Computational Developments

Lead Research Organisation: Earlham Institute
Department Name: UNLISTED

Abstract

State-of-the-art technologies are generating unprecedented amounts of complex data, from genomes, to proteomes and transcriptomes, thus spanning mechanistic and functional diversity. Handling, interpreting and integrating these large scale data into descriptive models that interpret the molecular functions at a system level requires continued development of algorithms, robust computational models, and interoperable analytical frameworks. Supported by our core capability, In this work package, we will contribute to the newest developments in the data sciences and facilitate the extrapolation of meaningful signals from often noisy data.

We will continue to develop efficient, reproducible and robust assembly and scaffolding algorithms, and robust statistical models to handle diverse complex genomic and metagenomics datasets. We will improve and further develop software to facilitate orthology assignment across complex and highly divergent species. We will also incorporate machine learning approaches to integrate the conservation of functional signals across species to infer functionality and improve annotation. We are also developing new statistical and network analytical approaches will be applied to track temporal and spatial changes across and within species to further inform phenotypic complexity.

Our algorithm optimisation expertise will enable us to drive computational advances in accuracy and efficiency across our research into assembly and variant calling, annotation and, network analysis. These efforts will put the platforms in place to consistently collect and rapidly feed datasets into downstream integrative analyses, enabling the extensive and complex data interrogation processes required for bringing together multiple heterogeneous datasets. We will also apply these strategies to investigate and implement low power consumption computing technologies for data acquisition and analysis that will be deployed in environmental situations at a previously unavailable scale.

We will carry out fundamental research into software engineering methods to manage, share, visualise and integrate the large and complex datasets. We will develop research data management and dissemination layers, underpinned by community standards, that provide the granularity and searchability of EI’s large-scale and diverse data outputs that we are generating, and integrate the statistical, machine-learning, and network-based models developed under this programme. We will also build semantic knowledge graphs annotated with ontology-based descriptions in order to represent the body of information gathered through harmonised data and network integration. These will comprise metadata that describe reusable interconnected research datasets, and we will feed these methods into appropriate information systems to enable national and international collaborative research through open multi-omics platforms.

This will lay the foundations for an interconnected network of hardware and software to deliver real-time monitoring of crop development and pathogen detection and screening. Subsequent federation of these activities with national and international services will be facilitated through the EI NCG in e-Infrastructure (NC3), and interactions with the ELIXIR-UK community for pan-European life science infrastructures. This will also underpin the computational biology needs of the QIB Microbes in the Food Chain ISP in standardised and interoperable analysis systems.

Organisations

Publications

10 25 50
 
Description 1. Our research on pre-term baby diagnostics using nanopore sequencing was published in Nature Microbiology (https://www.nature.com/articles/s41564-019-0626-z). This includes publication of the NanoOK RT tool for performing real-time analysis of metagenomic samples from nanopore sequencing.
2. Our Reverse Metagenomics method was published in Methods in Ecology and Evolution (https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13265). It is now the subject of a UEA i-Teams project looking to investigate commercial applications of the method.
3. We developed a tool called Alvis for assembly and long read alignment visualisation and chimera detection. This can provide analysis that can help to improve long-read genome assemblies.
3. We continued to develop Sequence Distance Graph (SDG, https://github.com/bioinfologics/sdg) allowing the integration of short reads, linked reads, and long reads for genome assembly. SDG also enables the user to navigate the sequence graph (https://doi.org/10.12688/f1000research.20233.1).
4. We have published a pipeline to conduct full transcript annotation and quantification from long read nanopore data enabling the identification of novel exons and transcripts (https://doi.org/10.1038/s41380-019-0583-1, https://github.com/twrzes/TAQLoRe)
5. We are developing a data integration tool to allow parallel visualisation of multi-modal single cell data - for example integrating long- and short- read RNA sequencing from the same single cell. We anticipate developing this further to allow parallel analysis of genetic, epigenetic and transcriptional information.
6. We have continued to develop the COPO data brokering platform to help researchers submit data to public repositories. COPO has now been chosen to be the data broker system for sample collection information into the EBI ENA databases for the whole Darwin Tree of Life project. This will result in more consistent and more richly annotated genomic metadata being available alongside data that arises from the project.
7. We have continued to improve internal data management processes inside our High Performance Computing environments, implementing more rigorous project planning structures that feed directly into day-to-day management of data at the institute. This will lead to clearer data publication routes, as well as easier deposition of data outputs into our institutional CKAN digital repository and other public databases.
8. We have developed a machine learning classifier based on convolutional neural networks to reliably identify species of Tilapia fishes from images. The classifier is roughly 90% accurate in identifying over 30 species of fish.
9. Together with partners at Natural History Museum and the engineering company Kromek Plc, we obtained funding from DARPA worth up to $8m in total ($1m to EI, staged over 5 years) to develop vehicle mounted sensors for detection of bioterrorism threats. This DARPA grant has been running since April 2019 and work continues on updating the NanoOK RT (real-time Metagenomics tool developed for the pre-term work) back-end in order to link it to the new MARTi web-based front-end developed as part of Ned Peel's PhD.
Exploitation Route Our data management and analysis platforms will greatly improve the quality of well-described data originating from our CSP. Researchers, industrial partners, and the public will be able to see the full provenance of data generated at EI through our digital repository solutions in development.

Our technological outputs for single-cell data generation and analysis, and nanopore analysis, will enable EI to lead the field in precision and real-world application of these new technologies. These findings represent EI's commitment to producing advances in data generation, description, and integration powering our science. These impacts will be delivered to our academic and industrial communities through our National Capability programmes.

COPO is an open source tool, so can help any institution wishing to improve their descriptions of data that they manage and subsequently submit into a public or institutional repository. The CGIAR project has seen COPO's implementation as a proof-of-concept data broker for international CG centres. We are working with data managers within the CGIAR consortium to aid uptake.

Our Tilapia species classifier can be further developed to identify sex. This would be of use to breeders whose customers often want specific sex of fingerling.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment

URL http://www.earlham.ac.uk/science-strategy
 
Description The impact of our computational work has been seen across not just the academic sector, but particularly across the policy and governance space (see Influence on Policy and Practice) showing that EI's strategy for life sciences, informatics, and international research is noted by policymakers, Ministers in government, and industrioal stakeholders. Similarly, our large public engagement efforts have shown EI to be able to translate its science into events and information fit for public consumption, highlighting the multidisciplinarity of our CSP3 staff. This year alone, our open data portal, including the DFW data portal, has served over 54TB data to the community, comprising 151,794 files. Our CropSight platform paper was published in Gigascience, and the CropQuant patent was granted for licensing crop imaging and analysis technology (patent no. GB2553631). This year, the COPO platform submitted 43 publicly available ENA data projects for EI, comprising 6769 samples and 13827 datafiles which are now publicly available for anyone to use. We delivered the initial CGIAR CGCore v2 schema within COPO. We have met with key CG data managers both face to face at workshops (Rome) and conferences (Hyderabad) and through online webinars to deomnstrate the functionality and to gather feedback for improvements.
First Year Of Impact 2018
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment
Impact Types Cultural,Societal,Economic

 
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 Contribution to the National Food Strategy Public Consultation
Geographic Reach National 
Policy Influence Type Participation in a national consultation
URL https://consult.defra.gov.uk/agri-food-chain-directorate/national-food-strategy-call-for-evidence/
 
Description Input into "Balance and Effectiveness of Research and Innovation Spending" inquiry by the House of Commons Science and Technology Select Committee
Geographic Reach National 
Policy Influence Type Citation in other policy documents
URL https://publications.parliament.uk/pa/cm201719/cmselect/cmsctech/1453/145303.htm#_idTextAnchor000
 
Description Letter to Rt Hin Chris Skidmore to discuss science funding and science immigration post-brexit
Geographic Reach National 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
 
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 Wilfried Haerty - meeting with French Embassy representatives to provide evidence to French Government review, gain visibility of research park and potential source of funding between France and UK
Geographic Reach Europe 
Policy Influence Type Gave evidence to a government review
 
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 Artificial intelligence and deep learning in image based crop phenomics for predicting seed quality
Amount £99,034 (GBP)
Funding ID BB/S507441/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 09/2022
 
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 Building capacity in third-generation genomics and bioinformatics for agricultural biosciences in Africa
Amount £99,952 (GBP)
Funding ID BB/T017422/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2020 
End 03/2021
 
Description DNA sequencing for biological threat monitoring
Amount $5,270,000 (USD)
Funding ID HR001119C0031 
Organisation Defense Advanced Research Projects Agency (DARPA) 
Sector Public
Country United States
Start 12/2018 
End 12/2023
 
Description Darwin Tree of Life
Amount £9,360,421 (GBP)
Funding ID 218328/Z/19/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 11/2019 
End 05/2022
 
Description Developing capabilities in high performance digital infrastructure for data intensive scientific innovation in Colombia
Amount £29,500 (GBP)
Funding ID IAPP18-19\294 
Organisation Royal Academy of Engineering 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2019 
End 12/2020
 
Description Grand Challenges Research Fund (GCRF) Data & Resources (EI) - extension
Amount £160,963 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2017 
End 07/2018
 
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 Identification of prognostic indicators of healthy ageing with a machine learning based systems biology approach using gut microbiome data
Amount £99,034 (GBP)
Funding ID BB/S50743X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 09/2022
 
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 Interactive real-time metagenomics algorithms for Nanopore sequencing (LEGGETT_E17DTP1)
Amount £90,000 (GBP)
Funding ID 1937486 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2017 
End 09/2021
 
Description John Innes Centre Institute Strategy Funding - The elucidation of transcription factor networks underling internode extension in wheat
Amount £13,911 (GBP)
Organisation John Innes Centre 
Sector Academic/University
Country United Kingdom
Start 01/2018 
End 12/2018
 
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 New software for nanopore based diagnostics and surveillance
Amount £151,571 (GBP)
Funding ID BB/R022445/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2018 
End 01/2020
 
Description OpenPlant - Developing a frugal transcription factor relative affinity measurement pipeline (TRAMP)
Amount £5,000 (GBP)
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 09/2018 
End 07/2019
 
Description Ship-seq: Nanopore sequencing of polar microbes on board icebreakers
Amount £90,000 (GBP)
Funding ID 1942119 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 09/2017 
End 05/2021
 
Description UKRI - Earth Biogenome Project
Amount £600,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2019 
End 03/2022
 
Title CGCore v2 Improvements 
Description As part of the collaboration between the EI COPO project and the CGIAR Big Data Platform, we worked with CGIAR and Crop Ontology developers to improve the CG Core v2 schema for describing CGIAR digital outputs. 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? Yes  
Impact Globally, this work will affect all CGIAR Data Managers and users of the COPO platform to deposit data into CG Centre repositories. 
URL https://github.com/collaborative-open-plant-omics/cgcore_schema
 
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 MulEA: An R package for Multi Enrichment Analysis 
Description Bioinformatics, genomics analysis tool MulEA is a comprehensive gene set overrepresentation and enrichment Bioconductor R package and Galaxy tool Github link : https://github.com/TGAC/Mulea 
Type Of Material Improvements to research infrastructure 
Year Produced 2017 
Provided To Others? No  
Impact MulEA will provide extensive analytical means using diverse databases, statistical models and p-value correction procedures that can extend our understanding of the results of various high-throughput analyses. 
 
