter days (10:00-15:00), which are better suited for virtual learning and maintaining concentration. Around XX% of attendees were PhD students, in line with our target audience and XX% of those providing feedback rated the workshop overall as 'Very Good' or 'Excellent', rated the trainers as 'Very Good' or 'Excellent' and would recommend the workshop. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/data-carpentry-virtual-workshop-2022 |
| Description | Data Carpentry 5-6 March 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Of the 13 attendees, 11 were PhD students, the majority of which are based at the University of east Anglia (UEA). Feedback shows that 100% of the attendees would recommend the course and 100% rated the trainers as "very good" or "excellent". An attendee from BBSRC-strategically funded institute Rothamsted, showed interest in engaging with the community to host similar workshops at their own institution. |
| Year(s) Of Engagement Activity | 2016,2017,2019 |
| URL | http://www.earlham.ac.uk/data-carpentry-workshop-2019 |
| Description | Data Carpentry Workshop - 21-22 November 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Data Carpentry's aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. The workshops are are for any life scientist or computational science researcher who has data they want to analyse, and no prior computational experience is required. This hands-on workshop taught basic concepts, skills, and tools for working more effectively with data. Topics included data organisation in spreadsheets, data cleaning, SQL, the command line, and R for data analysis and visualisation, all using examples from biology. Participants bring their own laptops and are encouraged to actively participate. The intention for such workshops is that by the end of the workshop, delegates would have the skills to more effectively manage and analyse data, and that they would be able to apply the tools and approaches directly to their ongoing research. PhD students comprised over 45% of the audience for this workshop and feedback was good with 100% of delegates identifying the trainers as excellent, almost 90% rating the training overall as 'very good' to 'excellent' and 100% saying that they would recommend the course to others. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/data-carpentry-workshop-2017 |
| Description | Data Carpentry training |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Participants were given a training about how to organize and work efficiently with data, with a focus on the use of Excel and R for scientific research. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/data-carpentry-workshop-2017 |
| Description | Data Stewardship in the Life Sciences |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I spoke at the "Challenges and Opportunities in Plant Science Data Management" workshop on the subject of data management in the life sciences. Open data and integrative data sharing are fundamental factors in order to address the challenges of modern data-intensive science. There is a clear need to develop and maintain community-focussed, semantically-aware data stewardship and management platforms, such as COPO, that are able to cope with the description and sharing of potentially huge datasets arising from the life sciences. Once made available, it is not sufficient to assume that researchers around the globe have requisite skills and resources to analyse these data. Therefore, we need to provide large-scale data analysis environments that are fit for purpose, incorporating state-of-the-art interfaces and programmatic layers to meet broad end-user requirements, such as CyVerse and Galaxy. Finally, this can only happen when there are community-led efforts into implementing solutions for data standardisation, best practice, and FAIR data policy. We are now only just starting to take advantage of groundbreaking opportunities to make integrated data a reality, and thus enabling scientists to store, manage, and share their data as a first-class citizen of the scientific process. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://app.core-apps.com/pag_2017/event/e2bec353017762d275ce250c23e011e6 |
| Description | Data, Data, Data Everywhere (Pint of Science talk, Norwich) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Dr Davey delivered a talk as part of the Norwich 2017 Pint of Science series about the challenges and solutions for modern data management in the life sciences, including recent data developments, high-performance computing, and software tools. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://pintofscience.co.uk/event/crops-crystals-and-computers-technology-for-food-security |
| Description | Differential Expression Analysis and Visualisation using Galaxy (Genome 10K and Genome Science 2017) - 1 September 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Organised as part of a series of workshops aimed to encourage and support early careers researchers attending the Genome 10K and Genome Science 2017 conferences, this workshop provided a fantastic introduction both to the Galaxy platform, but also to RNAseq analyses. A lot of material was covered in this one day event, however, the vast majority of delegates believed the balance of detail to be perfect given the duration of this introductory, one-day course. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/genome-10k-and-genome-science-conference#Day4-4 |
| Description | Digital oral presentation at 14th congress of European Crohn's and colitis organisation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Conference oral presentation at the 14th congress of European Crohn's and colitis organisation. Presentation tited "the regulatory landscape of intestinal cells - investigating the transcriptional effect of autophagy impairment observed in Crohn's disease using organoid and network biology approaches". Digital oral presentation at main congress and also an oral presentation at the Y-ECCO basic science workshop. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.ecco-ibd.eu/ecco19.html |
| Description | Discovery and visualisation of homologous genes and gene families using Galaxy |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | More than 100 people attended this talk in 18th The Bioinformatics Open Source Conference (BOSC), which sparked questions and discussion afterwards during the poster session at the same conference. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Discovery and visualisation of homologous genes and gene families using Galaxy |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented this talk as a part of 25th International Plant and Animal Genome Conference 2017 in a GMOD workshop, had some discussion with other professional working in the same area, and made plans for further development |
| Year(s) Of Engagement Activity | 2017 |
| Description | DivSeek Partner's Meeting (PAG 2019) |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Davey attended the DivSeek Partner's Meeting in the Courtyard Marriott hotel at PAG 2019. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Divseek Working Group - Data Standards for Interoperable Tools |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | As part of the "DivSeek - Addressing the challenges and opportunities for information and data sharing associated with plant germplasm" session at PAG, I spoke about the DivSeek Data Standards for Interoperable Tools Working Group. This WG will promote best practice in data sharing in the plant sciences, through the use of open and interoperable software powered by the adoption of open standards, i.e. programmatic interoperability standards (APIs), controlled vocabularies, trait dictionaries, metadata standards, and ontologies. We aim to highlight gaps in interoperability that impede workflows important to the communities supported by DivSeek partners, by liaising with research development groups, other DivSeek working groups, and consortia with relevance to DivSeek. We will educate and train data generators about standards and the tools and resources that use them, in order to promote and foster standards-compliance for long-term open data stewardship. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://pag.confex.com/pag/xxv/meetingapp.cgi/Paper/26202 |
| Description | Down The Tubes! Talk at the Norwich Science Festival |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Dr Davey gave a talk on the internet and data science entitled "Down The Tubes!" at the 2018 Norwich Science Festival. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://norwichsciencefestival.co.uk/events/down-the-tubes/ |
| Description | EI Innovate annual stakeholder engagement event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | EI Innovate is an annual engagement event that provides insight into the Earlham Institute's research, exploring opportunities for innovation and collaboration. Specialising in agri-food, biotech, med-tech and public health, we have a wealth of experience collaborating with others to develop potential solutions to urgent industrial and societal challenges. EI Innovate events foster exciting and valuable conversations between academia and industry. An example of an exciting collaboration that resulted from a previous EI Innovate is the Hybrid Wheat Initiative, which connects 25 breeding companies and research institutes worldwide, to resolve the critical challenge of hybrid wheat. In 2023, we showcased our two new strategic programmes of research - Cellular Genomics and Decoding Biodiversity - and two National Bioscience Research Infrastructures (NBRIs) - Transformative Genomics and the Earlham Biofoundry. The programme included talks about Earlham expertise and capabilities, examples of collaborations, panel discussions, Innovation Showcase, exhibition, tours of the two National Bioscience Research Infrastructures (NBRIs) - Transformative Genomics and the Earlham Biofoundry, and networking. |
| Year(s) Of Engagement Activity | 2019,2020,2021,2022,2023 |
| URL | https://www.earlham.ac.uk/events/ei-innovate-2023 |
| Description | EI Innovate: a platform for collaboration and new ideas |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | EI Innovate: a platform for collaboration and new ideas |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/ei-innovate-platform-collaboration-and-new-ideas |
| Description | EI Socioeconomic impact report 2022 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | News story to publicise a socioeconomic impact report undertaken on the Institute's research. In forecasting future impact, the report was designed to demonstrate the quality and breadth of our work to our funders, stakeholders, and the wider public. Figures from the report have since been used in presentations and at other events. Feedback has been positive and demonstrates an increased awareness of EI impact and the areas of research we're engaged in. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/news/earlham-institute-economic-impact |
| Description | ELIXIR 2024-28 Programme - Consultation with Community Leads |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | As part of the process to prepare its 2024-28 Programme, ELIXIR held consultations with relevant stakeholders. On 09/04/2022, Dr Nicola Soranzo participated as a representative of the ELIXIR Galaxy Community to the meeting dedicated to ELIXIR Community Leads, providing input and suggestions to the ELIXIR Head of Strategy and colleagues. |
| Year(s) Of Engagement Activity | 2021 |
| Description | ELIXIR 5th Anniversary |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The "ELIXIR 5th Anniversary - Open Data for Impact and Innovation" event celebrated achievements from the past five years, provided updates on recent activities from the ELIXIR Nodes, Platforms and the ELIXIR Hub, described the priorities for the next Scientific Programme (2019-2023), alongside discussions of future resources, events and challenges. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.elixir-europe.org/events/elixir-5th-anniversary-event-2018 |
| Description | ELIXIR BioHackathon 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Soranzo participated at "ELIXIR BioHackathon 2018", Campus des berges de Seine, Seine Port, France, 12-16/11/2018 where he collaborated with other researchers on the hackathon project "CWL support in Galaxy" to improve the support of the Common Workflow Language (CWL) in the Galaxy bionformatics analysis platform. Dr. Soranzo also introduced himself as new ELIXIR UK Technical Coordinator to other members of the ELIXIR UK community. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://2018.biohackathon-europe.org/ |
| Description | ELIXIR Compute Platform F2F Meeting |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | There were discussion about how to proceed to develop a european cloud infrastructure for life science, both in technical terms and in terms of policies. |
| Year(s) Of Engagement Activity | 2018 |
| Description | ELIXIR Compute Platform F2F Meeting |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was a meeting to delineate the next steps in achieving the tasks of the ELIXIR computing platform. Particular attention was given to the creation of an European hybrid cloud with common AAI to enable life research and the integration with EOSC. Plans were made to engage with the community to develop pilots. |
| Year(s) Of Engagement Activity | 2019 |
| Description | ELIXIR Data Management Network F2F Meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo participated to this meeting in Brussels, Belgium, 26/02/2020.This was the second meeting of the new ELIXIR Data Management Network of experts, which is being established as part of Work Package 1 of the ELIXIR Converge project. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.eventbrite.co.uk/e/elixir-converge-kick-off-meeting-tickets-84730383859 |
| Description | ELIXIR Data Management Network Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo participated to this workshop in Noordwijkerhout, Netherlands, 14-15/10/2019. This meeting had the goal of establishing a network of Data Management experts across ELIXIR Nodes and beyond, in particular as part of the Work Package 1 of the ELIXIR Converge project. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://docs.google.com/document/d/1D7Tuwl_9Yg1JYtE6hEHko0NLCmhPTf5qCbevT5RF33E/edit?usp=sharing |
| Description | ELIXIR Europe All Hands 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Annual meeting to discuss how Elixir can benefit industry and how industry can engage. Additional logistical support for registration, provided by Earlham Institutes Advanced Training team (NC4) |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://elixir-europe.org/events/elixir-excelerate-all-hands-meeting-2019 |
