Enabling and Advancing Life Scientists in data-driven research through Advanced Genomics and Computational Training

Lead Research Organisation: Earlham Institute
Department Name: UNLISTED

Abstract

A number of recent studies (BBSRC and MRC review of vulnerable skills (2015) and BBSRC review of Bioinformatics (2013)) and other publications have identified specific skills gaps in early-career scientists that are core strengths of EI. Higher Education curricula stagnation in fast-moving, technological growth areas such as genomics has led to insufficient skills to meet researchers’ demands. This National Capability in Advanced Training (NC4) aims to address this skills gap and is in line with BBSRC’s strategic enabling themes ‘Enhance skills and capacity to explore new tools and approaches’.
Delivered to suit topics and applications, hands-on training courses primarily focus on skill sets required for supporting a defined research goal. Core skills are advanced through workshops that address specific tools and resources, serving local research community needs and disseminating knowledge developed at EI. Delivery of this national capability is bolstered by dedicated training suites and IT servers, allowing delegates secure access to our computing resources to analyse data in real time.

Aimed at those engaged in data-driven research projects across genomics, complex systems, systems and network biology. EI delivers courses enabling individuals to become multidisciplinary scientists. Targeted, rapidly evolving, courses can respond to new technologies, data and paradigms. EI’s programme is demand-led, addressing PhD students and early career Postdocs providing impact on future research. The expertise that drives our own research is reflected in the diversity and advanced content of our training.

EI is one of only a few places in the world that carries out high-throughput research from sample, to data analysis, to publication. The expertise that drives this approach to our own research is reflected in both the diversity and the advanced nature of our training courses. We provide in-depth knowledge from DNA extraction, library preparation and sequencing, to data QC, genome assembly, variant analysis, annotation, through to highly specialised expertise in areas such as population genomics, immuno-genomics, algorithm development, data management and visualisation.

Publications

10 25 50
 
Description We have delivered training courses, workshops, and symposia during the first two years of the award to approximately 730 delegates, plus held the parallel conferences to 350 delegates in summer of 2017 (Genome 10K and Genome Science conferences). Feedback has been collected immediately post-event, and long-term impact is being gathered to assess the overall effect on delegates (improved skills applied to research projects, different approaches to projects, new collaborations etc.).

The institute has engaged formally with the Nuffield Research Foundation to offer Nuffield Research Placements to students alongside our work experience visiting students, Year in Industry and other internship opportunities.
Exploitation Route Feedback is used to help develop training courses further to address the needs of delegates. This has helped with annual re-development of existing courses, such as de novo assembly, which integrates the newest findings and pipelines from Earlham Institute faculty into course material, and for development of new courses such as Single Cell RNAseq.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment,Healthcare,Other

 
Description submission to UKRI infrastructure review
Geographic Reach National 
Policy Influence Type Participation in a national consultation
URL https://www.ukri.org/files/infrastructure/progress-report-summary-document-final-march-2019-pdf/
 
Description BBSRC Flexible Talent Mobility Account - Earlham Institute UKRI Innovation Fellowships
Amount £90,000 (GBP)
Funding ID BB/R50659X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2017 
End 03/2019
 
Description BTT EAGER - Breakthrough Technologies to Advance Crop Breeding
Amount £400,000 (GBP)
Funding ID BB/S020853/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2019 
End 02/2021
 
Description Brazilian PhD Sandwich Programs Abroad - PDSE/CAPES
Amount £9,000 (GBP)
Organisation Government of Brazil 
Department Coordination of Higher Education Personnel Training (CAPES)
Sector Public
Country Brazil
Start 03/2017 
End 08/2017
 
Description Development of single-cell sequencing technology for microbial populations
Amount £149,610 (GBP)
Funding ID BB/R022526/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2018 
End 06/2019
 
Description NRP Seed fund
Amount £16,000 (GBP)
Organisation Norwich Research Park 
Sector Private
Country United Kingdom
Start 01/2018 
End 01/2019
 
Description Single-cell cancer evolution in the clinic - zero rating
Amount £2,024,295 (GBP)
Funding ID C309/A26815 
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2018 
End 10/2023
 
Title Genotyping of 150 CIMMYT wheat lines (paper DOI 
Description 35K affymetrix array data for the High Biomass Association Panel of 150 spring wheat lines from CIMMYT. A paper explaining the panel and the use we made of these snps is available here: http://dx.doi.org/10.1111/pbi.13052 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Facilitated the identification of multiple marker trait associations which have now been incorporated into CIMMYT spring wheat marker assisted selection program. 
 