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 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 Supporting data for "A Galaxy-based training resource for single-cell RNA-seq quality control and analyses" 
Description It is not a trivial step to move from single-cell RNA-seq (scRNA-seq) data production to data analysis. There is a lack of intuitive training materials and easy-to-use analysis tools, and researchers can find it difficult to master the basics of scRNA-seq quality control and the later analysis.
We have developed a range of practical scripts, together with their corresponding Galaxy wrappers, that make scRNA-seq training and quality-control accessible to researchers previously daunted by the prospect of scRNA-seq analysis. We implement a 'visualise-filter-visualise' paradigm through simple command-line tools that use the Loom format to exchange data between the tools. The point-and-click nature of Galaxy makes it easy to assess, visualise, and filter scRNA-seq data from short-read sequencing data.
We have developed a suite of scRNA-seq tools that can be used for both training and more in-depth analyses. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
 
Title Supporting data for "Aequatus: An open-source homology browser" 
Description Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, including the identification of ancestral gene duplication events as well as regions under positive or purifying selection within lineages. Gene family and orthogroup characterisation enables the identification of syntenic blocks, which can then be visualised with various tools. Unfortunately, currently available tools display only an overview of syntenic regions as a whole, limited to the gene level, and none provide further details about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes.
We present Aequatus, a standalone web-based tool that provides an indepth view of gene structure across gene families, with various options to render and filter visualisations. It relies on pre-calculated alignment and gene feature information typically held in, but not limited to, the Ensembl Compara and Core databases. We also offer Aequatus.js, a reusable JavaScript module that fulfils the visualisation aspects of Aequatus, available within the Galaxy web platform as a visualisation plugin, which can be used to visualise gene trees generated by the GeneSeqToFamily workflow.
Aequatus is an open-source tool freely available to download under the MIT license at https://github.com/TGAC/Aequatus. A demo server is available at http://aequatus.earlham.ac.uk/. A publicly available instance of the GeneSeqToFamily workflow to generate gene tree information and visualise it using Aequatus is available on the Galaxy EU server at https://usegalaxy.eu 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
 
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 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 C3Biodiversidad: Colombian Cyberinfrastructure Consortium for Biodiversity (Consorcio Colombiano de Ciberinfraestructura para la Biodiversidad) 
Organisation Alexander von Humboldt Biological Resources Research Institute
Country Colombia 
Sector Charity/Non Profit 
PI Contribution C3Biodiversidad was created in a visionary workshop in Bogota from 26th to 28th June organised by GROW by a panel of experts from the Science, Technology and Innovation (STI) system of Colombia, with the assistance of a panel of independent international experts . C3Biodiversidad is open to any stakeholder interested in the development of a scientific cyberinfrastructure in Colombia.
Collaborator Contribution C3Biodiversidad aims to develop a scientific cyberinfrastructure in Colombia for the analysis of scientific data, especially biological, genomic and socioeconomic data. The objectives of C3Biodiversidad are: Growth skills in data analysis in Colombia, accelerate data-oriented research in Colombia, facilitate data-supported decision-making, secure the engagement of diverse stakeholders in the previous objectives.
Impact The Colombian Consortium of Cyberinfrastructure for Biodiversity aims to produce the following products for dissemination: A statement about its objectives and constitution, a strategy or white paper for the dissemination of the conclusions of the workshop in policy-making institutions, especially in Colombia and the United Kingdom, instruments for the coordination of the consortium using social networks (Slack, WhatsApp, Twitter @C3Biodiversidad, etc.), an informative note for dissemination in the national media, especially from Colombia and the United Kingdom, and an article in an international scientific journal.
Start Year 2018
 
Description C3Biodiversidad: Colombian Cyberinfrastructure Consortium for Biodiversity (Consorcio Colombiano de Ciberinfraestructura para la Biodiversidad) 
Organisation CGIAR
Department International Center for Tropical Agriculture
Country Colombia 
Sector Charity/Non Profit 
PI Contribution C3Biodiversidad was created in a visionary workshop in Bogota from 26th to 28th June organised by GROW by a panel of experts from the Science, Technology and Innovation (STI) system of Colombia, with the assistance of a panel of independent international experts . C3Biodiversidad is open to any stakeholder interested in the development of a scientific cyberinfrastructure in Colombia.
Collaborator Contribution C3Biodiversidad aims to develop a scientific cyberinfrastructure in Colombia for the analysis of scientific data, especially biological, genomic and socioeconomic data. The objectives of C3Biodiversidad are: Growth skills in data analysis in Colombia, accelerate data-oriented research in Colombia, facilitate data-supported decision-making, secure the engagement of diverse stakeholders in the previous objectives.
Impact The Colombian Consortium of Cyberinfrastructure for Biodiversity aims to produce the following products for dissemination: A statement about its objectives and constitution, a strategy or white paper for the dissemination of the conclusions of the workshop in policy-making institutions, especially in Colombia and the United Kingdom, instruments for the coordination of the consortium using social networks (Slack, WhatsApp, Twitter @C3Biodiversidad, etc.), an informative note for dissemination in the national media, especially from Colombia and the United Kingdom, and an article in an international scientific journal.
Start Year 2018
 
Description C3Biodiversidad: Colombian Cyberinfrastructure Consortium for Biodiversity (Consorcio Colombiano de Ciberinfraestructura para la Biodiversidad) 
Organisation Catholic University of Colombia
Country Colombia 
Sector Academic/University 
PI Contribution C3Biodiversidad was created in a visionary workshop in Bogota from 26th to 28th June organised by GROW by a panel of experts from the Science, Technology and Innovation (STI) system of Colombia, with the assistance of a panel of independent international experts . C3Biodiversidad is open to any stakeholder interested in the development of a scientific cyberinfrastructure in Colombia.
Collaborator Contribution C3Biodiversidad aims to develop a scientific cyberinfrastructure in Colombia for the analysis of scientific data, especially biological, genomic and socioeconomic data. The objectives of C3Biodiversidad are: Growth skills in data analysis in Colombia, accelerate data-oriented research in Colombia, facilitate data-supported decision-making, secure the engagement of diverse stakeholders in the previous objectives.
Impact The Colombian Consortium of Cyberinfrastructure for Biodiversity aims to produce the following products for dissemination: A statement about its objectives and constitution, a strategy or white paper for the dissemination of the conclusions of the workshop in policy-making institutions, especially in Colombia and the United Kingdom, instruments for the coordination of the consortium using social networks (Slack, WhatsApp, Twitter @C3Biodiversidad, etc.), an informative note for dissemination in the national media, especially from Colombia and the United Kingdom, and an article in an international scientific journal.
Start Year 2018
 
Description C3Biodiversidad: Colombian Cyberinfrastructure Consortium for Biodiversity (Consorcio Colombiano de Ciberinfraestructura para la Biodiversidad) 
Organisation Colombian Agricultural Research Corporation
Country Colombia 
Sector Charity/Non Profit 
PI Contribution C3Biodiversidad was created in a visionary workshop in Bogota from 26th to 28th June organised by GROW by a panel of experts from the Science, Technology and Innovation (STI) system of Colombia, with the assistance of a panel of independent international experts . C3Biodiversidad is open to any stakeholder interested in the development of a scientific cyberinfrastructure in Colombia.
Collaborator Contribution C3Biodiversidad aims to develop a scientific cyberinfrastructure in Colombia for the analysis of scientific data, especially biological, genomic and socioeconomic data. The objectives of C3Biodiversidad are: Growth skills in data analysis in Colombia, accelerate data-oriented research in Colombia, facilitate data-supported decision-making, secure the engagement of diverse stakeholders in the previous objectives.
Impact The Colombian Consortium of Cyberinfrastructure for Biodiversity aims to produce the following products for dissemination: A statement about its objectives and constitution, a strategy or white paper for the dissemination of the conclusions of the workshop in policy-making institutions, especially in Colombia and the United Kingdom, instruments for the coordination of the consortium using social networks (Slack, WhatsApp, Twitter @C3Biodiversidad, etc.), an informative note for dissemination in the national media, especially from Colombia and the United Kingdom, and an article in an international scientific journal.
Start Year 2018
 
Description C3Biodiversidad: Colombian Cyberinfrastructure Consortium for Biodiversity (Consorcio Colombiano de Ciberinfraestructura para la Biodiversidad) 
Organisation Colombian Sugarcane Research Center
Country Colombia 
Sector Public 
PI Contribution C3Biodiversidad was created in a visionary workshop in Bogota from 26th to 28th June organised by GROW by a panel of experts from the Science, Technology and Innovation (STI) system of Colombia, with the assistance of a panel of independent international experts . C3Biodiversidad is open to any stakeholder interested in the development of a scientific cyberinfrastructure in Colombia.
Collaborator Contribution C3Biodiversidad aims to develop a scientific cyberinfrastructure in Colombia for the analysis of scientific data, especially biological, genomic and socioeconomic data. The objectives of C3Biodiversidad are: Growth skills in data analysis in Colombia, accelerate data-oriented research in Colombia, facilitate data-supported decision-making, secure the engagement of diverse stakeholders in the previous objectives.
Impact The Colombian Consortium of Cyberinfrastructure for Biodiversity aims to produce the following products for dissemination: A statement about its objectives and constitution, a strategy or white paper for the dissemination of the conclusions of the workshop in policy-making institutions, especially in Colombia and the United Kingdom, instruments for the coordination of the consortium using social networks (Slack, WhatsApp, Twitter @C3Biodiversidad, etc.), an informative note for dissemination in the national media, especially from Colombia and the United Kingdom, and an article in an international scientific journal.
Start Year 2018
 
Description C3Biodiversidad: Colombian Cyberinfrastructure Consortium for Biodiversity (Consorcio Colombiano de Ciberinfraestructura para la Biodiversidad) 
Organisation CorpoGen
Country Colombia 
Sector Private 
PI Contribution C3Biodiversidad was created in a visionary workshop in Bogota from 26th to 28th June organised by GROW by a panel of experts from the Science, Technology and Innovation (STI) system of Colombia, with the assistance of a panel of independent international experts . C3Biodiversidad is open to any stakeholder interested in the development of a scientific cyberinfrastructure in Colombia.
Collaborator Contribution C3Biodiversidad aims to develop a scientific cyberinfrastructure in Colombia for the analysis of scientific data, especially biological, genomic and socioeconomic data. The objectives of C3Biodiversidad are: Growth skills in data analysis in Colombia, accelerate data-oriented research in Colombia, facilitate data-supported decision-making, secure the engagement of diverse stakeholders in the previous objectives.
Impact The Colombian Consortium of Cyberinfrastructure for Biodiversity aims to produce the following products for dissemination: A statement about its objectives and constitution, a strategy or white paper for the dissemination of the conclusions of the workshop in policy-making institutions, especially in Colombia and the United Kingdom, instruments for the coordination of the consortium using social networks (Slack, WhatsApp, Twitter @C3Biodiversidad, etc.), an informative note for dissemination in the national media, especially from Colombia and the United Kingdom, and an article in an international scientific journal.
Start Year 2018
 