| Description | ELIXIR Galaxy Community F2F meeting 2024 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Nicola Soranzo co-organised the 2024 meeting of the ELIXIR Galaxy Community ( https://elixir-europe.org/communities/galaxy ), a satellite event of the 2024 Galaxy Community Conference (GCC2024), Brno, Czechia, 26/06/2024. He also chaired this workshop and gave a talk titled "ELIXIR Science Tiers Open Call for Commissioned Services". |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://docs.google.com/document/d/1H0BfBVvjKf0TjW-hYxBdpPptm1xnf2VUDR4O8Rsozq8/edit?usp=sharing |
| Description | ELIXIR Technical Coordinators Group Meeting 2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo participated to this hybrid meeting, 26-27/04/2023, in his role of Technical Coordinator for ELIXIR-UK. This is the yearly meeting of the Technical Coordinators of all ELIXIR Nodes. The topics presented and discussed during this event included the findability and life cycle of Node Services, requirements and best practices for Services, dependencies on external services, and the role of Technical Coordinators. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://docs.google.com/document/d/10Fzg81_V7cu4habxRhaoPHuLjp2GBdMI3A4tY3d1LsM/edit?usp=sharing |
| Description | ELIXIR Training/Technical Coordinators Groups F2F Meeting 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo participated to this meeting in Barcelona, Spain, 12-13/11/2019, in his role of Technical Coordinator for ELIXIR-UK. This is the yearly face-to-face meeting of the Technical and Training Coordinators of all ELIXIR Nodes. During this event we discussed Human Genomics and Translational Data activities, the new concept of Service Bundles, the ELIXIR Industrial strategy, and the plan for the upcoming ELIXIR Converge project. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://docs.google.com/document/d/1CBFtxj8aVqC56ym5psS78-5ZPxqilhhyhUDQbmc3f4c/edit?usp=sharing |
| Description | ELIXIR Training/Technical Coordinators Groups Meeting 2020 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo participated to this virtual meeting, 24-25/11/2020, in his role of Technical Coordinator for ELIXIR-UK. This is the yearly meeting of the Training and Technical Coordinators of all ELIXIR Nodes. During this event Dr. Soranzo presented the Node Update for ELIXIR-UK. Other participants presented various COVID-19 initiatives across ELIXIR Nodes, updates about ongoing ELIXIR projects (e.g. Federated EGA), and reports from several Focus Groups. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://docs.google.com/document/d/15ZgeKIAK7XY2XAgfOKCLo7s62VWJx8Ecrn6R8ptYH-M/edit?usp=sharing |
| Description | ELIXIR Workshop for Galaxy training material and skills improvement |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. N. Soranzo, Mr. A. Thanki and Dr. E. Angiolini organised the workshop, which was attended by 16 participants coming from across Europe. During the first day, participants attended a Train-the-Trainer course delivered by Sarah Morgan (EBI, ELIXIR Training Platform). In the following 2 days, participants worked together and in groups on improving and extending the existing training materials for teaching Galaxy. A report is available at https://galaxyproject.eu/posts/2018/06/05/gtn-hackathon/ |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/elixir-workshop-galaxy-training-material-and-skills-improvement |
| Description | ELIXIR all hands 2020 - poster: the Cyverse UK cyberinfrastructure offer to support open science and FAIRness |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | We presented a poster to highlight what the CyVerse UK infrastructure is supporting in term of all the services hosted (COPO, grassroots and Galaxy in particular) to improve the FAIRness of the data landscape. We also showed how the data is shared with collaborators trough federation of iRODS instances. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://f1000research.com/posters/9-525 |
| Description | ELIXIR compute platform meeting |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | meeting to discuss what's been going on since March and what progresses we have made in the different working groups of the platform. Especially participated in the discussion about the creation of an hybrid cloud which researchers could submit to directly from any ELIXIR institution/country. |
| Year(s) Of Engagement Activity | 2020 |
| Description | ELIXIR-STEERS Kick-Off Meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The ELIXIR-STEERS Kick-off Meeting, Brussels, Belgium, 7-8/02/2024 brought together researchers from the 23 countries involved in this newly started EU-funded project. This collaborative three-year initiative aims to enhance large-scale, cross-border federated analysis in the life sciences within the European Research Area. Dr. Nicola Soranzo presented the plans for Task 3.4 ("Integrating optimisation criteria for environmental impact in commonly used workflow management systems") of the project. The ELIXIR-UK involvement in ELIXIR-STEERS is described in a news post: https://elixiruknode.org/news/2024/elixir-steers-launches/ |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://docs.google.com/document/d/102z0qPhjh5QEidhtWCqLGgryWwkgJVhme6EeafXYAgc/edit?usp=sharing |
| Description | ELIXIR-UK ALL-HANDS MEETING 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | The ELIXIR-UK All Hands Meeting provided updates on recent activities from the ELIXIR UK Node and ELIXIR Hub, alongside discussions of future resources, events and roadmapping breakouts.Dr Davey presented the COPO project and CyVerse UK infrastructure as UK-specific resources that were being developed as national infrastructure for UK researchers. There was much interest from the participants in both projects, and conversations at this event led to the submission of a BBSRC TRDF with Gos Micklem (Cambridge), Dr Davey and Dr Shaw (EI). |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.elixir-europe.org/events/elixir-uk-all-hands-meeting-2017 |
| Description | ELIXIR-UK All Hands 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | This award provided the majority of funding for the logistics (accommodation, room hire, catering, travel) for the event. ELIXIR-UK Member Organisation staff were invited to join to learn more about ELIXIR-UK activities over the previous year, present their work, and discuss together ideas for the future of ELIXIR-UK. Funders, staff from potential future ELIXIR-UK Member Organisations, and representatives from the ELIXIR Hub also participated. Aim was to promote networking amongst the ELIXIR-UK community, and to further develop plans for future work of ELIXIR-UK. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/elixir-uk-all-hands-2019 |
| Description | ELIXIR-UK All Hands 2025: Cardiff |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | The ELIXIR-UK All Hands Meeting 2024, held at Cardiff's iconic Principality Stadium on November 19-20, brought together 70 attendees from across almost all members of ELIXIR-UK, and representatives from the Welsh Government, BBSRC and MRC. Participants joined in to reflect on achievements and discuss the future and direction of our efforts. Hosted by our members at Cardiff University, the event showcased the power of collaboration in advancing research infrastructure and building a culture of collaboration in the life sciences. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://elixiruknode.org/news/2024/elixir-uk-all-hands-2024-a-celebration-of-collaboration-and-innov... |
| Description | ELIXIR-UK All Hands Meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | This award provided the majority of funding for the logistics (accommodation, room hire, catering, travel) for the event. ELIXIR-UK Member Organisation staff were invited to join to learn more about ELIXIR-UK activities over the previous year, present their work, and discuss together ideas for the future of ELIXIR-UK. Funders, staff from potential future ELIXIR-UK Member Organisations, and representatives from the ELIXIR Hub also participated. Aim was to promote networking amongst the ELIXIR-UK community, and to further develop plans for future work of ELIXIR-UK. |
| Year(s) Of Engagement Activity | 2016,2017,2018 |
| URL | http://www.earlham.ac.uk/elixir-all-hands-2018 |
| Description | ELIXIR-UK Hackathon 2021 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | We ran the second UK hanckathon to bring together UK participants to onboard ELIXIR standards (like Bioschemas), contribute to resources (like RDMkit) and integrate resources towards a common infrastructure. This Hackathon was led by Nicola Soranzo, who is the Node Technical Coordinator and Co-lead of the Galaxy Platform |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://elixiruknode.org/uncategorized/elixir-uk-fosters-collaboration-at-our-second-hackathon/ |
| Description | ELIXIR-UK Scientific Development Group: Review Meeting 2023 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo is a current member of the ELIXIR-UK Scientific Development Group, a small panel of experts tasked with reviewing the applications for new ELIXIR-UK Node Services to ensure high service quality and match UK priorities as identified by its funders. In July 2023, the Group met virtually to review several submissions and approved no new UK Node Services. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Earlham institute attendendance at ELIXIR-UK All Hands November 2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Earlham Institite attendees at the ELIXIR-UK All Hands 2023 in Norwich: Aaliya Providence, Anthony Hall, Eva Wan, Jazz Urog, Martin Ayling, Neil Hall, Nichola Wong, Nicola Soranzo, SEanna McTaggart, Yuk Chiu Ku, Catherine Knox |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/events/elixir-uk-all-hands-2023 |
| Description | Engagement with General Public: Royal Norfolk Show 2022 - Will Nash |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Engagement activities with the general public as part of the Royal Norfolk Show 2022, demonstrating our activities focusing on the application of new technologies to characterise biodiversity |
| Year(s) Of Engagement Activity | 2022 |
| Description | Engagement with industry - KWS UK Ltd. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Industry/Business |
| Results and Impact | Representatives from KWs were given an overview of the wheat projects and NC3 infrastructures and discussed the possibility to be involved. |
| Year(s) Of Engagement Activity | 2018 |
| Description | European Galaxy Administrator Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The European Galaxy Administrator Workshop was a 5-days course organised by ELIXIR and dedicated to Galaxy server administrators. Participants learned how to install, configure, customize, and extend their own Galaxy servers. Topics included basic and advanced server setup, tool configuration, data managers, authentication and user management, using heterogeneous storage and compute services, Ansible, server monitoring and maintenance. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.elixir-europe.org/events/european-galaxy-administrator-workshop |
| Description | European Galaxy Days 2023 (EGD2023) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The European Galaxy Days 2023 (EGD2023), Freiburg im Brisgau, Germany, 04-06/10/2023, brought together close to 80 researchers, trainers, tool developers, software engineers, and computational infrastructure providers interested in the Galaxy platform, all working in and supporting data intensive science that is accessible, sharable and reproducible. The ELIXIR Galaxy Community had its 2023 Face-to-face (F2F) meeting as part of this event. Dr. Nicola Soranzo chaired (with José Manuel Domínguez) the "Reducing the environmental impact of Galaxy workflows" Birds of a Feather (BOF) session. Dr. Soranzo also led the "Add support for Python 3.12" project at the CoFest that closed the event. A report of the event is available as a blog post at: https://galaxyproject.org/news/2023-10-13-egd-2023-the-wrapup/ |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://galaxyproject.org/events/2023-10-egd/ |
| Description | European consortium launched to reverse biodiversity loss through genomics research |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article about a new collaborative project for biodiversity genomics, jointly written with other European partners. Primary objectives were to promote the initiative and raise awareness of our involvement and expertise in data science and genomics, which we saw through the development of the article and in engagement online |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/news/european-consortium-launched-reverse-biodiversity-loss-through-genomi... |
| Description | Excellent science? It's in the technical detail |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article on the Institute's status as a Technician Commitment signatory, designed to inform and influence the opinions of internal and external audiences. We saw a positive response internally as people felt recognised and saw visibility given to colleagues who may have been overlooked for their past contributions. The piece also invited ideas for follow-up content on the different kinds of technical roles and their contributions. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/articles/excellent-science-its-technical-detail |
| Description | Focus on the future at EI Innovate |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Write-up of the EI Innovate event held at the Earlham Institute in November 2022, designed to provide an overview of the topics discussed to those who were unable to attend or may want to follow up with speakers having been here. The piece received some positive engagement and comments on social and will be a valuable tool for encouraging registration for the 2023 event. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/articles/focus-future-ei-innovate |
| Description | GCC2017 - Conda and Containers for Tool Dependencies - A Developer's Perspective |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This training workshop was part of the Galaxy Community Conference 2017 (GCC2017, https://gcc2017.sched.com ) and was aimed at people with some experience developing tools and deployers who need to manage complex sets of dependencies for tools. Galaxy tools define the applications and other dependencies they require to run using their requirements section. This training session covered the elements of the requirements section and how Galaxy can be configured to utilize these. The current best practice for resolving these dependencies is using Conda and Bioconda, and so a substantial amount of time will be spent on these topics. We went through the process of creating, testing, and publishing a Bioconda package. We worked through an example of connecting these packages to Galaxy. We also discussed how the Biocontainers project constructs Docker containers from Bioconda packages and how to emulate this process for local testing before publication. Finally, we reviewed approaches to leveraging these containers from Galaxy to run jobs within containers. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://gcc2017.sched.com/event/9mzb/conda-and-containers-for-tool-dependencies-a-developers-perspec... |
