Development and deployment of versatile digital platforms for 'omics-based data sharing and analysis

Lead Research Organisation: Earlham Institute
Department Name: UNLISTED

Abstract

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.
 
Description For the last 5 years, we have deployed and maintained a Galaxy server, used by researchers at the Earlham Institute and at the Quadram Institute. Over 565 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 and computational chemistry. A Docker image of Galaxy containing the GeneSeqToFamily workflow and all dependencies is also available from DockerHub. The Aequatus plugin in Galaxy is now integrated into the core codebase and comes with every Galaxy instance since version 19.01.

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. As the number of users increased over time to over 320, we organised 3 dedicated workshops and have provided guidance and support for 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 and metadata CyVerse users can share with collaborators, as well as a Data Commons repository for curated DFW data.

The CyVerse UK cloud was recently used for the first time to provide virtual machines for a hands-on bioinformatics training in Kenya; we are building on this experience to further develop our offer of training support on the platform.

The CyVerse UK e-infrastructure is now supporting EI training courses that requires trainees to work in a virtual environment. We have so far run 2 courses. The set up 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 in the EI system, and trainees have access to a ready-to-use desktop like environment with all relevant software and data pre-installed.

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. This project also represented a proof of concept for the usage of object storage in the cloud, which is now also being used by Grassroots and investigated for use with COPO.

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 developments.

Since 2017, our work on Galaxy and related technologies have underpinned the publication of 8 peer-reviewed papers. In particular, the paper describing Aequatus was successfully submitted to the GigaScience Prize Track, and first author A. Thanki from EI was invited to present it at BGI's International Conference on Genomics (ICG13) conference in Shenzhen, China.

Our group delivered several training workshops about Galaxy, CyVerse and basic computational skills: "Single-cell RNAseq Training Course" at EI, "Software Carpentry 2019" at EI, "Data Carpentry 2019" at EI. We also organised, together with the Training Team at EI, the "ELIXIR Workshop for Galaxy training material and skills improvement", which combined a Train-the-Trainer event with a hackathon on training material development, and the 1st ELIXIR-UK Hackathon in Cambridge, where participants worked on the integration of various ELIXIR-supported resources. Since 2018, we increased our involvement with ELIXIR (the intergovernmental organisation that brings together life science resources from across Europe) by attending other 4 ELIXIR-sponsored events and with the appointment of Dr N. Soranzo as Technical Coordinator for ELIXIR UK.

The CyVerse UK virtual machine offer, both as "single use" environment and as web hosting, is now part of the EOSC marketplace catalogue.

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 modeling problems. 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.
Exploitation Route GeneSeqToFamily gives users the opportunity to readily analyse not only complete genomes available through the Ensembl core databases, but also incomplete and/or non-model genomes of interest not yet available through public databases such as the precomputed Ensembl Compara hosted at EBI. Users can gain access to a broad yet sensitive analysis package to compare gene families within the genomes of their own research. Users can also visualise and interrogate gene families in detail, e.g. identify exon/intron boundary changes and mutations, using the Aequatus plugin that is now installed with Galaxy by default (from v19.01).

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 provides a reusable database and interface for mining regulatory networks, freely accessible for international researchers.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education

URL http://www.earlham.ac.uk/national-capability-e-infrastructure
 
Description The EI Galaxy server has more than 60 users (30 active) from EI and QIB, which ran over 1 million successful jobs in the last year, thanks to the high-performance compute resources funded by EI's recent Core Capability Grant awarded by BBSRC. GeneSeqToFamily is being used by researchers at EI to identify gene families across 19 rodent species, 24 vertebrate species, 9 bird transcriptomes, and also, in collaboration with UC Davis, on a set of 18 monocot and dicot plant genomes. The CyVerse UK cyberinfrastructure is currently hosting projects such as COPO and the Designing Future Wheat Grassroots infrastructure, as well as the BecA-Hub Galaxy instance for researchers in Nairobi, Kenya. It also hosts virtual machines to collaborators on and off site, providing them with custom compute and storage resources for their projects. As of today, 320 users worldwide, with the biggest group represented by UK and US researchers, have been using applications hosted and run on the CyVerse UK HPC system. We advertised the availability of the resource to DFW and other UK researchers and created additional resources as ORCA. Successive users have also provided positive feedback that shaped the SLA, guide and offer. We have been hosting 3 web servers in the CyVerse cloud for external users, thus multiplying the impact and allowing the community to be able to access resources such as CerealsDB and knetminer. The cyberinfrastructure is supporting the bioinformatics training of dozen of users thanks to the training offer at EI. Since 1 April 2018, the SignaLink website, which is also accessible from major web portals such as Uniprot, Flybase, Wormbase, attracted nearly 5000 visits (100-120 visits per week), and 85% of these were new users. The majority of users were from the US, UK, France, China, India and Brazil. The complete open database has been downloaded more than 120 times for analyses to be run within users' institutions.
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 BEIS/UKRI/RCUK Cloud Workshop, London, 24-10-2017
Geographic Reach National 
Policy Influence Type Participation in a national consultation
 
Description BecA-ILRI Hub & Strategic Partner Alignment 2019
Geographic Reach Africa 
Policy Influence Type Participation in a advisory 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 UKRI Data Infrastructure Roadmap
Geographic Reach National 
Policy Influence Type Participation in a national consultation
 
Description UKRI Supercomputing Roadmap
Geographic Reach National 
Policy Influence Type Participation in a national consultation
 
Description UKRI e-Infrastructure Expert Panel
Geographic Reach National 
Policy Influence Type Participation in a national consultation
Impact The UKRI Infrastructure landscape analysis and report constitutes the largest review of UK infrastructure across academic, industrial and the third sector. Davey and Hall N (EI) and Fretter (NBIP CiS) contributed key information to the analysis and reports to reflect the views and future strategy of the UK bioscience sector. This report has now been used to formulate the 2020 UK Budget with an announcement of large scale investment in infrastructure.
URL https://www.ukri.org/research/infrastructure/
 
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 08/2017 
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 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 05/2017 
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 04/2018 
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 04/2018 
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 09/2018 
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 06/2017 
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 10/2017 
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
 
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 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
 
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 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 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 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 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 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 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://github.com/galaxyproject/tools-iuc/tree/master/tools/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 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. 
 
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 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 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 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 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 2008
 
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 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 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://www.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 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 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 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 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, 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 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 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 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 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 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://bh2018paris.info/
 
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 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 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-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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 - 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: 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 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 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 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 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 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 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 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 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: 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: 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: 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 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 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 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 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