Description C3Biodiversidad: Colombian Cyberinfrastructure Consortium for Biodiversity (Consorcio Colombiano de Ciberinfraestructura para la Biodiversidad) 
Organisation EAFIT University
Country Colombia 
Sector Academic/University 
PI Contribution C3Biodiversidad was created in a visionary workshop in Bogota from 26th to 28th June organised by GROW by a panel of experts from the Science, Technology and Innovation (STI) system of Colombia, with the assistance of a panel of independent international experts . C3Biodiversidad is open to any stakeholder interested in the development of a scientific cyberinfrastructure in Colombia.
Collaborator Contribution C3Biodiversidad aims to develop a scientific cyberinfrastructure in Colombia for the analysis of scientific data, especially biological, genomic and socioeconomic data. The objectives of C3Biodiversidad are: Growth skills in data analysis in Colombia, accelerate data-oriented research in Colombia, facilitate data-supported decision-making, secure the engagement of diverse stakeholders in the previous objectives.
Impact The Colombian Consortium of Cyberinfrastructure for Biodiversity aims to produce the following products for dissemination: A statement about its objectives and constitution, a strategy or white paper for the dissemination of the conclusions of the workshop in policy-making institutions, especially in Colombia and the United Kingdom, instruments for the coordination of the consortium using social networks (Slack, WhatsApp, Twitter @C3Biodiversidad, etc.), an informative note for dissemination in the national media, especially from Colombia and the United Kingdom, and an article in an international scientific journal.
Start Year 2018
 
Description C3Biodiversidad: Colombian Cyberinfrastructure Consortium for Biodiversity (Consorcio Colombiano de Ciberinfraestructura para la Biodiversidad) 
Organisation EAFIT University
Country Colombia 
Sector Academic/University 
PI Contribution C3Biodiversidad was created in a visionary workshop in Bogota from 26th to 28th June organised by GROW by a panel of experts from the Science, Technology and Innovation (STI) system of Colombia, with the assistance of a panel of independent international experts . C3Biodiversidad is open to any stakeholder interested in the development of a scientific cyberinfrastructure in Colombia.
Collaborator Contribution C3Biodiversidad aims to develop a scientific cyberinfrastructure in Colombia for the analysis of scientific data, especially biological, genomic and socioeconomic data. The objectives of C3Biodiversidad are: Growth skills in data analysis in Colombia, accelerate data-oriented research in Colombia, facilitate data-supported decision-making, secure the engagement of diverse stakeholders in the previous objectives.
Impact The Colombian Consortium of Cyberinfrastructure for Biodiversity aims to produce the following products for dissemination: A statement about its objectives and constitution, a strategy or white paper for the dissemination of the conclusions of the workshop in policy-making institutions, especially in Colombia and the United Kingdom, instruments for the coordination of the consortium using social networks (Slack, WhatsApp, Twitter @C3Biodiversidad, etc.), an informative note for dissemination in the national media, especially from Colombia and the United Kingdom, and an article in an international scientific journal.
Start Year 2018
 
Description C3Biodiversidad: Colombian Cyberinfrastructure Consortium for Biodiversity (Consorcio Colombiano de Ciberinfraestructura para la Biodiversidad) 
Organisation Jorge Tadeo Lozano University
Country Colombia 
Sector Academic/University 
PI Contribution C3Biodiversidad was created in a visionary workshop in Bogota from 26th to 28th June organised by GROW by a panel of experts from the Science, Technology and Innovation (STI) system of Colombia, with the assistance of a panel of independent international experts . C3Biodiversidad is open to any stakeholder interested in the development of a scientific cyberinfrastructure in Colombia.
Collaborator Contribution C3Biodiversidad aims to develop a scientific cyberinfrastructure in Colombia for the analysis of scientific data, especially biological, genomic and socioeconomic data. The objectives of C3Biodiversidad are: Growth skills in data analysis in Colombia, accelerate data-oriented research in Colombia, facilitate data-supported decision-making, secure the engagement of diverse stakeholders in the previous objectives.
Impact The Colombian Consortium of Cyberinfrastructure for Biodiversity aims to produce the following products for dissemination: A statement about its objectives and constitution, a strategy or white paper for the dissemination of the conclusions of the workshop in policy-making institutions, especially in Colombia and the United Kingdom, instruments for the coordination of the consortium using social networks (Slack, WhatsApp, Twitter @C3Biodiversidad, etc.), an informative note for dissemination in the national media, especially from Colombia and the United Kingdom, and an article in an international scientific journal.
Start Year 2018
 
Description C3Biodiversidad: Colombian Cyberinfrastructure Consortium for Biodiversity (Consorcio Colombiano de Ciberinfraestructura para la Biodiversidad) 
Organisation National University of Colombia
Country Colombia 
Sector Academic/University 
PI Contribution C3Biodiversidad was created in a visionary workshop in Bogota from 26th to 28th June organised by GROW by a panel of experts from the Science, Technology and Innovation (STI) system of Colombia, with the assistance of a panel of independent international experts . C3Biodiversidad is open to any stakeholder interested in the development of a scientific cyberinfrastructure in Colombia.
Collaborator Contribution C3Biodiversidad aims to develop a scientific cyberinfrastructure in Colombia for the analysis of scientific data, especially biological, genomic and socioeconomic data. The objectives of C3Biodiversidad are: Growth skills in data analysis in Colombia, accelerate data-oriented research in Colombia, facilitate data-supported decision-making, secure the engagement of diverse stakeholders in the previous objectives.
Impact The Colombian Consortium of Cyberinfrastructure for Biodiversity aims to produce the following products for dissemination: A statement about its objectives and constitution, a strategy or white paper for the dissemination of the conclusions of the workshop in policy-making institutions, especially in Colombia and the United Kingdom, instruments for the coordination of the consortium using social networks (Slack, WhatsApp, Twitter @C3Biodiversidad, etc.), an informative note for dissemination in the national media, especially from Colombia and the United Kingdom, and an article in an international scientific journal.
Start Year 2018
 
Description C3Biodiversidad: Colombian Cyberinfrastructure Consortium for Biodiversity (Consorcio Colombiano de Ciberinfraestructura para la Biodiversidad) 
Organisation Saint Thomas Aquinas University
Country Colombia 
Sector Academic/University 
PI Contribution C3Biodiversidad was created in a visionary workshop in Bogota from 26th to 28th June organised by GROW by a panel of experts from the Science, Technology and Innovation (STI) system of Colombia, with the assistance of a panel of independent international experts . C3Biodiversidad is open to any stakeholder interested in the development of a scientific cyberinfrastructure in Colombia.
Collaborator Contribution C3Biodiversidad aims to develop a scientific cyberinfrastructure in Colombia for the analysis of scientific data, especially biological, genomic and socioeconomic data. The objectives of C3Biodiversidad are: Growth skills in data analysis in Colombia, accelerate data-oriented research in Colombia, facilitate data-supported decision-making, secure the engagement of diverse stakeholders in the previous objectives.
Impact The Colombian Consortium of Cyberinfrastructure for Biodiversity aims to produce the following products for dissemination: A statement about its objectives and constitution, a strategy or white paper for the dissemination of the conclusions of the workshop in policy-making institutions, especially in Colombia and the United Kingdom, instruments for the coordination of the consortium using social networks (Slack, WhatsApp, Twitter @C3Biodiversidad, etc.), an informative note for dissemination in the national media, especially from Colombia and the United Kingdom, and an article in an international scientific journal.
Start Year 2018
 
Description C3Biodiversidad: Colombian Cyberinfrastructure Consortium for Biodiversity (Consorcio Colombiano de Ciberinfraestructura para la Biodiversidad) 
Organisation The National Academic Network of Advanced Technology
Country Colombia 
Sector Public 
PI Contribution C3Biodiversidad was created in a visionary workshop in Bogota from 26th to 28th June organised by GROW by a panel of experts from the Science, Technology and Innovation (STI) system of Colombia, with the assistance of a panel of independent international experts . C3Biodiversidad is open to any stakeholder interested in the development of a scientific cyberinfrastructure in Colombia.
Collaborator Contribution C3Biodiversidad aims to develop a scientific cyberinfrastructure in Colombia for the analysis of scientific data, especially biological, genomic and socioeconomic data. The objectives of C3Biodiversidad are: Growth skills in data analysis in Colombia, accelerate data-oriented research in Colombia, facilitate data-supported decision-making, secure the engagement of diverse stakeholders in the previous objectives.
Impact The Colombian Consortium of Cyberinfrastructure for Biodiversity aims to produce the following products for dissemination: A statement about its objectives and constitution, a strategy or white paper for the dissemination of the conclusions of the workshop in policy-making institutions, especially in Colombia and the United Kingdom, instruments for the coordination of the consortium using social networks (Slack, WhatsApp, Twitter @C3Biodiversidad, etc.), an informative note for dissemination in the national media, especially from Colombia and the United Kingdom, and an article in an international scientific journal.
Start Year 2018
 
Description C3Biodiversidad: Colombian Cyberinfrastructure Consortium for Biodiversity (Consorcio Colombiano de Ciberinfraestructura para la Biodiversidad) 
Organisation University of Antioquia
Country Colombia 
Sector Academic/University 
PI Contribution C3Biodiversidad was created in a visionary workshop in Bogota from 26th to 28th June organised by GROW by a panel of experts from the Science, Technology and Innovation (STI) system of Colombia, with the assistance of a panel of independent international experts . C3Biodiversidad is open to any stakeholder interested in the development of a scientific cyberinfrastructure in Colombia.
Collaborator Contribution C3Biodiversidad aims to develop a scientific cyberinfrastructure in Colombia for the analysis of scientific data, especially biological, genomic and socioeconomic data. The objectives of C3Biodiversidad are: Growth skills in data analysis in Colombia, accelerate data-oriented research in Colombia, facilitate data-supported decision-making, secure the engagement of diverse stakeholders in the previous objectives.
Impact The Colombian Consortium of Cyberinfrastructure for Biodiversity aims to produce the following products for dissemination: A statement about its objectives and constitution, a strategy or white paper for the dissemination of the conclusions of the workshop in policy-making institutions, especially in Colombia and the United Kingdom, instruments for the coordination of the consortium using social networks (Slack, WhatsApp, Twitter @C3Biodiversidad, etc.), an informative note for dissemination in the national media, especially from Colombia and the United Kingdom, and an article in an international scientific journal.
Start Year 2018
 