| Description | GCC2017 - Writing & Publishing Galaxy Tools |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This training workshop was part of the Galaxy Community Conference 2017 (GCC2017, https://gcc2017.sched.com ). This session walked developers and bioinformaticians through the process of taking a working script or application and turning it into a Galaxy tool. It also covered the basics of using Planemo, a command-line utility to assist in building and publishing Galaxy tools. We investigated wrapping, common parameters, tool linting, best practices, loading tools into Galaxy, citations, and publishing tools to Github and the Galaxy Tool Shed. Common tips and tricks were discussed, as well as insights from experienced tool developers. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://gcc2017.sched.com/event/9mzP/writing-publishing-galaxy-tools |
| Description | Galaxy Admin Training 2021 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo was one of the trainers at the virtual Galaxy Admin Training workshop, 25-29/01/2021. Over the course of 5 intense days, 88 attendees from all over the world participated asynchronously (each in their time zone, at their own pace) with remote support from 11 instructors, communicating via Slack. Attendees were provided with videos, slides and tutorials, and learned how to install and manage a production-level Galaxy server and related services. Participants reported high level of satisfaction: in the post-workshop survey, 87.5% of the attendees rated the course 5 out of 5 when asked "How useful was the training?". More details are available in the blog post: https://gallantries.github.io/posts/2021/02/01/gat/ |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://galaxyproject.org/events/2021-01-admin-training/ |
| Description | Galaxy Admin Training 2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo was one of the trainers at the Galaxy Admin Training 2023 workshop, Gent, Belgium, 17-21/04/2023. The course was held in person over 5 intense days, with 16 attendees from different countries and background. The training covered the basic and advanced topics needed to know to setup and maintain a production, high-performance and multi-user Galaxy instance. A short report is available in the blog post: https://galaxyproject.org/news/2023-09-27-galaxy-admin-training/ |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://galaxyproject.org/events/2023-admin-training/ |
| Description | Galaxy Admin Training @ GTN Tapas 2022 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo was one of the 6 trainers for this online asynchronous training course, part of the "Smörgåsbord 2022: Tapas Edition", 14-18/03/2022. Over the course of 5 intense days, 19 attendees learned how to install and manage a production-level Galaxy server and related services. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://gallantries.github.io/video-library/events/smorgasbord2/gat.html |
| Description | Galaxy Community Conference 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Moderated the Session 3 "Tools and Workflows" at the Galaxy Community Conference 2017. Participated actively in the "Hack the Galaxy: Dev" hackathon. Interacted with other Galaxy users and developers throughout the 5-days event. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://gcc2017.sched.com/event/B57S/session-3-tools-and-workflows |
| Description | Galaxy Project meeting 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Meeting with the Principal Investigators, Core Team members and "committers" of the Galaxy project (https://galaxyproject.org/galaxy-team/ ) to discuss current Galaxy issues and establish the roadmap for the next 6 months of development. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://github.com/galaxyproject/galaxy/projects/8 |
| Description | Galaxy Project planning meeting 2022 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo participated to this strategic meeting, held in Montepellier, France, with the Principal Investigators, Core Team members and "committers" of the Galaxy Project ( https://galaxyproject.org/ ) to collectively update its technical roadmap, with links to major efforts such as the Vertebrate Genomes Project ( https://galaxyproject.org/projects/vgp/ ) and COVID-19 ( https://galaxyproject.org/projects/covid19/ ). |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://docs.google.com/document/d/1NlH_tL8BG9hvCgnLzJI4GLhKMk7TsQAXp8WkggbIGrg/edit?usp=sharing |
| Description | Genomic characterisation of wild tilapia populations |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The presentation took place as part of a workshop organised in Bogota (Colombia) between UK and Colombia scientific Institutions. The audience was composed of UK and Colombia university lecturers, Colombian industry partners. The presentation helped raising the international profile of Wilfried Haerty, Federica Di Palma and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Giving a talk at the ELIXIR All Hands 2020 Mini Symposium |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Rob Davey: Gave a talk at the ELIXIR All Hands 2020 Mini Symposium: FAIRification for knowledge management: COPO: Extending the frontiers of FAIRness in life science data |
| Year(s) Of Engagement Activity | 2020 |
| Description | Grassroots Infrastructure and the Wheat Information System (RDA Interest Group on Agricultural Data (IGAD), Barcelona) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Davey delivered a talk about the Grassroots software infrastructure for the dissemination of wheat data through federation and integration of storage and compute e-infrastructure. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.rd-alliance.org/rda-interest-group-agricultural-data-igad-pre-plenary-meeting-3-4-april-... |
| Description | HDR UK & ELIXIR-UK Joint Hackathon |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | We co-hosted the first joint Hackathon with HDR UK to tackle projects at the intersection of health data and life sciences research. 50 people attended to co-work on 12 projects. The event had a waiting list of 50 people, clearly showing the need for larger events engaging the community on boths ides. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://elixiruknode.org/news/2025/innovation-in-action-first-hackathon/ |
| Description | HPC and Cloud Computing training course, Module 7 of the Bioinformatics Community of Practice |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | About 15 researchers from Eastern Africa attended a 1 week training course, as part of the "Bioinformatics Community of Practice" training and networking program, to learn about High Throughput and High Performance Computing, the Galaxy analysis platform and related tools. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://acaciaafrica.org/bioinformatics-community-practice/ |
| Description | Hackathon on Galaxy Tools and Workflows for Metabolomics |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo participated to this Hackathon held at EBI, Hinxton, UK, 2-4/10/2019. The hackathon, organised by the MetaboFlow consortium, brought together developers from MetaboFlow, PhenoMeNal, usegalaxy.eu, workflow4metabolomics and beyond with the goal of integrating tools, in high demand by the Metabolomics community, into Galaxy. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://docs.google.com/document/d/1jy3ywXPdgzh3PHLWAtB9TyP1c5KSjyI6bLnVq-zCtLA/edit?usp=sharing |
| Description | Hosted a workshop at BioHackathon 2023: Increasing the findability, visibility, and impact of Galaxy tools for specialised scientific Communities |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Nicola Soranzo Co-led on Project No. 25: Increasing the findability, visibility, and impact of Galaxy tools for specialised scientific Communities |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://2023.biohackathon-europe.org/projects.html |
| Description | How to create a Galaxy Tool (GCC2019) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This training workshop was presented by Dr. Nicola Soranzo (together with John Chilton from Penn State University) at the 2019 Galaxy Community Conference (GCC2019), Freiburg im Brisgau, Germany, 02/07/2019. The session walked bioinformaticians, developers, and admins through the process of taking a working script, app, or software and turning it into a Galaxy Tool. It covered the basics of using Planemo, a command-line utility that assists in building and publishing Galaxy Tools. Common tips and tricks were discussed as well as insights from experienced tool developers. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://gcc2019.sched.com/event/MCxQ/how-to-create-a-galaxy-tool |
| Description | Industry Seminar Precision Life 5/12/2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | The day was made up of 1:1 appointments for EI colleagues in the morning followed by a 60 minute seminar. The afternoon was a meeting with AIP colleagues. The day lead to follow up; conversations and looking at ways of working. |
| Year(s) Of Engagement Activity | 2023 |
| Description | International Conference Oral Presentation: Discovery and visualisation of homologous genes and gene families using Galaxy |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The oral presentation at the International Plant and Animal Genomes Conference (San Diego, USA) conference was selected on abstract submission. The presentation was delivered in front of industry participants, donors, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Anil Thanki, Nicola Soranzo, Wilfried Haerty, Robert Davey and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | International Conference Poster Presentation: Evolution of tissue-specific regulatory programs in cichlids. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The poster presented at the Cold Spring Harbour Biology of Genomes conference was selected on abstract submission. The poster was presented in front of university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Tarang Metha, Luca Penso Dolfin, Tomasz Wrzesinski, Will Nash, Padhmanand Sudhakar, Wilfried Haerty, Tamas Korcsmaros, Federica Di Palma and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | International Conference Poster: Binding sites within long non-coding RNAs discriminate between RNA- and transcription mediated mechanism. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The poster presented at the Cold Spring Harbour Biology of Genomes conference was selected on abstract submission. The poster was presented in front of university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Tomasz Wrzesinski, Wilfried Haerty and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | International Conference poster presentation: Discovery and visualisation of homologous genes and gene families using Galaxy |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The poster presentation at the 18th The Bioinformatics Open Source Conference (BOSC), 25th Intelligent Systems for Molecular Biology (ISMB) and 16th European Conference on Computational Biology - ISMB/ECCB conference was selected on abstract submission. The poster was presented in front of industry participants, donors, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Anil Thanki, Nicola Soranzo, Wilfried Haerty, Robert Davey and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Introduction to Galaxy Administration (BCC2020) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo was one of the trainers at this full-day workshop, part of the Bioinformatics Community Conference 2020 (BCC2020), virtual, 17-25/07/2020. Participants learned how to install and manage a production-level Galaxy server and related services. Materials for the training are available at: https://github.com/galaxyproject/admin-training/tree/2020-bcc |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://bcc2020.sched.com/event/c3e1/introduction-to-galaxy-administration-i |
| Description | Introduction to Multiomics Data Integration |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Tamas Korcsmaros delivered a talk on the nature of different data types, and provided a training on Cytoscape |
| Year(s) Of Engagement Activity | 2009,2018 |
| URL | https://www.ebi.ac.uk/training/events/2018/introduction-multiomics-data-integration-0 |
| Description | Invited seminar: Characterization of transcriptional complexity of Voltage Gated Calcium Channels in the human brain using Nanopore long read sequencing |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited seminar at the Division of Evolution & Genomic Sciences, University of Manchester. The audience was composed of group leaders, University lecturers, postdoctoral researchers, graduates and undergraduates students interested in RNA biology. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Invited seminar: Comparative genomics of Australian marsupials: Expansion of gene families and signatures of selection following an ancient divergence |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited seminar at University College Dublin presented by Will Nash. The audience was composed of University professors and Lecturers, postdoctoral researchers, graduates and undergraduates students. Outcomes: Increased the international profile of Will Nash and Wilfried Haerty and increased the international profile of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Invited seminar: Nanopore cDNA sequencing reveals transcriptional complexity of CACNA1C gene in human brain |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited seminar at the MRC Institute of Genetics and Molecular Medicine. The audience consisted group leaders, University professors, University Lectures, postdoctoral researchers, graduates and undergraduates students. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Invited seminar: Nanopore cDNA sequencing reveals transcriptional complexity of CACNA1C gene in human brain |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited seminar in the satellite meeting of The Americal Society for Human Genetics organised by Oxford Nanopore. The audience of the seminar was composed of industrial professionals, group leaders, university professors and lecturers, postdoctoral researchers, graduates and undergraduate students. The seminar allowed to raise the personal profile of Wilfried Haerty and to raise the profile of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Invited speaker International Institution: Characterization of functional long non-coding RNAs and their expression in the developing human brain |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The presentation took place as the result of an invitation to present at the ICenter for Regenerative Therapies Dresden. The audience was composed of university lecturers, graduate and undergraduate students. The presentation helped raising the international profile of Wilfried Haerty and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | JRS Biodiversity R workshop, Nairobi |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Davey travelled to Nairobi, Kenya, as part of a JRS Biodiversity funded programme to teach a day R workshop to 23 representatives from the African Conservation Centre, Kenya Wetlands Biodiversity Reseach Centre, National Museums of Kenya, University of Nairobi, and the Jomo Kenyatta University. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Laying the Foundations; Why are Semantics in Agriculture Difficult? - PAG 2020 talk in Plant Phenotypes workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Davey gave an invited talk to approx 90 attendees at the PAG 2020 workshop "Plant Phenotypes" |