Description GROW Colombia partnerships 
Organisation Aberystwyth University
Department Institute of Biological, Environmental and Rural Sciences (IBERS)
Country United Kingdom 
Sector Academic/University 
PI Contribution The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity
Collaborator Contribution The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products
Impact Further funding: RCUK-GROW programme BB/P028098/1; Multidisciplinary programme involving biological sciences, agricultural sciences, economics, social sciences, political science
Start Year 2017
 
Description GROW Colombia partnerships 
Organisation Administrative Department of Science, Technology and Innovation (Colciencias)
Country Colombia 
Sector Public 
PI Contribution The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity
Collaborator Contribution The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products
Impact Further funding: RCUK-GROW programme BB/P028098/1; Multidisciplinary programme involving biological sciences, agricultural sciences, economics, social sciences, political science
Start Year 2017
 
Description GROW Colombia partnerships 
Organisation Alexander von Humboldt Biological Resources Research Institute
PI Contribution The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity
Collaborator Contribution The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products
Impact Further funding: RCUK-GROW programme BB/P028098/1; Multidisciplinary programme involving biological sciences, agricultural sciences, economics, social sciences, political science
Start Year 2017
 
Description GROW Colombia partnerships 
Organisation CGIAR
Department International Center for Tropical Agriculture
Country Colombia 
Sector Charity/Non Profit 
PI Contribution The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity
Collaborator Contribution The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products
Impact Further funding: RCUK-GROW programme BB/P028098/1; Multidisciplinary programme involving biological sciences, agricultural sciences, economics, social sciences, political science
Start Year 2017
 
Description GROW Colombia partnerships 
Organisation Colombian Agricultural Research Corporation
PI Contribution The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity
Collaborator Contribution The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products
Impact Further funding: RCUK-GROW programme BB/P028098/1; Multidisciplinary programme involving biological sciences, agricultural sciences, economics, social sciences, political science
Start Year 2017
 
Description GROW Colombia partnerships 
Organisation Colombian Sugarcane Research Center
PI Contribution The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity
Collaborator Contribution The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products
Impact Further funding: RCUK-GROW programme BB/P028098/1; Multidisciplinary programme involving biological sciences, agricultural sciences, economics, social sciences, political science
Start Year 2017
 
Description GROW Colombia partnerships 
Organisation CorpoGen
Country Colombia 
Sector Private 
PI Contribution The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity
Collaborator Contribution The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products
Impact Further funding: RCUK-GROW programme BB/P028098/1; Multidisciplinary programme involving biological sciences, agricultural sciences, economics, social sciences, political science
Start Year 2017
 
Description GROW Colombia partnerships 
Organisation EAFIT University
Country Colombia 
Sector Academic/University 
PI Contribution The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity
Collaborator Contribution The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products
Impact Further funding: RCUK-GROW programme BB/P028098/1; Multidisciplinary programme involving biological sciences, agricultural sciences, economics, social sciences, political science
Start Year 2017
 
Description GROW Colombia partnerships 
Organisation John Regan Associates Ltd
PI Contribution The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity
Collaborator Contribution The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products
Impact Further funding: RCUK-GROW programme BB/P028098/1; Multidisciplinary programme involving biological sciences, agricultural sciences, economics, social sciences, political science
Start Year 2017
 
Description GROW Colombia partnerships 
Organisation National University of Colombia
Country Colombia 
Sector Academic/University 
PI Contribution The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity
Collaborator Contribution The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products
Impact Further funding: RCUK-GROW programme BB/P028098/1; Multidisciplinary programme involving biological sciences, agricultural sciences, economics, social sciences, political science
Start Year 2017
 
Description GROW Colombia partnerships 
Organisation Natural History Museum
Country United Kingdom 
Sector Public 
PI Contribution The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity
Collaborator Contribution The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products
Impact Further funding: RCUK-GROW programme BB/P028098/1; Multidisciplinary programme involving biological sciences, agricultural sciences, economics, social sciences, political science
Start Year 2017
 
Description GROW Colombia partnerships 
Organisation The Eden Project
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity
Collaborator Contribution The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products
Impact Further funding: RCUK-GROW programme BB/P028098/1; Multidisciplinary programme involving biological sciences, agricultural sciences, economics, social sciences, political science
Start Year 2017
 
Description GROW Colombia partnerships 
Organisation University of East Anglia
Country United Kingdom 
Sector Academic/University 
PI Contribution The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity
Collaborator Contribution The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products
Impact Further funding: RCUK-GROW programme BB/P028098/1; Multidisciplinary programme involving biological sciences, agricultural sciences, economics, social sciences, political science
Start Year 2017
 
Description GROW Colombia partnerships 
Organisation University of Sydney
Department Faculty of Veterinary Science
Country Australia 
Sector Academic/University 
PI Contribution The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity
Collaborator Contribution The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products
Impact Further funding: RCUK-GROW programme BB/P028098/1; Multidisciplinary programme involving biological sciences, agricultural sciences, economics, social sciences, political science
Start Year 2017
 
Description GROW Colombia partnerships 
Organisation University of the Andes
Country Colombia 
Sector Academic/University 
PI Contribution The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity
Collaborator Contribution The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products
Impact Further funding: RCUK-GROW programme BB/P028098/1; Multidisciplinary programme involving biological sciences, agricultural sciences, economics, social sciences, political science
Start Year 2017
 