Description C3Biodiversidad: Colombian Cyberinfrastructure Consortium for Biodiversity (Consorcio Colombiano de Ciberinfraestructura para la Biodiversidad) 
Organisation University of the Andes
Country Colombia 
Sector Academic/University 
PI Contribution C3Biodiversidad was created in a visionary workshop in Bogota from 26th to 28th June organised by GROW by a panel of experts from the Science, Technology and Innovation (STI) system of Colombia, with the assistance of a panel of independent international experts . C3Biodiversidad is open to any stakeholder interested in the development of a scientific cyberinfrastructure in Colombia.
Collaborator Contribution C3Biodiversidad aims to develop a scientific cyberinfrastructure in Colombia for the analysis of scientific data, especially biological, genomic and socioeconomic data. The objectives of C3Biodiversidad are: Growth skills in data analysis in Colombia, accelerate data-oriented research in Colombia, facilitate data-supported decision-making, secure the engagement of diverse stakeholders in the previous objectives.
Impact The Colombian Consortium of Cyberinfrastructure for Biodiversity aims to produce the following products for dissemination: A statement about its objectives and constitution, a strategy or white paper for the dissemination of the conclusions of the workshop in policy-making institutions, especially in Colombia and the United Kingdom, instruments for the coordination of the consortium using social networks (Slack, WhatsApp, Twitter @C3Biodiversidad, etc.), an informative note for dissemination in the national media, especially from Colombia and the United Kingdom, and an article in an international scientific journal.
Start Year 2018
 
Description C3Biodiversidad: Colombian Cyberinfrastructure Consortium for Biodiversity (Consorcio Colombiano de Ciberinfraestructura para la Biodiversidad) 
Organisation University of the Llanos
Country Colombia 
Sector Academic/University 
PI Contribution C3Biodiversidad was created in a visionary workshop in Bogota from 26th to 28th June organised by GROW by a panel of experts from the Science, Technology and Innovation (STI) system of Colombia, with the assistance of a panel of independent international experts . C3Biodiversidad is open to any stakeholder interested in the development of a scientific cyberinfrastructure in Colombia.
Collaborator Contribution C3Biodiversidad aims to develop a scientific cyberinfrastructure in Colombia for the analysis of scientific data, especially biological, genomic and socioeconomic data. The objectives of C3Biodiversidad are: Growth skills in data analysis in Colombia, accelerate data-oriented research in Colombia, facilitate data-supported decision-making, secure the engagement of diverse stakeholders in the previous objectives.
Impact The Colombian Consortium of Cyberinfrastructure for Biodiversity aims to produce the following products for dissemination: A statement about its objectives and constitution, a strategy or white paper for the dissemination of the conclusions of the workshop in policy-making institutions, especially in Colombia and the United Kingdom, instruments for the coordination of the consortium using social networks (Slack, WhatsApp, Twitter @C3Biodiversidad, etc.), an informative note for dissemination in the national media, especially from Colombia and the United Kingdom, and an article in an international scientific journal.
Start Year 2018
 
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 Genome 10K Consortium 
Organisation University of California, Davis
Department UC Davis Genome Cente
Country United States 
Sector Academic/University 
PI Contribution The G10K consortium is an international consortium of tissue curators, biologists, conservationists, genome scientists, computer scientists, outreach educators, and more. Federica Di Palma is a council member of the Consortium and has provided advice to the current ongoing projects. Organised meetings and contributed talks to several workshops and meetings.
Collaborator Contribution The G10K leadership and community of scientists built an infrastructure from sample collection to genome sequencing, assembly, annotation, alignments, public data releases, and analyses for publications.
Impact Collaboration is multidisciplinaryand includes tissue curators, biologists, conservationists, genome scientists, computer scientists, outreach educators, and more from different countries. Outputs include press releases, workshops, meetings, publications.
Start Year 2011
 
Description HPE AI workshop 2019 
Organisation Hewlett Packard Enterprise (HPE)
Country United Kingdom 
Sector Private 
PI Contribution We worked with HPE staff to organise and host an AI Workshop at EI. We opened the course up for national delegates to attend and discover more about how AI and Machine Learning techniques can be applied to biological research data.
Collaborator Contribution HPE provided the trainers and staff to teach the materials.
Impact We will continue to work with HPE to supply our institutlonal HPE equipment. We have also put forward HPE as a potential partner in the upcoming DTP3 bid.
Start Year 2019
 
Description Integration of COPO and CGCore Schemas and Associated Repositories 
Organisation CGIAR
Country France 
Sector Charity/Non Profit 
PI Contribution We have developed a proof-of-concept platform to streamline metadata attribution and dataset deposition into CGIAR repositories using the BBSRC-funded COPO software. Drs Etuk and Shaw, two Research Software Engineers in the Davey group at Earlham Institute and the original core developers, have implemented various new features into COPO to allow CGIAR Data Managers to harmonise and streamline the submission of CG-relevant metadata and data into the CG digital data repositories. All software and infrastructure is hosted within the CyVerse UK cloud. We have: - Implemented support of CG Core v.2.0. (http://repo.mel.cgiar.org/handle/20.500.11766/4764) metadata annotation of various data types, including publications, produced at the CGIAR institutes via the existing COPO wizard system. - Implemented support of submissions of annotated objects to institutional instances of the following repositories: dSpace (https://www.duraspace.org/dspace/), CKAN (https://ckan.org/) and Dataverse (https://dataverse.org/). - Designed and implemented a mechanism within COPO which controls which users can submit to which repositories. - Implemented support the annotation of variables within data sets (i.e. column headings; experiment condition descriptors etc) with terms and URIs from ontologies or controlled vocabularies/trait dictionaries (AGROVOC and GACS).
Collaborator Contribution CGIAR have provided coordination contributions with key members in the CG Centres to gather feedback on developed elements, as well as provided funds to allow a core CGCore metadata schema developer to travel to EI and work with Drs Etuk and Shaw to improve the CGCore schema.
Impact This collaboration has seen rapid development of key functionality in the COPO platform to support CG centre Data Managers. This has required technical skills to develop the software, biocuration expertise provided by CGIAR to improve and refine the CGCore metadata schema, ontology expertise from the Bioversity team in Montpellier, and coordination expertise from Dr Davey (EI) and Medha Devare (CGIAR). Software and Technical Products (Webtool/Application - Collaborative Open Plant Omics (COPO) (2017)): All software code developed is open source and can be found within the COPO Github repository: https://github.com/collaborative-open-plant-omics/COPO
Start Year 2018
 
Description Kromek 
Organisation Kromek Group plc
Country United Kingdom 
Sector Private 
PI Contribution Kromek approached us about applying for DARPA funding for a project to sequence airborne DNA for threat monitoring (see separate grant). We supplied expertise in sequencing, bioinformatics and molecular biology and helped to write a grant proposal.
Collaborator Contribution Kromek have engineering expertise and have previously delivered a DARPA radiation detector contract.
Impact Successful application of funding to DARPA. Continued discussions on future work.
Start Year 2018
 
Description The 200 mammals project: sequencing genomes by a novel cost-effective method, yielding a high resolution annotation of the human genome. 
Organisation Broad Institute
Country United States 
Sector Charity/Non Profit 
PI Contribution Part of the consortium which is analysing the data.
Collaborator Contribution Proposal submitted to NHGRI and funded
Impact In combination with the ~50 already existing high quality placental mammalian assemblies, the project produced the sequence of one placental mammal per family for a total of 150 species. The new assembly method: DISCOVAR de novo, was used to allow the production of a good quality novel genome assembly using only a single sequencing library type.
Start Year 2016
 
Description University of Los Andes, Universy del Rosario and Earlham Institute (RAEng partnership) 
Organisation Del Rosario University
Country Colombia 
Sector Academic/University 
PI Contribution This is a consortium to promote capacity building in data science in Colombia. Funding was awarded by the Newton Fund - Royal Academy of Eng.
Collaborator Contribution This is a consortium to promote capacity building in data science in Colombia. Funding was awarded by the Newton Fund - Royal Academy of Eng.
Impact two training workshops held at Uniandes campus in 2019 one Data Science summer school in 2020
Start Year 2020
 
Description University of Los Andes, Universy del Rosario and Earlham Institute (RAEng partnership) 
Organisation University of the Andes
Country Colombia 
Sector Academic/University 
PI Contribution This is a consortium to promote capacity building in data science in Colombia. Funding was awarded by the Newton Fund - Royal Academy of Eng.
Collaborator Contribution This is a consortium to promote capacity building in data science in Colombia. Funding was awarded by the Newton Fund - Royal Academy of Eng.
Impact two training workshops held at Uniandes campus in 2019 one Data Science summer school in 2020
Start Year 2020
 
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
 
Title Air-seq IP 
Description Methods for DNA extraction, sequencing and analysis of aerosol samples. 
IP Reference  
Protection Protection not required
Year Protection Granted 2018
Licensed Yes
Impact As part of the DARPA funding (see funding), we are licensing our Air-seq technology to Kromek to build devices for biological threat monitoring.
 
Title Data Processing of images of a crop 
Description A method of processing images of a crop, particularly a cereal crop, is described. The method comprises retrieving a series of images of a crop captured over a period of time, selecting from the series of images one to serve as a reference and identifying in said image a reference system against which other images can be compared, the reference system including an extent of a crop plot and/or one or more reference points, such as height markers which may be a ranging pole. For each of at least one other image in the series of images, calibrating the image using the reference system, and determining a height of a canopy of the crop in the image, a main orientation of the crop and/or a value indicative of vegetative greenness. A quality measure may be made of the images in the sequence, possibly involving brightness, size of image file, sharpness or the proportion of dark areas in the image, to determine if an image is to be included in the images to be processed. The image capture device may be a camera and the images may be transferred to a processing unit via a wireless network with only images meeting the quality requirement being transferred. 
IP Reference GB2553631 
Protection Patent granted
Year Protection Granted 2018
Licensed Yes
Impact It was formally licensed to Nanjing Agricultural University in China, including for commercial use in South East Asia. It was licensed for commercial use in South East Asia, but we don't have any further reports on additional impacts. Filed applications for European and Chinese patents in December 2019. https://worldwide.espacenet.com/publicationDetails/biblio?DB=EPODOC&II=0&ND=3&adjacent=true&FT=D&date=20180314&CC=GB&NR=2553631A&KC=A
 
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 Alvis 
Description Tool to produce a range of production quality alignment diagrams based on the output of common aligner tools. Will also spot chimeric contigs/reads. 
Type Of Technology Software 
Year Produced 2019 
Open Source License? Yes  
Impact An earlier version was used to create diagrams for the RenSeq paper. The tool is currently being used for analysis of genome assembly quality within EI. A paper on the tool will be submitted during 2019. 
 
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 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 Legopore 
Description Software to control the Lego DNA sequencer model built for public engagement. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact Hundreds of members of the public, adults and children, have used the software at one of our engagement events. 
 