| Year(s) Of Engagement Activity | 2020 |
| Description | Lightning Talk: Adding Python 3 support to Galaxy: a status report 2018 (GCC2018) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. N. Soranzo presented "Adding Python 3 support to Galaxy: a status report 2018" at the "2018 Galaxy Community Conference (GCC2018)", Portland, OR, USA, 26-30/06/2018, had some discussion with other professional working in the same area, and made plans for further development. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://gccbosc2018.sched.com/event/Eix2/adding-python-3-support-to-galaxy-a-status-report |
| Description | Meet the GigaScience ICG Prize Winners, Pt. 1: Aequatus |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Press release from GigaScience Journal introducing ICG Prize winners (Aequatus) |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://gigasciencejournal.com/blog/aequatus-icg-prize/ |
| Description | Microbial Community Analysis Workshop 29 - 31 March 2022 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | This was a three-day course covering microbiome analysis - going from samples, to sequencing, to numerical ecology analysis. It provided an overview from raw sequencing reads to publication ready analysis and figures. Lecture materials comprised the theory of DNA extraction, sample storage and existing pipelines for amplicon sequencing. Use of the LotuS2 pipeline was applied to an example dataset via a Galaxy interface. R was also used to explore abundance data from producing diversity measures to visualisation of taxonomic differences. We had 25 participants comprising PhD students (~53%), Postdocs (~30%), Professors/PIs (12%) and other representatives from research organisations in attendance. The overall quality of the course was rated as 'Very Good' or 'Excellent' (92%) and there are plans to host this again in Q4 2023. Participants reported this allowed them unique hands-on experience with 16S/amplicon sequencing data, and that after attending the course it allowed them to present papers in the field of bioinformatics. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/events/microbial-community-analysis-workshop-2022 |
| Description | Monogram Bioinformatics Workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Workshop to present results of the SeeD/UK infrastructure project (including new data and bioinfomatics tools). |
| Year(s) Of Engagement Activity | 2018 |
| Description | NRPDTP Student Elective: Artificial Intelligence and Advanced Digital Literacy |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Dr. Nicola Soranzo and Jazz Urog were the trainers for the "Artificial Intelligence and Advanced Digital Literacy" elective course, part of the Training Programme for the Norwich Research Park Doctoral Training Partnership (NRPDTP) PhD programme. They presented the CyVerse UK infrastructure, the CyVerse Discovery Environment and the Galaxy web platform for data analysis. Then Dr. Soranzo guided the students through 2 tutorials: "A short introduction to Galaxy" and "Basics of machine learning in Galaxy". |
| Year(s) Of Engagement Activity | 2023 |
| Description | Norwich science festival |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | A number of member from the public attended the Norwich science festival, where the Earlham institute presented the work being done in Norwich. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://norwichsciencefestival.co.uk/ |
| Description | Open source data management: Sherlock open for all - 14/06/2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Website article on customisable method of data management for smaller research groups who don't have the resources to develop a modern, big data solution using software developed at EI and made open-source. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/sherlock-open-source-data-management |
| Description | Oral Presentation: Aequatus.js: a plugin to visualise gene trees in Galaxy |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | More than 300 people attended the conference and had a good discussion after the talk about the way it is integrated with Galaxy. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://gcc2019.sched.com/ |
| Description | Oral presentation at international conference: Characterization of functional long non-coding RNAs in human |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The presentation at the Genome 10K / Genome Science conference was selected on abstract submission. The presentation was delivered in front of industry participants, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The presentation helped raising the international profile of Wilfried Haerty and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Organisation and Attendance at the Alan Turing Institute for AI for Wheat Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Rob Davey helped organise the Alan Turing Institute - AI For Wheat Workshop 9th & 10th March 2020 This two day workshop will bring members of the UK wheat community and data science researchers together to identify suitable and exciting biological problems (with associated datasets) that could be further developed and made ready for a future wheat-focussed Data Study Group (DSG). DSGs are week-long intensive interdisciplinary workshops which explore a small number of topics in greater depth to seed longer-term collaborations which could lead to joint publications or research proposals. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.rothamsted.ac.uk/events/ai-wheat-workshop |
| Description | Organiser of Challenges and Opportunities in Plant Science Data Management PAG workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Co-organiser of Challenges and Opportunities in Plant Science Data Management PAG workshop, which saw 6 international speakers deliver presentations on various aspects of data management in the plant sciences. Approx 50 attendees. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Organoid transcriptomics to study cell regulation Internal research presentation at the Earlham Institute |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Organoid transcriptomics to study cell regulation Internal research presentation at the Earlham Institute |
| Year(s) Of Engagement Activity | 2019 |
| Description | Panel discussion at RCUK cloud workshop about virtual laboratories and research environments |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Discussion about virtual laboratories and their limitations. Similarities and differences were discussed and a conversation about the sharing of data and their management between platforms started. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://cloud.ac.uk/2017/12/15/rcuk-cloud-workshop-2018/ |
| Description | Participation in a Webinar: Introduction to the UK Data Service |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Webinar: Introduction to the UK Data Service April 2021 Description: The UK Data Service holds the UK's largest collection of research data. This introductory webinar is for anyone with an interest in social research who wants to hear about the vast array of resources we offer. Participants will learn about the different types of quantitative and qualitative data we hold, how to find those data collections using our online resource discovery tools, and how to register to access datasets in a number of different formats. We will also demonstrate how some of our data collections can be viewed and analysed online, as well as providing an overview of our support and training resources for students, researchers and teachers |
| Year(s) Of Engagement Activity | 2021 |
| Description | Participation of a ELIXIR Webinar: Towards professionalising data stewardship |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Participation of a ELIXIR Webinar: Towards professionalising data stewardship |
| Year(s) Of Engagement Activity | 2021 |
| Description | Participation of the ELIXIR Environmental Impact Focus Group |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Nicola Soranzo is part of the ELIXIR Environmental Impact Focus Group. This group will explore ways to assess and minimise the environmental impact of ELIXIR, and of data handling in general. We will raise awareness about the issues and solutions. We will also explore how ELIXIR can help interdisciplinary research on the environmental impact on human health and biodiversity. |
| Year(s) Of Engagement Activity | 2023,2024 |
| URL | https://elixir-europe.org/focus-groups/environmental-impact |
| Description | Poster "ELIXIR-UK at 10: new members and activities" at the ELIXIR All Hands 2024 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Nicola Soranzo and Xènia Pérez Sitjà (Earlham Institute & ELIXIR-UK) presented the poster "ELIXIR-UK at 10: new members and activities" during the "ELIXIR All Hands 2024" meeting, Uppsala, Sweden, 10-12/06/2024. The poster describes the ELIXIR-UK Node, its four UK-wide communities of practice, its community engagement activities, the four ELIXIR-UK services newly recognised as ELIXIR Core Data Resources and the three added as Recommended Interoperability Resources, the work done in improving Trusted Research Environments (TREs), and how it conceived and supported the new digital research infrastructure BioFAIR. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://f1000research.com/posters/13-632 |
| Description | Poster "Implementing a new Galaxy integration to export datasets to COPO" at the 2024 Galaxy Community Conference (GCC2024) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Nicola Soranzo (Earlham Institute) presented the poster "Implementing a new Galaxy integration to export datasets to COPO" at the 2024 Galaxy Community Conference (GCC2024), Brno, Czechia, 24-29/06/2024. The poster describes the effort to integrate the currently separate processes of production of genome assemblies in Galaxy with their deposition via the COPO brokering portal. This work will extend the Galaxy backend and user interface, together with the COPO Application Programming Interface (API), to allow users to easily export their Galaxy datasets to the COPO platform, from which they can then start the metadata validation and submission process to the European Nucleotide Archive (ENA). |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://f1000research.com/posters/14-283 |
| Description | Poster Presentation - Intelligent Systems for Molecular Biology - Scaling up GeneSeqToFamily to handle pan transcriptomes and million of genes |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation as part of the Intelligent Systems for Molecular Biology 2022 conference |
| Year(s) Of Engagement Activity | 2022 |
| Description | Poster Presentation: Aequatus.js: a plugin to visualise gene trees in Galaxy |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a poster in addition to an oral presentation at GCC 2019, it had good feedback from audience. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://gcc2019.sched.com/ |
| Description | Poster presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the annual PopGroup meeting |
| Year(s) Of Engagement Activity | 2021 |
| Description | Poster presentation - Characterising and visualising gene families within Galaxy using GeneSeqToFamily and Aequatus |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the SMBE Annual Meeting 2019, Manchester, UK 21-25 July 2019 |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation : Pathway Analysis to Study the Effect of Bifidobacteria on Autophagy in the Intestine 2nd Interdisciplinary Signaling Workshop 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Treveil A. T., Korcsmaros T. K. (2017) Pathway Analysis to Study the Effect of Bifidobacteria on Autophagy in the Intestine 2nd Interdisciplinary Signaling Workshop |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://signalingworkshop.org/ |
| Description | Poster presentation : SalmoNet: an integrated multi-layered network for Salmonella 2nd Interdisciplinary Signaling Workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Olbei M. L. O., Metris A. M., Sudhakar P. S., Fazekas D. F., Demeter A. D., Ari E. A., Branchu P. B., Kingsley R. K., Baranyi J. B., Korcsmaros T. K. (2017) SalmoNet: an integrated multi-layered network for Salmonella 2nd Interdisciplinary Signaling Workshop |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://signalingworkshop.org/ |
| Description | Poster presentation : SalmoNet: an integrated multi-layered network for Salmonella Genome 10K and Genome Science Conference. Genome 10K and Genome Science Conference 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Olbei M. L. O., Metris A. M., Sudhakar P. S., Fazekas D. F., Demeter A. D., Ari E. A., Branchu P. B., Kingsley R. K., Baranyi J. B., Korcsmaros T. K. (2017) SalmoNet: an integrated multi-layered network for Salmonella Genome 10K and Genome Science Conference |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://genome10k.soe.ucsc.edu/node/130 |
| Description | Poster presentation at 2nd Interdisciplinary signalling workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Poster presentation titled "Pathway Analysis to Study the Effect of Bifidobacteria on Autophagy in the Intestine" at the 2nd Interdisciplinary Signaling Workshop 2017. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/2nd-interdisciplinary-signaling-workshop-isw |