Title MISO: An open-source LIMS for NGS sequencing centres 
Description MISO (Managing Information for Sequencing Operations) is an open-source Lab Information Management System (LIMS) started at the Earlham Institute, specifically designed for tracking next-generation sequencing experiments. Sequencing centres differ not only in terms of their scale and output, but also their requirements for information management. Sequencing platforms are becoming more accessible, and the efficient storage of genomic metadata is vital for large and small sequencing centres alike. Off-the-shelf solutions are often very expensive and not cost-effective for the smaller centre. Furthermore, support contracts are often required, and the extensibility of these systems is not in the hands of the metadata generators. In terms of implementation, as well as the desire to tailor an information system in-house, data formats can change and platforms can evolve rapidly. These are valid concerns for both large centres characterised by high-throughout data production and smaller scale laboratories with constrained expenditure for IT solutions, and potentially project specific metadata requirements. Hence, we are developing MISO, an open-source LIMS for recording sequencing metadata. We are using freely available tools that are industry standard, well documented, and easy to set up on minimal hardware. As a bare system, MISO can store relevant metadata based on a wide array of NGS sequencing platforms (e.g. Illumina GA, HiSeq and MiSeq, Roche 454, ABI SOLiD and PacBio RS) and public repository data submission schemas (e.g. the Sequence Read Archive at the EBI), and has many features common to bespoke and proprietary LIMS, such as secure authentication, fine-grained access control, barcode tracking, and reporting. 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact A number of new MISO releases have been made available this year, the latest being 0.2.109. The project has seen over 140 releases in its 7 year existence, and the project is 100% open source, allowing sequencing centres to have the option of a completely free solution for managing their instruments and sample tracking. 
URL https://github.com/TGAC/miso-lims/releases/tag/v0.2.109
 
Title NanoOK RT software tool 
Description A real-time analysis tool for metagenomic classification and identification of antimicrobial resistances form nanopore sequence data. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact The software was developed for and initially used in our work with pre-term babies suffering from Necrotizing Enterocolitis. We are now working to apply it to a wide range of other application areas and have had discussions with a number of interested parties at national and international institutes. 
 
Title SDG 
Description SDG is a framework to analyse sequence graphs such as those generated by various genome assemblers. It provides a workspace that can contains a graph and datastores for paired, linked and long reads. These reads can be mapped to the graph, and can be used to untangle or scaffold the graph. A SWIG API enables SDG to be used as a Python module, and there is experimental Julia and R support. 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact We are currently producing genome assemblies of: multiple wheat cultivars, multiple strawberry cultivars, and more. 
URL https://f1000research.com/articles/8-1490
 
Title SKM-tools 
Description These are a series of tools to compare skip-mers (cyclic spaced-seeds) spectra between different datasets. It can be used to study conservation of sequence across evelotuonary distant organisms. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact We are using skm-tools to study conservation in the context of EI's CSP and BBSRC's DFW projects. 
URL https://github.com/bioinfologics/skm-tools
 
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 aequatus.js 
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. 
Type Of Technology Webtool/Application 
Year Produced 2017 
Open Source License? Yes  
Impact This development of Aequatus.js allows its implementation to any web based tools without relying on full Aequatus software. One of example is implementation within Galaxy Server at EI. 
URL https://github.com/TGAC/aequatus.js
 
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 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 w2rap 
Description w2rap is a genome assembly pipeline for complex genomes from short reads. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact W2rap has enabled wheat genomics to jump into a new era of high-quality genomes from short reads. While there are some alternative tools from private companies, w2rap remains the standard for quality reconstruction across the genome. W2rap has already been used to assemble 5 wheat genomes in the public domain, putting the UK at the forefront of wheat genomics. With tens of genomes being assembled now, new modules veing developed for new data types, and 5 wheat lines assembled in a £1M private project, w2rap is one of the flagship projects for Earlham Institute. 
URL https://github.com/bioinfologics/w2rap/
 
Description Evolutionary History and Domestication of the Ferret (Mustela putorius furo). Genome Science 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The domestic ferret (Mustela putorius furo) models biological processes that are highly relevant to human disease and health research such as influenza, cystic fibrosis and asthma. The recently completed draft of the ferret genome and associated annotation project (Peng et al 2014) allows us to extend research and examine the domestication of the ferret. Most domestic animals were domesticated ~10,000 years ago, but the history of the ferret's domestication is uncertain. It is likely that ferrets have been domesticated for at least 2,000 years, a similar time to the domestication of the rabbit, of which the ferret was domesticated to hunt. We have sequenced the genomes of a further eight domestic ferrets along with 12 European Polecats (M. putorius), 2 Steppe Polecats (M. eversmanii) and 4 Black-footed Ferrets (M. nigripes). In order to examine the genetics underpinning ferret domestication and compare the genomes of domestic and wild ancestor, we first need to identify the ancestral species of the domestic ferret, the identification of which is not fully resolved.
Year(s) Of Engagement Activity 2016
 
Description 10 years of impact: Keeping living things healthy - 23/05/2019 
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 Website article highlighting the impact of our research so far including working delivered through the CSP from a report commissioned by EI (Brookdale Consulting).
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/10-years-impact-keeping-living-things-healthy
 
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 Activity - DNA sequencer at Great Hockham Primary School 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Activity at the Great Hockham Primary School
Year(s) Of Engagement Activity 2019
 
Description Activity - Pink Pigeon Trail at the Norfolk Show 
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 Activity Pink Pigeon Trail at the Norfolk Show
Year(s) Of Engagement Activity 2019
 
Description Activity - Where have you BEEn? 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Activity at the Norwich Science Festival
Year(s) Of Engagement Activity 2019
 
Description Agritech East Week 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact In order to stimulate a dialogue and discussion between scientists, farmers, breeders and more, we organised an interactive, show-and-tell style workshop for members of AgriTech East, who came to EI for three hours on a Tuesday evening.

The event showcased the latest advances in genome sequencing and bioinformatics, while then allowing groups to explore themes relevant to modern agriculture and research together.
Year(s) Of Engagement Activity 2018
 
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 BAMBI Diagnosing infections earlier in preterm babies with real time genomic analysis - 16/12/2019 
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 Website article highlighting a new method for profiling the microbiome of preterm babies that can significantly speed-up the identification of infections and indicate more effective treatments developed in collaboration with Quadram Bioscience and NNUH. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. This story generated 293K estimated coverage reads and 298K social shares.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/newsroom/diagnosing-infections-earlier-preterm-babies-real-time-genomic-an...
 
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 Cataloging genetic diversity in the Black-footed Ferret Black-footed Ferret Genetics Symposium, Fort Collins, Colorado, USA. 19-20 Jan 15. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation of EI's work on Black-footed Ferret.
Year(s) Of Engagement Activity 2015
 
Description Cheap and robust genomes using the PDABS pipeline Advances in Genome Biology and Technology 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Advances in next-generation sequencing (NGS) technologies and the subsequent reduction in cost have enabled the research community to sequence the genomes of many non-model organisms. Genome assemblies using next generation technologies such as Illumina show high quality nucleotide level information, but are fragmented due to the inability to retain contiguity. The absence of low-cost methods for creating high quality genome sequences from a wide range of organisms currently hampers the generation of de novo genomes for comparative genomic studies, and new methodologies and data types need to be tested to achieve this goal. We have integrated NGS with nano-channel genome mapping and developed the PCR-free Discovar Assembly BioNano Scaffolding (PDABS) pipeline to assemble cheap, contiguous and robust genomes.
Year(s) Of Engagement Activity 2016
 
Description Conference talk: Tackling microbial diseases using MinION diagnostics and NanoOK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited plenary speaker at the Bern Nanopore Technology Day.
Year(s) Of Engagement Activity 2017
 
Description Cyberinfrastructure and the Carpentries - Workshop in Bogota, Colombia 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact We delivered a Carpentries instructor training in Bogota, Colombia, as part of the GROW Colombia project.
Year(s) Of Engagement Activity 2018
URL https://froggleston.github.io/2019-10-22-ttt-colombia/
 
Description Decision support systems for sustainable farming - breaking down the barriers to behaviour change - 23/07/2019 
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 The aims of the workshop were threefold:
• Establish the state of play with respect to the use of data to support decision-making on farms
• Explore the barriers to more/better use of data/information/insight on farms
• Identify the scope for a pilot project involving key organisations from the Eastern Region, to gain a better understanding of on-farm decision-making and actual (as opposed to claimed or reported) behaviour with respect to the use of key inputs and their impact on performance
A total of 19 people attended the workshop (see appendix for details), with four representatives from three of the largest agricultural businesses in Norfolk, two regional agri-business consultants, one global agri-chemical manufacturer, one global farm machinery manufacturer and a regional farm machinery distributor, the Agricultural and Horticultural Development Board (AHDB), two companies working in the area of data warehousing, aggregation and visualisation, two computer scientists and a business development manager from the Earlham Institute, three senior academics (two from the School of Environment and one from Norwich Business School) and a relationship manager from the UEA.
The entire workshop was run in plenary, over three hours, split into three parts. The first re-visited the context (as summarised above), the second covered the current state of data use on farms, and the third explored the need for further research into on the efficacy of data use on farms to support decision-making and improve performance.
Year(s) Of Engagement Activity 2019
 
Description Dialogo industria-academia (Industry-academia dialogue) Bogota 2019 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact "Dialogo Industria-academia (Industry-academia dialogue)" was a workshop to promote partnerships between industry, University and Government, using the "triple helix model", in the areas of big data and bio-economy in Colombia. The event was held at Universidad de Los Andes campus and facilitated by trained facilitators from the Earlham Institute. The event included 16 participants from industry and Governmental institutions and 16 participants from Universities. During two days, they analysed the challenges and opportunities for the "big data" sector in Colombia and the tentative role of this sector in the socio-economic growth of Colombia. The 32 participants were selected from 123 applicants. The event included opportunities for "speed networking" between industry and Universities, and group activities to discuss the priorities for the data-driven innovation and economic growth.

"Dialogo Industria-academia (Industry-academia dialogue)". The workshop included two plenary speakers from the "Mision de Sabios", which is a panel of experts reporting to the President of Colombia about Science and Innovation policy. This event allowed us, participants and facilitators to engage with policymakers. The main objective of this event aligns with our aim to build partnerships between industry and academia.
Year(s) Of Engagement Activity 2019
 
Description Dialogue: food and health, what matters to you? - 24/10/2019 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Dialogue: food and health, what matters to you? was a new event at the Norwich Science Festival supported by Professor Neil Hall and Dr Nicola Patron. The event was an invitation to the public to join Norwich Research Park scientists and work together with them to solve the problems that you see, and inspire the science of the future.
Year(s) Of Engagement Activity 2019
URL https://docs.google.com/document/d/13yGwFkzh-9YDVUYMBzkhm7i_E4NnytZt74LBFrmjhNU/edit?usp=sharing
 
Description Down The Tubes! Talk at the Norwich Science Festival 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Dr Davey gave a talk on the internet and data science entitled "Down The Tubes!" at the 2018 Norwich Science Festival.
Year(s) Of Engagement Activity 2018
URL https://norwichsciencefestival.co.uk/events/down-the-tubes/
 
Description EI Innovate - 09/01/2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Website article highlighting the importance of knowledge exchange, reflecting on the success of the first EI Innovate KEC focussed event which including showcasing the CSP.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/articles/ei-innovate-why-knowledge-exchange-important
 
Description EI Innovate event - 13/11/2019 
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 The inaugural EI innovate event showcased EIs capabilities and expertise in genomics, bioinformatics, synthetic biology, crop phenotyping, and high-performance computing including the CSP. This event aimed to help industry, academics, charity and voluntary organisations fully understand the opportunities for collaboration with EI, and how engaging with EI science and services can be of benefit. EI Innovate: genomics data to advance bioscience, held on 13th November 2019, was a success. It was attended by 82 people, 26 EI staff who delivered talks, tours and discussion sessions, prepared posters and came to network, 31 representatives from industry (across agri-food, biotech and life sciences sectors), 2 BBSRC staff, 2 representatives from Food Standards Agency, representatives from KTN, NALEP, National Biofilms Centre and Centre for Process Innovation, and 14 representatives from (9 from UEA) academic institutions. We attracted 3 high profile external speakers from: Natural History Museum (Director of Research); Royal Botanic Gardens Kew (Director of Science); and Oxford Nanopore Technologies (Vice President for Applications). We delivered 5 talks, prepared 11 posters, led 2 tours of Genomics Pipelines and Bio-Foundry to showcase EI expertise and capabilities. The afternoon programme had 3 breakout sessions, aiming to explore opportunities for collaborative projects: 1. New Frontiers in Next-Generation Sequencing 2. Data Mining of the UK Tree of Life to Understand and Utilise Biodiversity of British Species 3. A guided discussion about the value of data for driving research, innovation and commercialisation This was EI's first externally-facing KEC event, bringing together various stakeholders to learn about EI expertise and how it can add value to their projects. We received a lot of informal positive feedback and following upon the interactions that this event enabled. A date has already been secured for November 2020.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/innovate2019-0
 
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 Earlham Institute at the Royal Norfolk Show 
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 Using our work in robotics and artificial intelligence as a launch pad, we were able to engage with a large swathe of the general public in the Innovation Zone at the Royal Norfolk Show.

The aim: to promote awareness of the important work that Earlham Institute does across all of its CSPs and NCs, particularly emphasising our computational, data-driven approach.

The outcome: hundreds of members of the public, as well as certain interested stakeholders, engaged in the work that we do. The setting was perfect to have a dialogue with particular groups of interest, including breeders and farmers, while opening the discussion about the role of genomics research and associated projects in influencing and advancing UK agriculture now and in the future.
Year(s) Of Engagement Activity 2018
 
Description Earlham Institute takes part in ambitious 'Tree of Knowledge' to map the genomes of all life in UK - 08/11/2019 
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 Website article highlighting that Earlham Institute (EI) has been awarded over 700k from the Wellcome Trust for the Darwin Tree of Life Project, aiming to produce a complete genomic UK biota as part of the wider Earth Biogenome Project (EBP). The remarkable study will understand all living species to preserve our planet's rich biodiversity and discover new biomaterials for pharmaceuticals. Some knowledge and expertise to deliver project based on the CSP-led advances. This story generated an estimated coverage views of 1.74M and 1.28K social shares.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/newsroom/earlham-institute-tree-knowledge-genomics-biota
 
Description Emma's Antarctic Diary - 15/04/2019 
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 Website blog article highlighting the work of Emma Langan, a PhD student in EI's Leggett group who has been on a six-week expedition to Antarctica to analyse the effects of climate change on coccolithophores with real-time DNA sequencing algorithms. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media and showcase the work of our staff
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/emma-langan-antarctic-adventure-algae-climate-change
 
Description Event - DNA Detectives 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Activity at the Eden project
Year(s) Of Engagement Activity 2019
 
Description Extreme environments: genome sequencing & space 
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 EI website article on our fieldwork in Iceland
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/extreme-environments-genome-sequencing-space
 
Description Genetic Diversity of the Mustelidae: Implications for understanding Evolution, Domestication and Conservation. Genome 10K 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The ferret (Mustela putorius furo) models biological processes that are highly relevant to human disease and health research such as influenza, cystic fibrosis (CF) and asthma. Since CF is a multi-organ disorder, research using CF ferrets span a range of organs, thus the impact of research in this model is broad and allows for the analysis of early stages of the diseases.

The recently completed draft of the ferret genome has allowed us to look more closely into ferret domestication and examine the underpinning processes of domestication from the ancestral European Polecat (M. putorius). We have sequenced eight domestic ferrets genomes and will sequence samples from European Polecat. Beneficial genetic variants increase in frequency due to positive selection together with linked neutral variants resulting in genomic islands of reduced heterozygosity between populations. By examining fixation indexes and heterozygosity between wild and domestic ferrets we can find genomic regions that have undergone selective sweeps.

Using whole genome sequencing also allows us to leverage the ferret genome sequence to look into the genetic diversity and evolution of other species of wild Mustelidae. The current population of the endangered Black-footed Ferret (M. nigripes) from North America stems from only seven individuals. Using whole genome sequencing of Black-footed Ferrets from both before and after the population crash we will identify genetic diversity not present in the current population with a view to reintroducing it via genome editing technology.

About two million years ago, the ancestral species of modern day Steppe Polecats (M. eversmanni) from Asia entered North America via the Bering Land Bridge and speciated into what is now Black-footed Ferret. Using a reference-free unbiased kmer approach, we will examine how closely-related Steppe Polecat is to both Black-footed Ferret and its sister species the European Polecat.
Year(s) Of Engagement Activity 2015
 
Description George Freeman MP, Minister for Transport visit - 20/09/2019 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Policymakers/politicians
Results and Impact In September 2019, George Freeman MP, Transport Minister, visited EI and address NRP staff. EI and CSP researchers lobbied him on our priorities and policy asks and staff were able to question him on the Government's Brexit policy as well as its wider science strategy
Year(s) Of Engagement Activity 2019
URL https://www.georgefreeman.co.uk/content/earlham-institute-visit
 
Description Host-microbe interactions in oral cavity Conference: Unilever Microbiology Symposium Location: Unilever R&D Colworth Science Park, Bedfordshire Date: 4-5 July, 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Industry/Business
Results and Impact Host-microbe interactions in oral cavity Conference: Unilever Microbiology Symposium Location: Unilever R&D Colworth Science Park, Bedfordshire Date: 4-5 July,
Year(s) Of Engagement Activity 2019
 
Description Improving the Koala genome using the PDABS pipeline AGBT 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Advances in next-generation sequencing (NGS) technologies and the subsequent reduction in cost have enabled the research community to sequence the genomes of many non-model organisms. Genome assemblies using next generation technologies such as Illumina show high quality nucleotide level information, but are fragmented due to the inability to retain contiguity. The absence of low-cost methods for creating high quality genome sequences from a wide range of organisms currently hampers the generation of de novo genomes for comparative genomic studies, and new methodologies and data types need to be tested to achieve this goal. We have integrated NGS with nano-channel genome mapping and developed the PCR-free Discovar Assembly BioNano Scaffolding (PDABS) pipeline to assemble cheap, contiguous and robust genomes.
Year(s) Of Engagement Activity 2016
 
Description Inside EI - 21/05/2019 
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 Public/other audiences
Results and Impact Inside EI is an open day when the public are invited to learn more about the work at the Earlham Institute, meet our team and engage with our research and understand its relevance and impact. There were talks and posters based on CSP-led research.
Year(s) Of Engagement Activity 2019
URL https://earlhaminstitute.coveragebook.com/b/0ee62ba7
 
Description Inside EI: Public engagement with impact - 06/08/2019 
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 Website highlighting the Inside EI event for the public to explore our fascinating and diverse range of important scientific research projects including talks and posters on our CSP work and the importance and impact of public engagement in research
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/inside-ei-public-engagement-science-impact
 
Description Integrating omic-based technologies for the valorisation of Peruvian crop biodiversity 
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 three-day workshop aimed to understand the potential application of high-throughput "omics-technologies" for the characterization and valuation of the genetic biodiversity of Peruvian crop in a more holistic and integrated approach.
The workshop convened UK and Peruvian leading researchers and early-career researchers, with the aim of outlining the best strategies to integrate omic approaches in the research of Peruvian crop biodiversity. This contributed to developing resilience in local agriculture under the context of climate change and the current demand for healthier foods and natural compounds.
Developed in collaboration with Universidad Catolica de Santa María, this workshop has been granted by the Newton-Paulet fund under the program "Researcher Links - Workshop Grants - Talleres 2018-01". This grant is the result of an agreement between the British Council and the Consejo Nacional de Ciencia Tecnologia e Innovacion (CONCYTEC) from Peru.
Year(s) Of Engagement Activity 2019
 
Description Invited talk - Real-time sequencing and analysis of microbial communities with nanopores 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Research day on microbe research attended by approx. 200.
Year(s) Of Engagement Activity 2019
URL http://microbesinnorwich.org/
 
Description JRS Biodiversity R workshop, Nairobi 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Dr Davey travelled to Nairobi, Kenya, as part of a JRS Biodiversity funded programme to teach a day R workshop to 23 representatives from the African Conservation Centre, Kenya Wetlands Biodiversity Reseach Centre, National Museums of Kenya, University of Nairobi, and the Jomo Kenyatta University.
Year(s) Of Engagement Activity 2019
 
Description Keynote lecture: Assembling complex crop genomes for comparative analyses 
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 Bioinformatics for Plant Biology - EBI Cambridge, 6-9 November
Year(s) Of Engagement Activity 2018
URL https://www.ebi.ac.uk/training/events/2018/bioinformatics-plant-biology
 
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 Leszek Wysocki (Department for International Trade ) 10/06/2019 - visit to EI 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Policymakers/politicians
Results and Impact Leszek Wysocki (Department for International Trade) visited EI and met with CSP researchers to discuss their work in relation to International Trade
Year(s) Of Engagement Activity 2019
 
Description Lettuce Have It! - 10/06/2019 
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 Website article highlighting real-life applications for artificial intelligence based techniques to improve efficiency and precision on the farm developed at EI and through the CSP. Linked to the paper, titled: Combining computer vision and deep learning to enable ultra-scale aerial phenotyping and precision agriculture: A case study of lettuce production is published in Horticulture Research - Nature. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media, the article has estimated coverage views of 111K
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/newsroom/lettuce-have-it-machine-learning-cr-optimisation
 
Description NanoOK of the North and South 
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 EI website article about our work developing the nanopore analysis software NanoOK
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/nanook-north-south-life-in-antarctic
 
Description Network biology approaches to understanding life - 29/04/2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Website article highlighting the work of a PhD student in the Korcsmaros group on how systems biology approaches can help us to understand the interactions between living systems and how the information we can glean is important for improving human health and better understanding the evolution of host-specificity of bacteria, among many other things. This article also provide insight into carrying out a PhD at EI and working in the field of systems biology and Salmonella research.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/network-biology-approaches-to-understanding-life
 
Description New rapid test diagnoses pneumonia and lower respiratory tract infections - 24/06/2019 
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 Website article highlighting research carried out by Quadram Institute, University of East Anglia (UEA) and Earlham Institute (EI) to develop a new, rapid way of diagnosing bacterial lower respiratory tract infections in hours rather than days that could improve patient care and slow the spread of antimicrobial resistance. The MinION technology was applied using software developed at EI as part of the CSP. Article showcased collaborative work between the research institutes and NHS. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/newsroom/new-rapid-test-diagnoses-pneumonia-and-lower-respiratory-infectio...
 