| Description | Poster presentation at EI Inniovate 2019 - Tools to aid improved genome annotation |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Aroud 55 people attended the event and we presented a poster on "Tools to aid improved genome annotation" describing various tools developed at EI from Davey group and Swarbreck group. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/innovate2019-0 |
| Description | Poster presentation at ELIXIR UK All Hands 2018 meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | The annual ELIXIR-UK All Hands brings together people working at ELIXIR-UK consortium member institutions for this two-day meeting, which for 2018 is hosted by Birmingham University. I presented a poster on the network resources developed and maintained by the Korcsmaros group. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/elixir-all-hands-2018 |
| Description | Poster presentation at EMBO conference Modularity of signaling proteins and networks |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Poster presentation titled "Identifying signalling pathways regulating antimicrobial peptide production in the gut using network biology and organoid transcriptomics Modularity of signaling proteins and networks" at the EMBO conference Modularity of signaling proteins and networks. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://meetings.embo.org/event/18-modularity |
| Description | Poster presentation at Exploring Human Host-Microbiome Interactions in Health and Disease conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Poster presentation titled "Investigating regulation of intestinal function by Bifidobacteria using network biology and organoid approaches" at the Exploring Human Host-Microbiome Interactions in Health and Disease conference 2017. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://coursesandconferences.wellcomegenomecampus.org/our-events/exploring-human-host-microbiome-in... |
| Description | Poster presentation at National Conference: Expansion of gene families and signatures of selection in the Australian marsupials |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | The poster presented at the 50th Population Genetics Group meeting (Cambridge UK) was selected on abstract submission. The poster was presented in front of iuniversity professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of AWill Nash, Wilfried Haerty, and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Poster presentation at international conference: Binding sites within long non-coding RNAs discriminate between RNA- and transcription-mediated mechanism |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The poster presented at the Genome 10K / Genome Science conference was selected on abstract submission. The poster was presented in front of industry participants, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Tomasz Wrzesinski, Wilfried Haerty and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Poster presentation at international conference: Discovery and visualisation of homologous genes and gene families using Galaxy |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The poster presented at the Genome 10K / Genome Science conference was selected on abstract submission. The poster was presented in front of industry participants, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Anil Thanki, Nicola Soranzo, Wilfried Haerty, Robert Davey and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Poster presentation: : Characterising and visualising gene families with GeneSeqToFamily and Aequatus (GI2018) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | More than 300 people attended "Genome Informatics 2018" conference at Wellcome Genome Campus Conference Centre, Hinxton, Cambridge, UK. We had good discussion about this project with many attendees from various institute and university. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://coursesandconferences.wellcomegenomecampus.org/wp-content/uploads/2018/08/Genome-Informatics... |
| Description | Poster presentation: Discovery and visualisation of homologous genes and gene families using Galaxy |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | More than 300 people attended "Genome 10K and Genome Science Conference 2017" conference at Norwich, UK. We had good discussion about this project with many attendees from various institute and university. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/genome-10k-and-genome-science-conference |
| Description | Poster presentation: SignaLink 3, a tissue specific and extended multi-layered signaling network resource 2nd Interdisciplinary Signalling Workshop 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Fazekas D., Kadlecsik T., Sudhakar P., Modos D., Turei D., Csabai L., Gul L., Korcsmaros T. (2017) SignaLink 3, a tissue specific and extended multi-layered signaling network resource 2nd Interdisciplinary Signalling Workshop 2017 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://signalingworkshop.org/ |
| Description | Poster: BioFAIR: a new BioCommons infrastructure for UK life science (UKRI DRI Community Congress) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Nicola Soranzo (Earlham Institute) and Carole Goble (The University of Manchester) presented the poster "BioFAIR: a new BioCommons infrastructure for UK life science" during the "UKRI Community Congress", Birmingham, UK, 6-7 March 2023. The poster describes ELIXIR, ELIXIR-UK, the ELIXIR-UK DaSH Fellowship, the 2021 BioFAIR feasibility study, BioFAIR's high-level structure and its proposed components and services for the UK life science researchers. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://zenodo.org/record/7708304 |
| Description | Poster: BioFAIR: a new BioCommons infrastructure for the UK life science (ELIXIR All Hands 2023) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Nicola Soranzo (Earlham Institute & ELIXIR-UK) presented the poster "BioFAIR: a new BioCommons infrastructure for the UK life science" during the "ELIXIR All Hands" meeting, Dublin, Ireland, 5-8 June 2023. The poster describes the ELIXIR-UK Node, the 2021 BioFAIR feasibility study, international comparators and complementary research infrastructures, BioFAIR's high-level structure and its proposed components and services for the UK life science researchers. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://f1000research.com/posters/12-596 |
| Description | Poster: ELIXIR-UK (ELIXIR All Hands 2023) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Emily Delva and Catherine Know (Earlham Institute & ELIXIR-UK) presented the poster "ELIXIR-UK" during the "ELIXIR All Hands" meeting, Dublin, Ireland, 5-8 June 2023. The poster described the recent updates at the UK Node of ELIXIR, including new member organisations, new Node Services, recent projects, and latest news. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://f1000research.com/posters/12-640 |
| Description | Poster: ELIXIR-UK Node (ELIXIR All Hands meeting 2019) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This poster was presented by Prof. Neil Hall, Dr. Nicola Soranzo and Catherine Hunter at the ELIXIR All Hands meeting 2019, Lisbon, Portugal on 19th June 2019. The poster presents ELIXIR-UK and its mission to deliver on the national Funders vision for FAIR data infrastructure within the Life Sciences. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.eventbrite.co.uk/e/elixir-excelerate-all-hands-meeting-lisbon-2019-registration-55503335... |
| Description | Poster: Sharing data to reduce costs and time needed to deliver life science innovation (EI Innovate 2019) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | This poster was prepared by Dr. Nicola Soranzo and presented by Prof. Neil Hall at the EI Innovate event, Earlham Institute, Norwich, UK, 13/11/2019. The poster describes ELIXIR-UK, its goals and potential for technology transfer, and its role in bioinformatics training in the UK. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/innovate2019-0 |
| Description | Poster: Support open science and FAIRness through an integrated collaborative platform for life science: CyVerse UK and hosted services |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented as CyVerse, COPO, Galaxy and Grassroots icrease the level of FAIRNESS in the research process. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.igst.it/nettab/2018/ |
| Description | Poster: Support open science and FAIRness through an integrated collaborative platform for life science: CyVerse UK and hosted services |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | poster presentation of the projects supported by the CyVerse UK infrastructure and how they contribute to the FAIRness of data |
| Year(s) Of Engagement Activity | 2019 |
| Description | Practical use of the Galaxy API command line tools (GCC2018) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Galaxy has an always-growing API that allows for external programs to upload and download data, manage histories and datasets, run tools and workflows, and even perform admin tasks. This training session at the 2018 Galaxy Community Conference (GCC2018) and Bioinformatics Open Source Conference 2018 (BOSC2018) covered various approaches to access the API, in particular using the BioBlend Python library. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://gccbosc2018.sched.com/event/Dn9n/practical-use-of-the-galaxy-api-command-line-tools |
| Description | Presenattion: Using Docker to add flexible container support to CyVerse UK |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented the use of containerization and Docker in particular in the CyVerse UK ecosystem. Discussed how the cyberinfrastructure structure and the use of the API mitigate common security concerns. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.software.ac.uk/c4rr/agenda |
| Description | Presentation - Long Read Sequencing Uppsala - Comprehensive human brain transcriptome characterisation using long-read CaptureSeq |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation as part of the Annual Long Read Sequencing Uppsala meeting |
| Year(s) Of Engagement Activity | 2022 |
| Description | Presentation - Winter Conference on Brain Research - Characterisation of Transcript and Protein Diversity in Major Candidates for Neuropsychiatric Disorders |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation at the Winter Conference on Brain Research |
| Year(s) Of Engagement Activity | 2023 |
| Description | Presentation at DockerCon 2019: Value in simplicity - how Docker is helping Academia and non-dev |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A number of participants to the conference from different backgrounds were given an overview of the reproducibility issue in science and how the new containerization technology is proving useful. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.docker.com/dockercon/2019-videos?watch=value-in-simplicity-how-docker-is-helping-academi... |
| Description | Presentation at sanger Openstack Day: cyVerse UK: a cloud based infrastructure for life science |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | A talk to present CyVerse UK and the technology stack in used to other professionals in the same field. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation at the Plant clock Workshop: cyVerse UK: a platform for collaborative life science in the UK |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | a number of postgraduate students, postdocs and PIs involved in the plant clock research field were made aware of the opportunities available to them trough CyVerse UK. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation: CyVerseUK: widening the scope to the UK and beyond |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented the efforts to federate CyVerse UK with the parent US project, both in term of execution system and storage of data. Followed up with collaborators to continue working on flocking the resources. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4771 |
| Description | Presentation: The ELIXIR Galaxy Community |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Presented "The ELIXIR Galaxy Community" at the event "ELIXIR Innovation and SME Forum: Enabling Discoverability in Bio-Data Innovation" in the "Challenges in tools development" session, and participated in the following round table. Report of the event is available at https://www.elixir-europe.org/news/elixir-innovation-and-sme-forum-promotes-discoverability-biomedical-data |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.elixir-europe.org/events/elixir-innovation-and-sme-forum-enabling-discoverability-bio-da... |
| Description | Presented at Research Councils UK Cloud Workshop - CyVerse UK: a cloud cyberinfrastructure for life science |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented the use of the cloud and containerization in the CyVerse ecosystem, underlining some of the differences with virtual labs and the efforts to enable interoperability and sharing of data. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://cloud.ac.uk/2017/12/15/rcuk-cloud-workshop-2018/ |
| Description | Preserving, Restoring and Managing Colombian Biodiversity Through Responsible Innovation - GROW Colombia UK workshop 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Robert Davey gave a talk on the C3 Biodiversidad ConsortiumProject Coordination and Website |
| Year(s) Of Engagement Activity | 2020 |
| Description | Press Release - Network science unravels the secrets of the evolution of Salmonella's disease adaptations |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Press release to introduce SalmoNet, a systems biology approach that uses network biology and bioinformatic techniques to collate molecular interactions within Salmonella, and to link information on how genes and metabolic pathways are regulated in Salmonella, and how proteins interact with each other. -SOCIAL MEDIA- Engagement x45, Impressions x54800 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/newsroom/network-science-unravels-secrets-evolution-salmonella%E2%80%99s-di... |
| Description | Press article - Improved strain of tilapia genome sequencing highlighted by UKRI and BBSRC Impact Showcase of 2022 - Tarang Mehta, Will Nash, Adam Ciezarek, Graham Etherington |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article as part of BBSRC Impact showcase 2022 |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://preview.shorthand.com/uG7dbZH9ZkAyeO0M#group-section-Collaboration-Tv0V86lglL |