Description Newsletter - Developing a frugal and medium throughput method for assessing protein-DNA binding affinity 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact News Letter for Open Plant
Year(s) Of Engagement Activity 2019
URL https://www.openplant.org/blog/2019/4/4/developing-a-frugal-and-medium-throughput-method-for-assessi...
 
Description Norwich Research Park Day at the Norwich Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact This, a celebration of science from across the NRP, was a fantastic chance for us to showcase the work across our collective CSPs and NCs.

All in all, we had dozens of staff involved from across the institute who helped us to deliver a set of multiple activities, workshops and talks on the day. Activities included a live LEGO sequencer with BLAST analysis of genomes and a live DNA sequencing experiment. Additionally, there were talks on the Institute and how it applies big data and computational approaches to understanding life on earth, the interactions underpinning ecosystems and communities, as well as how we can better understand evolution to drive trait improvement.

The event was a spectacular success, with desired outcomes being a greater awareness of the important research undertaken by EI, as well as the value of applying computational approaches to tackling a swathe of biological questions. The specific feedback showed that this event had definitely increased understanding among participants, who numbered more than 8000, of the role that EI and its core programmes play at the cutting edge of science.

Social media coverage ensured that the activities we put on reached many thousands more people than just those who attended the event on the day.
Year(s) Of Engagement Activity 2018
URL https://www.youtube.com/watch?v=Uf0h8Q8PVxI
 
Description Norwich Science Festival - 22/10/2019 to 24/10/2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Norwich Science Festival is a wonderful showcase of science from Norwich and beyond for learning and excellent public engagement. This year, EI presented 11 talks and poems covering a fascinating range of science topics, from Salmonella and guts through to sequencing algae in the Antarctic, covering the whole tree of life in the process, bringing an innovative Bee Trail, LEGO sequencer, robots and more. Researchers from the CSP participated, presented their work and engaged with the public. Coverage on TV, radio and media with estimated coverage views of 698K
Year(s) Of Engagement Activity 2019
URL https://earlhaminstitute.coveragebook.com/b/02819684cc7da5de
 
Description Norwich Science Festival - Lego DNA sequencer 
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 We created a working Lego Mindstorms model of a DNA sequencer, along with software to run it. We arranged activities around it during the Norwich Science Festival and engaged lots of adults and children.
Year(s) Of Engagement Activity 2018
URL https://twitter.com/brickopore/status/1055043270999465985
 
Description Norwich Science Festival - The Nedome 
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 During Norwich Science Festival, we ran live demonstrations of nanopore sequencing in which we sequenced the "Ned-ome" (DNA kindly provided by Ned, a PhD student).
Year(s) Of Engagement Activity 2018
URL https://twitter.com/hashtag/nedome?lang=en
 
Description Norwich Science Festival Ops Note 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience 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 http://www.earlham.ac.uk/newsroom/first-ei-lego-sequencer-human-dna-and-endangered-species-earlham-i...
 
Description Norwich Science Park Open Day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Presented poster on work linked to Big Data Bioinformatics
Year(s) Of Engagement Activity 2016
 
Description Oceans Day at 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 Tarang Mehta gave a well-received talk on how he delves into cichlid fish diversity for the Norwich Science Festival.

He had given a similar talk the year before, and this was an update due to its roaring success the first time around.

The talk helped to promote an awareness of the importance of understanding the evolution of interesting groups of organisms such as cichlid fish, and how this can be applied to a number of interesting research projects, from better understanding human disease through to improving aquaculture practice in East Africa.
Year(s) Of Engagement Activity 2018
 
Description Open source data management: Sherlock open for all - 14/06/2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Website article on customisable method of data management for smaller research groups who don't have the resources to develop a modern, big data solution using software developed at EI and made open-source.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/sherlock-open-source-data-management
 
Description Oral Presentation - Characterization of noncoding expression and splicing diversity in the human brain 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Seminar at the Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
Year(s) Of Engagement Activity 2019
 
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 - Non-human genomes, why bother? 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Oral presentation at the EI Open Day
Year(s) Of Engagement Activity 2019
 
Description Oral presentation - Characterization of splicing diversity and gene fusions through Nanopore sequencing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral presentation at the Long Read Sequencing Meeting, SciLifeLab Uppsala, Sweden
Year(s) Of Engagement Activity 2019
 
Description Oral presentation - Characterization of splicing diversity in bulk samples and single cells using long read technologies 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Seminar at the Maurice Wohl Clinical Neuroscience Institute King's College London
Year(s) Of Engagement Activity 2019
 
Description Oral presentation - Enter the Nanoporium 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Oral presentation as part of the Pint of Science
Year(s) Of Engagement Activity 2019
 
Description Oral presentation - How well do you know your family tree? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Oral presentation at the Norwich Science Festival
Year(s) Of Engagement Activity 2019
 
Description Oral presentation - What Can We Learn from a High Koala-ty Genome?' 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Orap presentation as part of the EI Open Days
Year(s) Of Engagement Activity 2019
 
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 PRESS RELEASE: How to escape big data and cancer with data integration and broccoli 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact How to escape big data and cancer with data integration and broccoli
Year(s) Of Engagement Activity 2015
 
Description PRESS RELEASE: NGS expert leads world-class Institute's cutting-edge genome analysis 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact NGS expert leads world-class Institute's cutting-edge genome analysis
Year(s) Of Engagement Activity 2015
 
Description PRESS RELEASE: NanoOK: Quality Control for portable, rapid, low-cost DNA sequencing 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact NanoOK: Quality Control for portable, rapid, low-cost DNA sequencing
Year(s) Of Engagement Activity 2015
 
Description PRESS RELEASE: New big data pushes bioinformatics training in life sciences 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact New big data pushes bioinformatics training in life sciences
Year(s) Of Engagement Activity 2015
 
Description PRESS RELEASE: Novel online bioinformatics tool significantly reduces time of multiple genome analysis 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Novel online bioinformatics tool significantly reduces time of multiple genome analysis
Year(s) Of Engagement Activity 2015
 
Description PRESS RELEASE: TGAC's take on the first portable DNA sequencing 'laboratory' 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact TGAC's take on the first portable DNA sequencing 'laboratory'
Year(s) Of Engagement Activity 2015
 
Description Pint of Science 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Will Nash gave a well-received talk about his work understanding the koala genome, and what we can learn from understanding it - particularly how koalas can somehow withstand a toxic diet of eucalyptus.

Pint of Science is a great occasion to share information with the public in an informal setting, which stimulates and encourages debate and discussion, therefore the opportunity for a dialogue - which is a valuable outcome for any public engagement event.
Year(s) Of Engagement Activity 2018
 
Description Poster Presentation - 200 Genomes EI Open Days 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Poster Presentation EI Open Days
Year(s) Of Engagement Activity 2019
 
Description Poster Presentation - Analysing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Presentation in front of the Earlham Institute Scientific Advisory Board
Year(s) Of Engagement Activity 2018
 
Description Poster Presentation - Brain Isoforms EI Open Days 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Poster Presentation as part of EI Open Days
Year(s) Of Engagement Activity 2019
 
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 - Evolution of gene regulatory networks controlling traits under natural selection 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 Poster presentation at the volutionary Systems Biology Conference, Wellcome Trust Sanger Centre. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2018
 
Description Poster presentation - Characterising and visualising gene families with GeneSeqToFamily and Aequatus 
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 at the Genome Informatics 2018, Cambridge, UK . The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2018
 
Description Poster presentation - Examining genetic diversity and traits under selection in several aquaculture-relevant tilapia species 
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 Poster presentation at the Genome Science Conference, Nottingham, UK . The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2018
 
Description Poster presentation - Gene regulatory network evolution in East African lake 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 Poster presentation at the Evolution 2018 conference, Montpellier. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2018
 
Description Poster presentation - Identifying signalling pathways regulating antimicrobial peptide production in the gut using network biology and organoid transcriptomics 
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 Modularity of signaling proteins and networks conference Seefeld, Austria. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2018
 
Description Poster presentation - Networks to catch the difference: Construction and analysis of Regulatory Networks applied to East African Lake Cichlids 
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 Evolutionary Systems Biology conference, Wellcome Trust Sanger Centre. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2018
 
Description Poster presentation - The evolution of mammalian microRNAs 
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 Biology of Genomes, Cold Spring Harbor Laboratory. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 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 Poster presentation at the Galaxy Community Conference (GCC2019) - Freiburg, Germany
Year(s) Of Engagement Activity 2019
 
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 - Eukaryotic metagenomics: Identification and quantification of bee collected pollen 
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 London Calling conference, May 2018
Year(s) Of Engagement Activity 2018
 
Description Poster presentation - Gene regulatory network evolution in East African lake cichlids 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Poster presentation as part of the PopGroup 52, Oxford. The audience included group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2019
 
Description Poster presentation - Investigating regulation of intestinal function by Bifidobacteria using network biology and organoid approaches 
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 Poster presentation at the Microbes in Norwich workshop. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2019
 
Description Poster presentation - Nanopore sequencing reveals the transcriptional complexity of neuropsychiatric disease genes in human brain 
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 Biology of Genomes, Cold Spring Harbor Laboratory. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2018
 
Description Poster presentation - Real-time surveillance and diagnostics with NanoOK RT 
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 London Calling conference, May 2018
Year(s) Of Engagement Activity 2018
 
Description Poster presentation - The long and the short of eukaryotic metagenomics: Identification and quantification of plant species in bee pollen 
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 Advances in Genome Biology and Technology (AGBT) conference in Marco Island, Florida.
Year(s) Of Engagement Activity 2019
URL https://www.agbt.org
 
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 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 Presentation - Evolution of regulatory networks controlling adaptive traits in cichlids Network Biology CSHL, NY, USA Mar 19-23 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at the Network Biology meeting Cold Spring Harbor Laboratory. The audience included group leaders, university lecturers, postdoctoral researchers, graduate students and industry representatives.
Year(s) Of Engagement Activity 2019
 