| Description | Project "Reducing the environmental impact of Galaxy" at BioHackathon Europe 2024 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Nicola Soranzo led (with Paul De Geest) the project "Reducing the environmental impact of Galaxy" at the BioHackathon Europe 2024, organised by ELIXIR in La Roca del Vallès, Spain, 4-8/11/2024. Project description: https://github.com/elixir-europe/biohackathon-projects-2024/blob/main/26.md Slide with the outcomes of this hacking project: https://docs.google.com/presentation/d/1Kqk5NrHS1tfFI4I_8Kx0qoPYEytSLU0glSN-GZspOGc/edit#slide=id.g3078db21077_0_340 |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://biohackathon-europe.org/ |
| Description | Research Cyberinfrastructure Colombia Workshop 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The workshop involved a multidisciplinary team of Colombian and international experts to understand user needs and available resources, discuss innovative solutions, and design a strategy to grow research capacity for the high-throughput computational analysis of biological data in Colombia. This workshop was an opportunity for intensive discussions to uncover innovative solutions, identify critical partners and produce a realistic strategy and open vision for the creation of C3Biodiversidad (Consorcio Colombiano de Ciberinfraestructura) in Colombia. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.bridgecolombia.org/c3-biodiversidad/ |
| Description | Scientific Committee of the Galaxy Community Conference 2017 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The Scientific Committee of the Galaxy Community Conference 2017 evaluated and scored abstract submissions for oral presentations, posters, lightning talks and computer demonstrations. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://gcc2017.sched.com/ |
| Description | Scripting Galaxy through BioBlend (GCC2019) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This training workshop was presented by Dr. Nicola Soranzo (together with Marius van den Beek from Institute Curie) at the 2019 Galaxy Community Conference (GCC2019), Freiburg im Brisgau, Germany, 02/07/2019. This session introduced Galaxy's always-growing API that allows for external programs to upload and download data, manage histories and datasets, run tools and workflows, and even perform admin tasks. The training covered various approaches to access the API, in particular using the BioBlend Python library. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://gcc2019.sched.com/event/MDTD/scripting-galaxy-through-bioblend |
| Description | Scripting Galaxy with BioBlend (BCC2020) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo led this training workshop at the Bioinformatics Community Conference 2020 (BCC2020), virtual, 17-25/07/2020. This session introduced Galaxy's always-growing API that allows for external programs to upload and download data, manage histories and datasets, run tools and workflows, and even perform admin tasks. The training covered various approaches to access the API, in particular using the BioBlend Python library. Slides for the training are available at: https://training.galaxyproject.org/training-material/topics/dev/tutorials/bioblend-api/slides.html |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://bcc2020.sched.com/event/c3cW/scripting-galaxy-with-bioblend |
| Description | Sherlock: elementary genomics 18/03/2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Website article highlighting the Sherlock platform developed at EI to store and analyse bioinformatics data using modern big data technologies. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/sherlock-elementary-genomics |
| Description | Single-Cell RNAseq 1-4 November 2021 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Aimed at researchers who were in the experimental planning stages of a Single-Cell genomics project, the course required no previous experience in bioinformatics approaches with the najority of hands-on analysis delivered through the web-based, user-friendly interface - Galaxy. The course provided an introduction to single-cell genomics for researchers who are new to bioinformatics and covered: assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variations at the single-cell level. It consisted of a mixture of conceptual and methodological lectures and hands-on sessions, including best practices and tips as learned first-hand by Earlham Institute's faculty. The course was redeveloped from the course delivered in 2020 focusing on bioinformatics only, spread over 4, shorter days (10:00-15:00) and involved a number of new teaching faculty. The majority of attendees were national and outside of the Norwich Research park (50%), and from academia (94%). They rated the training overall as very good or excellent (91%) and the trainers very good or excellent (91%), with 91% saying that they would recommend the course. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/single-cell-rnaseq-training-course-2021 |
| Description | Single-Cell RNAseq 19-22 October 2020 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Aimed at researchers who were in the experimental planning stages of a Single-Cell genomics project, the course required no previous experience in bioinformatics approaches with the najority of hands-on analysis delivered through the web-based, user-friendly interface - Galaxy. The course provided an introduction to single-cell genomics for researchers who are new to bioinformatics and covered: assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variations at the single-cell level. It consisted of a mixture of conceptual and methodological lectures and hands-on sessions, including best practices and tips as learned first-hand by Earlham Institute's faculty. The course was converted from a 5-day course that was previously split 3 days of lab work and 2 days of bioinformatics into a bioinformatics only course, spread over 4, shorter days (10:00-15:00) and involved a number of new teaching faculty. The majority of attendees were national and outside of the Norwich Research park, and from academia (88%). They rated the training overall as very good or excellent (100%) and the trainers very good or excellent (100%), with 100% saying that they would recommend the course. Despite the virtual nature of the course, there were plenty of opportunities to to discuss matters with both trainers and discuss with other delegates and there were many requests during our introductory delegate 'flash' presentations where individuals wished to reach out to each other for longer-term collaborations and/or to discuss new techniques/approaches that were presented. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/single-cell-rnaseq-2020 |
| Description | Software Carpentry (12-14 December 2023) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | - |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/events/software-carpentry-workshop-dec23 |
| Description | Software Carpentry 07-10 February 2023 (In-person) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | This workshop is designed to help scientists become more productive by teaching them basic computing skills like program design, version control, testing and task automation. In this three-day bootcamp, short tutorials will alternate with hands-on practical exercises. Lessons included: using the shell to do more in less time; automating tasks and pipelines; writing structured programs; using Git to manage and share information; how (and how much) to test programs. Usually this syllabus is taught over two days, for this online only iteration we opted to run this as a four-day programme with shorter days (10:00-15:00). Attendees were all UK residents and predominantly from academic institutions, with one delegate from a global RnD company. The majority of attendees were from our local community across the Norwich Research Park. XX% of delegates rated the course as very good or excellent and XX% agreed or strongly agreed that trainers were knowledgeable and approachable (Note: Awaiting feedback collection from third party, The Carpentries). |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/events/software-carpentry-workshop-2023 |
| Description | Software Carpentry 18-21 January 2021 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | This workshop is designed to help scientists become more productive by teaching them basic computing skills like program design, version control, testing and task automation. Following discussions with trainers and review of the feedback from the first online iteration of this workshop in June 2020, the programme was redeveloped to run over the course of four, shorter days (10:00-15:00). This allowed for the short tutorials to continue as before, but with more time allowed for the hands-on practical exercises with which they alternated. Lessons included: using the shell to do more in less time; automating tasks and pipelines; writing structured programs; using Git to manage and share information; how (and how much) to test programs. In particular, there was more time to spend on the breakout groups for the Git collaboration lessons, and for Python tutorials. Attendees were predominantly UK residents (88%) and all were from academic institutions, with the majority from our local community across the Norwich Research Park (94%). 100% of delegates rated the course as very good or excellent and agreed or strongly agreed that trainers were knowledgeable and approachable. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/software-carpentry-virtual-workshop-2021 |
| Description | Software Carpentry 24-27 January 2022 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | This workshop is designed to help scientists become more productive by teaching them basic computing skills like program design, version control, testing and task automation. In this three-day bootcamp, short tutorials will alternate with hands-on practical exercises. Lessons included: using the shell to do more in less time; automating tasks and pipelines; writing structured programs; using Git to manage and share information; how (and how much) to test programs. Usually this syllabus is taught over two days, for this online only iteration we opted to run this as a four-day programme with shorter days (10:00-15:00). Attendees were all UK residents and predominantly from academic institutions, with one delegate from a global RnD company. The majority of attendees were from our local community across the Norwich Research Park. 91% of delegates rated the course as very good or excellent and 96% agreed or strongly agreed that trainers were knowledgeable and approachable. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/software-carpentry-virtual-workshop-2022 |
| Description | Software Carpentry 30 June-02 July 2020 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | This workshop is designed to help scientists become more productive by teaching them basic computing skills like program design, version control, testing and task automation. In this three-day bootcamp, short tutorials will alternate with hands-on practical exercises. Lessons included: using the shell to do more in less time; automating tasks and pipelines; writing structured programs; using Git to manage and share information; how (and how much) to test programs. Usually this syllabus is taught over two days, for this online only iteration we opted to run this as a three-day programme with shorter days (10:00-15:00). Attendees were all UK residents and from academic institutions, with the majority from our local community across the Norwich Research Park. 100% of delegates rated the course as very good or excellent and agreed or strongly agreed that trainers were knowledgeable and approachable. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/software-carpentry-2020 |
| Description | Software Carpentry Workshop - 10-11 October 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | The intention of this workshop is to help scientists become more efficient in data analysis through teaching basic computing skills such as programme design, version control, testing and task automation. The two-day workshop alternates short tutorials with hands-on practical exercises to reinforce concepts and best practice. This course is aimed at researchers in the life science and computational science disciplines and across all research stages. Delegates learned how to: use the shell to do more in less time, automate tasks and pipelines, write structured programmes, using Git to manage and share information, plus how and to what extent to test programmes. 100% of delegates rated the event overall as very good to excellent, 100% rated the trainers as very good to excellent and 100% said that they would recommend the course. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/software-carpentry-workshop-october-2017 |
| Description | Software Carpentry Workshop - 26-27 April 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | The intention of this workshop is to help scientists become more efficient in data analysis through teaching basic computing skills such as programme design, version control, testing and task automation. The two-day workshop alternates short tutorials with hands-on practical exercises to reinforce concepts and best practice. This course is aimed at researchers in the life science and computational science disciplines and across all research stages. Delegates learned how to: use the shell to do more in less time, automate tasks and pipelines, write structured programmes, using Git to manage and share information, plus how and to what extent to test programmes. Almost 50% of delegates in attendance were PhD students, in accordance with our target audience. Around 90% of delegates rated the training overall as very good top excellent, and 100% stated that they would recommend the course to others. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/software-carpentry-workshop-2017 |
| Description | Software Carpentry training |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Participants attended entry level lessons with exercise to start using Python, Git and R in their research. It was given an overview of good coding practices for science and how research can benefit from these tools. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/software-carpentry-workshop-october-2017 |
| Description | Software Development for Earth and Environmental Scientists: Reproducible Research through Reusable, Reliable Code |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Dr. Nicola Soranzo (Earlham Institute) attended this training workshop, organised by The University of Manchester in collaboration with the Software Sustainability Institute, as observer and additional helper with a view to potential redevelopment and delivery by other ELIXIR-UK partners, including at EI. This activity was supported by EI's FTMA4 award (BB/X017761/1). |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://research-it.manchester.ac.uk/news/2022/11/30/reproducible-environmental-research-from-resear... |
| Description | Software carpentry workshop 21-22 January 2020 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | With an overview of basic program design, version control, testing and automation, this workshop is designed to provide delegates with little or no prior programming experience and to teach how to improve efficiency using the command line, automation of tasks and how to manage and share your own code and information using Git. Aimed at early career researchers it is no surprise that almost all of the attendees were undergraduate students, postgraduate students or Postdoctoral scientists and almost 75% of these were from the local area (Norwich Research Park). Respondents to feedback surveys indicated that the trainers were knowledgeable and easy to interact with, with 100% rating as in 'Agree' or 'Strongly Agree' |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/software-carpentry-2020 |
| Description | Talk "BioFAIR Status Update" at the ELIXIR Tools Platform F2F 2024 meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Nicola Soranzo presented the short talk "BioFAIR Status Update" at the ELIXIR Tools Platform F2F 2024 meeting, Manchester, UK, 26-27/11/2024. The talk was part of a session dedicated to the interactions of the ELIXIR Tools Platform with other National projects, where Dr. Soranzo introduced the new UK digital research infrastructure BioFAIR, its objectives and delivery model, and an update on its delivery progress. Slides: https://docs.google.com/presentation/d/1iLn-7qILPRZ1tA0Tw9E-Xd1SVxagOQ0c766xB2QHM50/edit?usp=sharing |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://docs.google.com/document/d/163MxsxfwK2_wkO8_n16XjcQqLiSvRsn5t8UR2NepoSI/edit?usp=sharing |
| Description | Talk at EGD2022: Python type annotation of Galaxy and BioBlend: goals and progress |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This talk was presented by Dr. Nicola Soranzo at the European Galaxy Days 2022, Freiburg im Brisgau, Germany, 04/10/2022. Dr. Soranzo presented an introduction to Python type annotations and static type checking, and the current state of type annotations in the Galaxy ecosystem. Slides are available at https://docs.google.com/presentation/d/1gnFuTP-alIL1ZXRb-vAYq_irBqbaDUHTE2aNAsaYLRc/edit?usp=sharing |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://galaxyproject.org/events/2022-10-egd/egd/ |
| Description | Talk at ELIXIR All Hands 2023: Services and resources to facilitate the work of Galaxy tool developers and administrators |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This talk was presented by Dr. Nicola Soranzo (Earlham Institute, ELIXIR-UK) during the "Scaling user support: Galaxy from a service perspective" workshop at the ELIXIR All Hands 2023, Dublin, Ireland, 6/06/2023. Dr. Soranzo explained the scalability issues faced by Galaxy tool and workflow developers and admins, and presented the services and resources available to facilitate their work. Slides are available at https://docs.google.com/presentation/d/1uJuXGVTfmyMOjOOHqppdswfMsGkIa3C5sQcJSvul5ao/edit?usp=sharing |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://docs.google.com/document/d/1kTot1V-t7xJx5ftQJiWiht5e3ix3nAq3MkFKhU4_4lA/edit?usp=sharing |
| Description | Talk at GCC2022: Support for the Common Workflow Language in Galaxy: History, Progress and Remaining Challenges |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This talk was presented by Dr. Nicola Soranzo (together with Michael Crusoe from VU Amsterdam and ELIXIR-NL) at the 2022 Galaxy Community Conference (GCC2022), University of Minnesota, Minneapolis, MN, USA, 19/07/2022. Dr. Soranzo presented the history, design choices and progress made towards supporting the execution of the Common Workflow Language (CWL) tools and workflows in Galaxy and discussed the remaining challenges and the path towards merging the separate CWL branch into the upstream Galaxy repository. Slides are available at https://docs.google.com/presentation/d/1LbV3AthOJwxTCOA0WSbNsGhf6nw8W_yHgkRQ4WZj2F8/edit?usp=sharing |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://gcc2022.sched.com/event/135D9/support-for-the-common-workflow-language-in-galaxy-history-pro... |
| Description | Talk delivered at the ELIXIR Biodiversity working group Inaugural meeting - Milan 2020 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Organised as part of a new ELIXIR working group to address challenges in biodiversity data management and infrastructure. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Talk given at the ELIXIR All Hands 2022: Nicola Soranzo, Day 2 Workshop session 2 - Communities Connectedness |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | ELIXIR-UK Member Nicola Soranzo (Earlham) gave a talk entitled: The Galaxy Community: "Gateway for integration across Communities |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://docs.google.com/document/d/194CPrabfk0qd9uTnxOFB2WNkppyiRfIPZxp1o6XYlg4/edit# |
| Description | Talk given at the ELIXIR All Hands 2022: Nicola Soranzo, Day 3 Workshop session 3 - Science driven improvements to tools ecosystems |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | ELIXIR-UK Member Nicola Soranzo (Earlham) gave a talk entitled: Improving the FAIRness of workflows in Galaxy |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://docs.google.com/document/d/1VA_9_1TOECPL26exs4Nyow_Y2V9RGzOnzF0WYcmLxyo/edit# |
| Description | Talk given at the ELIXIR All Hands 2022: Nicola Soranzo, Day one Workshop session 2 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | ELIXIR-UK Member Nicola Soranzo (Earlham) gave a talk entitled: Updates from the Galaxy-verse |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://docs.google.com/document/d/1vcOkcp528S1auXjxqrXwhE1Gjgmf2o4kUF9i2MKH9Uw/edit# |
| Description | Talk: Beta Python 3 support for Galaxy in release 18.09, at last! (European Galaxy Days 2018) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. N. Soranzo presented "Beta Python 3 support for Galaxy in release 18.09, at last!" at the "European Galaxy Days", Freiburg im Brisgau, Germany, 19-20/11/2018, had some discussion with other professional working in the same area, and made plans for further development. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://galaxyproject.org/events/2018-europe-dev/ |
| Description | Talk: Galaxy and its Tool Shed on Python 3: conclusion of a long journey |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. N. Soranzo presented the "Galaxy and its Tool Shed on Python 3: conclusion of a long journey" talk at the Bioinformatics Community Conference 2020 (BCC2020), virtual, 17-24/07/2020. Dr. Soranzo recounted how Python 3 support was added in the course of multiple years without breaking the existing code under Python 2, and looked at the upcoming removal of Python 2 support. Slides are available at https://docs.google.com/presentation/d/1wVWZxyZzfVnkx0fi58LJh0NzvqV7pwoizrr4hoOolfw/edit?usp=sharing |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://bcc2020.sched.com/event/clA8/galaxy-and-its-tool-shed-on-python-3-conclusion-of-a-long-journ... |
| Description | Talk: Galaxy: linking ELIXIR Communities and Platforms (ELIXIR UK All Hands 2018) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. N. Soranzo presented "Galaxy: linking ELIXIR Communities and Platforms" at the "ELIXIR UK All Hands 2018", Birmingham, UK, 28-29/11/2018, had some discussion with other professional working in the same area, and made plans for further development. Dr. Soranzo also introduced himself as new ELIXIR UK Technical Coordinator to other members of the ELIXIR UK community. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/elixir-all-hands-2018 |
| Description | Talk: GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline (GCC2018) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. N. Soranzo presented "GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline" at the "2018 Galaxy Community Conference (GCC2018)", Portland, OR, USA, 26-30/06/2018, had some discussion with other professional working in the same area, and made plans for further development. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://gccbosc2018.sched.com/event/EYNE/geneseqtofamily-a-galaxy-workflow-to-find-gene-families-bas... |
| Description | Talk: Integrating new Galaxy tools for COVID-19 workflows |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo presented this talk at the ELIXIR All Hands 2020, virtual, 08-10/06/2020, https://elixir-europe.org/events/elixir-all-hands-2020 In this talk (part of the Tools Platform workshop), Dr. Soranzo reported about the progress made during the COVID-19 virtual Biohackathon (held virtually 05-11/04/2020) in developing tools and workflows for viral pangenome assembly in the Galaxy bioinformatics web platform. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://docs.google.com/document/d/1WmdvTFmqV56XY_ZJCplOmDck7_XEPrMf8rPkSd5IQdY/edit?usp=sharing |
| Description | Talk: Introduction to Galaxy and BCO submission |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo presented the talk "Introduction to Galaxy and BCO submission" at the "Building BioCompute Objects on three popular Bioinformatics platforms" workshop, online, 13/09/2022 (around 35 participants). Dr. Soranzo introduced the Galaxy web platform for reproducible data-intensive analysis and how to export a complete analysis from Galaxy to a BioCompute Object Database (BCO DB). He also actively participated in the discussion session that closed the workshop. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.eventbrite.com/e/building-biocompute-objects-on-three-popular-bioinformatics-platforms-t... |
| Description | Talk: Technical Coordinator update (ELIXIR-UK All Hands 2019) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr. Nicola Soranzo presented this talk at the ELIXIR-UK All Hands 2019, Dundee, UK, 9-11/12/2019. In this talk, Dr. Soranzo recounted his activities as Technical Coordinator for ELIXIR-UK and illustrated the outcomes of recent events like the 1st ELIXIR-UK Hackathon and BioHackathon Europe 2019. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://docs.google.com/presentation/d/1B7OdKVvOLfXYjk-WBaDSVDBAnI-NCEm5l3GwBAwNfYg/edit?usp=sharing |
| Description | The regulatory landscape of intestinal cells - investigating the transcriptional effect of autophagy impairment observed in Crohn's disease using organoid and network biology approaches 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Updating the Inflammatory Bowel Disease community about the regulatory landscape and the role of autophagy in various types of intestinal cells |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://academic.oup.com/ecco-jcc/article/13/Supplement_1/S031/5300677 |
| Description | Training at GCC2022: BioBlend |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This training workshop was presented by Dr. Nicola Soranzo (together with Dannon Baker from Johns Hopkins University) at the 2022 Galaxy Community Conference (GCC2022), University of Minnesota, Minneapolis, MN, USA, 19/07/2022. This session introduced Galaxy's always-growing API that allows for external programs to upload and download data, manage histories and datasets, run tools and workflows, and even perform admin tasks. The training covered various approaches to access the API, in particular using the BioBlend Python library. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://gcc2022.sched.com/event/xaD3/bioblend |
| Description | Training delivered - Single Cell RNA-Seq data analysis 2022 - Graham Etherington, David Wright, Yuxuan Lan, Wilfried Haerty, Iain Macaulay |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Training delivered as part of the Single Cell RNA-Seq data analysis 2022 |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/events/single-cell-rnaseq-data-analysis-2022 |
| Description | Training held at BeCA: Cyverse ecosystem, basic Sysadmin skills and dockerization |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | About 15 researchers from Easter Africa attended a 1 week training course, as part of a longer training in bioinformatics, to learn about virtual machines, Docker, basic Sysadmin skills and how to apply this knowledge using CyVerse. CyVerse UK also supplied the virtual machines for the training to take place. |
| Year(s) Of Engagement Activity | 2018 |
| Description | UK CBCB: an ELIXIR for cross-disciplinary collaboration in bioinformatics |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | UK CBCB: an ELIXIR for cross-disciplinary collaboration in bioinformatics |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/uk-cbcb-elixir-cross-disciplinary-collaboration-bioinformatics |
| Description | UK Node Chair of an ELIXIR All Hands 2021 Workshop | Strengthening the integration of Galaxy in the Tools Ecosystem |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Nicola Soranzo Co-Chaired this workshop Building on top of the content aggregated and curated over the last years, the ELIXIR Tools Platform has initiated the development of the "Tools Platform Ecosystem" metadata exchange platform to coordinate different ELIXIR registries and services using community-driven standards. In this workshop, members of the ELIXIR Galaxy Community and the Tools Platform will give updates on their latest developments and plans, and then discuss current and future collaborations in light of the funded Implementation Studies and Commissioned Services. In particular, we intend to concentrate on the integration of Galaxy into the Tools Ecosystem by exploring how Galaxy could become more interoperable with the various ELIXIR registries and services, and how the ELIXIR Communities can benefit from this. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://docs.google.com/document/d/1vmOwdlfHTERJudwhs9F6v3oYIAMi0wc5bJWsHDSqWRM/edit?usp=sharing |