Description Presentation - GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at the 2018 Galaxy Community Conference (GCC2018), Portland, OR, USA, 25-30/06/2018. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students and industry representatives
Year(s) Of Engagement Activity 2018
 
Description Presentation - The role of structural variants in the adaptive radiation of African Cichlids 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentatio at the Genome Informatics 2018 Conference, Hinxton, Cambridge. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2018
 
Description Presentation - Aequatus: An open-source homology browser 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited presentation at the 13th International Conference on Genomics (ICG13) Shenzhen, China. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students and industrial representatives.
Year(s) Of Engagement Activity 2018
 
Description Presentation - Characterization of noncoding expression and splicing diversity in the human brain 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Invited seminar at the Institute of Ophthalmology, University College London. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2019
 
Description Presentation - Characterization of splicing diversity and gene fusions through Nanopore sequencing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Selected presentation at AGBT2019, Marco Island Florida. The audience consisted of group leaders, postdoctoral researchers, graduate students, industry representatives.
Year(s) Of Engagement Activity 2019
 
Description Presentation - Genomics applications for conservation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Presentation as part of a training course for the use of genomic resources for species identification delivered to law enforcement officers in Cali, Colombia. The audience included university lecturers, graduate and undergraduate students, conservation organizations, law officers, representatives of the ministry of environment, ministry of justice,
Year(s) Of Engagement Activity 2018
 
Description Presentation - Lego sequencer at the Women of the Fututre event 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Activity at the Women of the Fututre event
Year(s) Of Engagement Activity 2019
 
Description Presentation - RCUK GROW Colombia Natural Diversity 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Presentation as part of FIMA 2018 in Bogota, Colombia. The audience included general public, conservation organization, schools, law officers
Year(s) Of Engagement Activity 2018
 
Description Presentation - What can we learn form a high Koala-ty genome? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Presentation as part of the Norwich Science Festival. The audience included general public and schools
Year(s) Of Engagement Activity 2018
 
Description Presentation - Working with sequences 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Lecture delivered to BBSRC DTP graduate students as part of the Computational & Systems Biology DTP course
Year(s) Of Engagement Activity 2019
 
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 Real time sequencing solutions: taking the lab to the sample and beyond 
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 Article on the EI website about our work with real-time nanopore sequencing
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/real-time-sequencing-solutions-taking-lab-sample-and-beyond
 
Description Science Camp 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Graham Etherington put on a a workshop on how to use bioinformatics tools, namely Galaxy, in the life sciences.

This is a very valuable introduction to the work undertaken at EI, and a chance to show the next generation of budding scientists the important role of computational-driven approaches to understanding life, evolution, and how we can improve crops through better understanding genetic diversity and variation.
Year(s) Of Engagement Activity 2018
 
Description Sherlock: elementary genomics 18/03/2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Website article highlighting the Sherlock platform developed at EI to store and analyse bioinformatics data using modern big data technologies. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/sherlock-elementary-genomics
 
Description Sixth Form Summer studentships 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact We hosted four biology students wishing to study medicine but who wanted to gain experience in working in a scientific background. The students where here for 2 weeks and carried out both taught and independent study.
Year(s) Of Engagement Activity 2017
 
Description Talk - Developing a Streamlined Field Protocol for In Situ Sequencing and Analysis of Extremophiles 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at American Geophysical Union Fall Meeting, Washington DC, 10-14 December 2018
Year(s) Of Engagement Activity 2018
 
Description Talk and poster presentation - Taking the lab to the sample: enabling new ways of working with nanopore sequencing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster and flash talk at the Advances in Genome Biology and Technology (AGBT) conference in Marco Island, Florida.
Year(s) Of Engagement Activity 2019
URL https://www.agbt.org
 
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 Teaching Data Science with The Carpentries (Bogota 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 "Teaching Data Science" was a train the training course aiming a data science trainers in Colombia. The course was held in the University of Los Andes in downtown Bogota, Colombia on 22nd and 23th October. The course was tough by two experts on data science and teaching from Earlham Institute. The training was free- to attend thanks to a grant from the Royal Academy of Engineering. Internal flights and accommodation in the University's student residence were provided to the attendants from outside Bogota DC on standard Grant conditions in order to foster equality and the development in peripheral regions of Colombia.
The training was attended by 22 permanent staff from 8 different Universities and four research institutions. Staff included Professors to support staff. The final 22 attendants were selected from approx. Eighty applicants based on the potential to use the training in the future to develop data science training events in their own institutions. This event directly contributed to objectives 1 and 2. Particularly, this two-day class fulfilled the following: (1) introducing the participants to evidence-based best-practices of teaching, (2) teach the participants how to create a positive environment for learners at data workshops, (3) provide opportunities for the participants to practice and build their teaching skills in roleplaying exercises, (4) helping them become integrated into the global data science community that uses the open access "Carpentries" syllabus to teach.
Year(s) Of Engagement Activity 2019
 
Description Technology Day at the 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 We reached over 8000 members of the public with an interactive workshop demonstrating the potential of computational biology and data-driven approaches to understanding life.

Through Rob Davey, we explored memes and ownership of data, where the public had the chance to directly interact with one of our group leaders.

We also demonstrated a live sequencing experiment, showcasing our work on software development for the MinION, which was hugely popular and drew significant crowds alongside our unique LEGO sequencer. Children and parents alike were able to explore the themes around computational biology and to have a dialogue with the researchers involved.

The purpose of public engagement is always to attempt to foster a dialogue, which first comes with increasing awareness and understanding of complex concepts and cutting edge techniques. Our specific feedback obtained suggested that, over the course of the science festival, participants came away with a better understanding of the work that we do in important areas relevant to every day life.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/celebration-science-norwich
 
Description The Earlham Institute LEGO sequencer 
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 Article on EI website about our engagement project in which we built a LEGO DNA sequencer
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/earlham-institute-lego-sequencer
 
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 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at the 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark . The audience included group leaders, university lecturers, postdoctoral researchers, graduate students, industry representatives
Year(s) Of Engagement Activity 2019
 
Description Training - Kmer Analysis (UC Davis) 
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 2 day course on using kmer analysis in denovo assembly. Delivered by Gonzalo Garcia Accinelli
Year(s) Of Engagement Activity 2018
 
Description Training - Single-Cell RNAseq Training Course 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Training delivered as part of the Single-Cell RNAseq Training Course at EI. The audience included postdoctoral researchers and graduate students
Year(s) Of Engagement Activity 2018
 
Description UKRI Darwin Tree of Life Project meeting, London 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Dr Davey travelled to London with other EI staff to discuss strategy for an SPF bid to UKRI for the UK Darwin Tree of Life Project.
Year(s) Of Engagement Activity 2018
 
Description Visit for potential collaboration - Richard Leggett 01/08/2019 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Visit to observe and receive training in nanopore technologies
Year(s) Of Engagement Activity 2017,2019
 
Description WEB ARTICLE: Building bridges for big data research 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Building bridges for big data research
Year(s) Of Engagement Activity 2015
 
Description WEB ARTICLE: Computing the path to success between TGAC and UEA 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Computing the path to success between TGAC and UEA
Year(s) Of Engagement Activity 2015
 
Description WEB ARTICLE: European bioinformatics consortium workshop opens science 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact European bioinformatics consortium workshop opens science
Year(s) Of Engagement Activity 2015
 
Description WEB ARTICLE: Open galaxy of biomedical research 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Open galaxy of biomedical research
Year(s) Of Engagement Activity 2015
 
Description WEB ARTICLE: Starting from scratch with de novo training 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Starting from scratch with de novo training
Year(s) Of Engagement Activity 2015
 
Description WEB ARTICLE: The power of Python for Life Scientists 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact The power of Python for Life Scientists
Year(s) Of Engagement Activity 2015
 
Description We're ten years old, leading the field in decoding complex, non-human genomes - 21/09/2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Website article highlighting contributions of EI, including work delivered through the CSP in decoding complex, non-human genomes. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/articles/ten-years-leading-decoding-complex-genomes
 
Description Web Article - BioJulia helping biologists surmount the "two language problem"' 
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 BioJulia is a community of biologists using a modern programming language to make programming more accessible to biologists, while providing a much more efficient platform for performing computer-driven research. This informative article focused on an interview with Dr. Ben Ward, visiting scientist at Earlham Institute, about his involvement in BioJulia. -SOCIAL MEDIA- Engagement x63, Impressions x107777
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/biojulia-helping-biologists-surmount-two-language-problem
 
Description Web Article - How our tools can help you: MIKADO - 23.05.2018 
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 article promotes Mikado is a novel algorithm that lets you integrate multiple RNA-Seq assemblies into a coherent transcript annotation. The performance of genomics RNA-Seq aligners and assemblers varies greatly across different organisms and experiments and the accuracy of the transcript reconstruction is boosted by combining multiple approaches.

The open-source bioinformatics tool can remove redundancies and select the best transcript models according to user-specific metrics while solving common genetic artefacts. Lead developer Luca Venturini explains how Mikado leverages multiple transcriptome assembly methods for improved gene structure annotation.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/how-our-tools-can-help-you-mikado
 
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 Technology Article - 'The machines are learning, and they're coming for bioscience' 
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 Web article to introduce 'Machine Learning' and how it is being used by EI. -SOCIAL MEDIA- Engagement x124, Impressions x89913
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/the-machines-are-learning-and-theyre-coming-for-bioscience
 
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 - How our tools can help you: BioJulia - 06.08.2018 
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 article focused on BioJulia a new tool in modern programming for computer science and biology; helping bioinformaticians navigate their way out of the infamous tool and file-format black hole.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/how-our-tools-can-help-you-biojulia
 
Description Web article - My week at Earlham Institute: more than just science - 29.08.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact This article promotes the experience of a work experience student to engage with others.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/my-week-earlham-institute-more-than-just-science
 
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 Where are the bees? Tracking down which flowers they pollinate - 07/08/2019 
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 Public/other audiences
Results and Impact Media article highlighting work carried out at EI and as part of CSP to develop a new method to rapidly identify the sources of bee pollen to understand which flowers are important for bees. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media, this story has estimated coverage views of 398K.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/newsroom/where-are-the-bees
 
Description Where bees roam: pollinate this! - 07/08/2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Website article highlighting reverse metagenomics project to track what plants bees have visited via the pollen grains they pick up, using data gleaned from next-, and third-generation genome sequencing technologies and software developed at EI supported through the CSP.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/where-bees-roam-pollinate-this
 
Description brickopore.co.uk 
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 Created a website to provide information on our Lego DNA sequencer, details of events and instructions to build. Designed to promote the institute's engagement and to encourage it elsewhere.
Year(s) Of Engagement Activity 2019
URL http://brickopore.co.uk
 
Description denovo assembly training in Kenya 
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 Denovo assembly training - Kenya - Delivered by Gonzalo Garcia Accinelli
Year(s) Of Engagement Activity 2017
 
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 Oral presentation at the Galaxy Community Conference (GCC2019) - Freiburg, Germany
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