| Description | UK-Conference of Bioinformatics and Computational Biology (UK-CBCB) 27-29 September 2022 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was the third iteration of the UK Conference of Bioinformatics and Computational Biology (UK-CBCB), organised in conjunction with ELIXIR-UK. The conference was designed to bring together biologists, bioinformaticians, computer scientists, software engineers and data scientists across the life sciences to discuss and present on how to manage biological data and use computational methods to power life science research. The 3-day programme combined a keynote lecture with presentations of use cases from researchers working at the cutting edge, plus breakout discussion groups at the end of each session. The breakout groups were intended for participants to exchange expertise and challenges with one another, in order to develop multidisciplinary solutions to complex problems together. Discussions and themes as a result of these breakout groups were then summarised by the facilitator at the end of each session. To maximise engagement across multiple disciplines we opted for a streamlined programme (no parallel sessions), and short introductory talks to support each session to encourage focus on the theme in question. Research facilitators also headed up each session to reinforce key themes, and encourage or stimulate conversation. The sessions covered: Metagenomics and Microbial Bioinformatics; Bioimaging and Artificial Intelligence; Sex and Gender Bias in Computational Disciplines; Federated Analytics/Learning; Structural Bioinformatics; Open Science and Spatial Transcriptomics. Over 130 delegates registered to attend the conference, the majority from the United Kingdom (~86%) however registrants were also based in the US and Europe, Asia, the Middle East and South Africa. Approximately half of these virtual attendees were Postdoctoral Researchers (52%) while other significant groups comprised PhD Students (19%) and Professor/PIs (11%). |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/uk-cbcb-2022#about-the-event |
| Description | UK-Conference of Bioinformatics and Computational Biology (UK-CBCB) 28-30 September 2021 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was the second iteration of the UK Conference of Bioinformatics and Computational Biology (UK-CBCB), organised in conjunction with ELIXIR-UK. The conference was designed to bring together biologists, bioinformaticians, computer scientists, software engineers and data scientists across the life sciences to share innovations, applications and best practice in their fields. Applicable to bioinformatics researchers working on core services or in research teams as well as computer scientists or bioinformaticians developing tools or maintaining data resources. Originally planned as an in-person event, as the pandemic progressed the decision was made to convert this to virtual only format. With all speakers happy to present for the event in this format, we continued with the planned 3-day event, and took abstract submissions for selected speakers for each of the sessions. We opted here for a nominal registration fee of £15 to cover the additional use of the Spatial chat platform for networking and poster sessions. Sessions included: Research Data Management; Metagenomics and Microbial Genomics; Computational Proteomics and Metabolomics; Bridging Genotype to Phenotype; Structural Bioinformatics; and Artificial Intelligence. The event also included a workshop session for the UKRI Innovation Scholars - Data Science Training in Health and Bioscience, to allow engagement across the various planned activities from this scheme, plus a short funder's perspective session on Data-intensive bioscience and artificial intelligence (UKRI-BBSRC). The sessions saw an even spread of attendees with similar numbers across all sessions. Three themes emerged from the conference: Theme 1: FAIR data Theme 2: COVID-19 response Theme 3: AI and Machine Learning. Attendees were predominantly national (non-Norwich Research Park) (85%) with some international (~17%) and from academia (92%) with the remainder (8%) from industry. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/uk-conference-bioinformatics-and-computational-biology-21 |
| Description | UKRI Data Infrastructure Club Show & Tell |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | ELIXIR-UK Joint Head of Node Prof. Carole Goble organised an informal Show & Tell meeting (online, 20/01/2023) with researchers from several UKRI Research Councils involved in planning and delivering Digital Research Infrastructures and Data Commons for UK researchers to exchange their experiences, technology choices and challenges encountered. During the event, the ELIXIR-UK Technical Coordinator Dr. Nicola Soranzo presented "BioFAIR: a new BioCommons infrastructure for UK life science". |
| Year(s) Of Engagement Activity | 2023 |
| Description | UKRI-BBSRC Workshop on Computing in the Biosciences |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | BBSRC ran a workshop to discuss the outcomes of its "Review of Data-Intensive Bioscience" and to better understand the scientifc computing needs of the bioscience community. Several EI researchers participated to the facilitated discussions, expressing their views on current needs and available opportunities. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://webarchive.nationalarchives.gov.uk/ukgwa/20210409080241/https://bbsrc.ukri.org/news/events/2... |
| Description | Visit from Collaborators from University of Melbourne; Andrew Lonie, Glen Mooney and Rhys Francis |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Visit from Collaborators from University of Melbourne; Andrew Lonie, Glen Mooney and Rhys Francis |
| Year(s) Of Engagement Activity | 2018 |
| Description | Web Article - The seven deadly sins of software documentation - 2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. Community engagement in best practice - Software development is time consuming, but it's vital to use proper documentation. Some tips on how to make life easier for those using your program. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/seven-deadly-sins-software-documentation |
| Description | Web Article - What is bioinformatics? - 16.10.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. Bioinformatics is a growing field of research, existing at the cutting-edge of the biological sciences. But what is it? Biology is going large. With the advent of next generation (and third generation) genome sequencing and along with it an explosion in the amount of biological data being produced daily, scientists are now playing with terabytes or even petabytes (lots and lots of zeros) of data at a time. It would take infinite infinities for a single person to analyse this digital abundance. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/what-is-bioinformatics |
| Description | Web Article - Why code? Bioinformatics for decoding living systems - 17.09.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | To celebrate National Coding Week, we ask some of our bioinformaticians here at EI why they code. Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/why-code-bioinformatics-decoding-living-systems |
| Description | Web Article - Women in computing: a journey into bioinformatics with Erin Baggs - 08.05.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. This is part of our women in computing to promote this as a career addressing the skill shortage and lack of gender balance in the UK For many in the bioinformatics world, coding is a leap into the unknown. This was the case for Erin Baggs, who has learned from scratch how to apply computational science to biology while doing her PhD with Ksenia Krasileva. She gives us an insight into what life is like for a PhD student, and how to negotiate the intrepid plunge into the choppy sea of coding. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/women-computing-journey-bioinformatics-erin-baggs |
| Description | Web article - A celebration of science in Norwich - 27.08.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. Promoting our engagement in the Noriwch Science festival beyond our region. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/celebration-science-norwich |
| Description | Web article - Aequatus - a free, open-source visualisation tool enabling in-depth comparison of homologous genes - 15.10.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. This article focused on Aequatus - a new bioinformatics tool developed at Earlham Institute (EI) - is helping to give an in-depth view of syntenic information between different species, providing a system to better identify important, positively-selected, and evolutionarily-conserved regions of DNA. It is to promote the use of this tool and illustrate the work that we do. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/aequatus-bioinformatics-data-visualisation-tool |
| Description | Web article - Bioinformatics for East Africa: Spotlight on Toni Etuk - 03.09.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. An article about Dr Anthony Etuk, a computer scientist at Earlham Institute, being appointed to the Scientific Advisory Board (SAB) of the East Africa Network for Bioinformatics Training (EANBiT) - helping to build capability and establish scientific computing expertise in the region. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/bioinformatics-east-africa |
| Description | Web article - Decoding Living Systems: from cell to ecosystem - 28.03.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/decoding-living-systems-cell-ecosystem |
| Description | Web article - Fostering symbiosis in the biosciences through multiscale modelling |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | News article to highlight the "Multiscale analysis of host-microbe interactions in plants, animals & humans" workshop and it's outcomes. -SOCIAL MEDIA- Engagement x102, Impressions x113433 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/articles/fostering-symbiosis-biosciences-through-multiscale-modelling |
| Description | Web article - Women in Computing: Alexandra Veress - 12.01.2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. This is part of our women in computing to promote this as a career addressing the skill shortage and lack of gender balance in the UK. Alexandra Veress came to study at Earlham Institute for three months as part of the Korcsmáros Group, where she learned how to apply computational approaches to biology. Working with Tamás and his group, as many can attest, is a great experience - and Alexandra left for Hungary with the desire to learn even more about the world of bioinformatics. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/women-computing-learning-ropes-bioinformatics |
| Description | Web article - Women in computing: Yuxuan Lan - 11.02.2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. This is part of our women in computing to promote this as a career addressing the skill shortage and lack of gender balance in the UK |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/women-computing-yuxuan-lan |
| Description | Website Article: An accessible single-cell RNA seq bioinformatics training suite using Galaxy |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Detailed the development of a workflow and related training materials via the user-friendly Galaxy interface to support biologists with no prior experience in command line. This was used as part of the training course in Single-Cell RNAseq bioinformatics earlier in the year. The workflow remains freely accessible and demonstrates the longer-term impact through continued availability of our training materials and courses developed through NC4. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/accessible-single-cell-rna-sequencing-bioinformatics-training-usi... |
| Description | Website Article: Is this the future of science conferences? |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Outlining the experience of both the training team and faculty members in the conversion to online, virtual training events, conferences and similar. Detailing the positives of going virtual (reducing carbon footprint, widening participation, shorter and more focussed programmes tailored to a more realistic attention span, inclusive networking, availability of recordings for playback and enhanced recollection) versus the down-sides (presenting to the void, ability to become distracted, lacking the social side and food, more time sat in front of a screen, technical issues) |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/future-science-conferences-if-we-are-serious-about-climate-action... |
| Description | Website article: We're ten years old; 21/09/2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Website article highlighting contributions of EI, including work delivered through the NC4. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/articles/ten-years-leading-decoding-complex-genomes |
| Description | Wheat Bioinformatics III workshop, South Africa |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | 25 people from across the crop industrial and academic sectors were trained in Wheat Bioinformatics, the third in a series of workshops organised by Diane Saunders, Burkhard SteuerNagel and Rob Davey, funded by the UK High Commission in South Africa. This workshops are valuable for the attendees to learn the up-to-date computational and analytical techniques to make the most of their own and publicly available wheat data, feeding these skills directly into their breeding programmes. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Why cloud computing is important for life science research |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article to highlight services and opportunities arising from the use of cloud computing in life science research |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/articles/why-cloud-computing-important-data-driven-bioscience-research |
| Description | Why statistics is important in a world of big data |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Why statistics is important in a world of big data |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/why-statistics-important-world-big-data |
| Description | Workshop Oral Presentation: Gene families dynamics associated with lineage specific adaptations in Vertebrates |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited presentation to the students of the Earth and Life Systems Alliance (Norwich Research Park). The audience of the seminar was mainly composed of graduate and undergraduate students as well as University Professors and Lecturers. The presentation helped raising the profile of Wilfried Haerty and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | computing platform ELIXIR F2F meeting |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Meeting to updates in the compute platform of ELIXIR and make plans for interactions with EOSC and start using AAI ELIXIR authentication system. |
| Year(s) Of Engagement Activity | 2019 |
| Description | web article - One day in New York: bioinformatics and family life - 13.08.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. This is part of our working in computing to promote this as a flexible career addressing the skill shortage and lack of gender balance in the UK |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/one-day-new-york-bioinformatics-and-family-life |