Description GROW Colombia partnerships 
Organisation Zoological Society of East Anglia
PI Contribution The Institute brought together partners from Colombia and the UK with an interest in biodiversity to develop and collaborate on research ideas and proposals relating to understanding the preserving Colombian Biodiversity
Collaborator Contribution The partnership is multidisciplinary, calling on the expertise of each of our partners to develop a series of research projects and goals to help understand Colombian biodiversity and develop recommendations for the continued preservation and sustainable use of natural products
Impact Further funding: RCUK-GROW programme BB/P028098/1; Multidisciplinary programme involving biological sciences, agricultural sciences, economics, social sciences, political science
Start Year 2017
 
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 2017 Youth STEMM Gold Awards 
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 Presentation on synthetic biology followed by a practical workshop on designing genetic circuits. Sudents then presented their ideas, asked technical questions and discussed the potential impacts of synthetic biology and biotechnology on society.
Year(s) Of Engagement Activity 2017
URL http://ysawards.co.uk
 
Description 17-21 July 2017_2nd Interdisciplinary Signaling Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact In this interdisciplinary workshop advanced science was combined with informal summer activities to solve multi-disciplinary scientific questions, by bringing early career scientists together with more established researchers in a relaxing and beautiful location.

Invited speakers presented talks on the topics of cell regulation, network modelling, genomics, systems biology, bioinformatics, structural biology, biochemistry, and cheminformatics. Then, selected talks from other participants will be followed by multi-disciplinary teamwork sessions in the afternoon, followed by cultural and social activities, such as medieval team building and handicraft activities in the Visegrad Castle. Poster sessions and plenty of informal opportunities allowed the participants to discuss complex and exciting questions as well as develop new collaborations. The renaissance surroundings of the venue nicely matched with the interdisciplinary nature of the workshop.
Year(s) Of Engagement Activity 2017
URL http://signalingworkshop.org/
 
Description 24-25 April 2017_Multiscale analysis of host-microbe interactions in plants, animals and humans 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact The aim of this workshop was to bring together key experts and early-stage scientists working on host-microbe interactions, including pathogen infections, commensals and microbiome level studies, to share novel scientific ideas on the multiscale investigation of host-microbe interactions and to provide an exciting opportunity to establish and improve cross-disciplinary and UK-wide collaborations.

After kick off with three keynote speakers on current challenges, the program provides structured study groups to discuss 1) novel methodological approaches; 2) potential future projects requiring participants from different disciplines; 3) the best ways to get funding for such multi-disciplinary projects. We facilitated these goals with short presentations and brainstorming opportunities in coordinated team works, and with panel discussion with representatives of key relevant funding agencies and charities.
Year(s) Of Engagement Activity 2017
URL http://www.multiscalebiology.org.uk/events/event/multiscale-analysis-of-host-microbe-interactions/
 
Description AI Discovery Workshop with HPE 31 January - 1 February 2019 
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 Earlham Institute hosted an Artificial Intelligence Discovery workshop lead by Hewlett Packard Enterprises (HPE). The workshop was developed by and came about given the existing strong connections that EI faculty and NC leads and our Computing Infrastructure for Science (CiS) group have with HPE. There was a particular focus on potential applications of AI and Machine Learning to image, time series and genomics data.

There was also some opportunity for delegates to discuss their own projects and data, which they brought along to the workshop, and to explore potential applications and approaches with the experts at HPE. Sessions covered included: An Introduction to AI and Strategies, Potential Use cases (round table discussion), How Deep Learning Works, Using Frameworks and Implementing Optimisations, Examples of AI application, Imaging data and AI Applications, Time series data and AI Applications, Brainstorming session: Genomics AI Applications.

There were 21 attendees, the majority from across the Norwich Biosciences Institutes, but also a couple of collaborators from each of Rothamsted and Wellcome Trust Sanger Institute. The attendees were a balanced mixture of PhD students, PostDoc, Project Leaders and Other researchers in support capacities e.g. statistician, Infrastructure support.

Feedback was overwhelmingly positive with 100% of delegates saying that they found the workshop useful and would recommend to others. Although a lot of ground was covered and the pace of the training was a little fast, delegates have shown great interest in follow-on workshops and discussions are underway to invite HPE back for future event(s).
Year(s) Of Engagement Activity 2019
 
Description BBSRC AI in Biology Workshop - 4 October 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Fifty one (51) delegates attended the full workshop including breakout groups with an additional twenty (20) attendees accessing the talks only. This workshop was part of a series of workshops supporting cross-institutional engagement and aligning research activities, this one in particular invited industry and other research institution representatives working in the application of AI to biology.
Breakout discussions were grouped by topic: Genotype-to-phenotype; DNA Motifs, Protein Structure and Function; Gene Mining; Network Inference; and Phenotyping. Potential projects were identified and discussed. Paper written to BBSRC outlining the workshop discussions and outcomes. The workshop initiated a AI working group across the BBSCR strategically funded institutes. Further funding was secured from Turing Institute for a collaborative project.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/bbsrc-artificial-intelligence-biology-workshop
 
Description BBSRC Plant Breeding workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation on Haplotype-specfic genome assembly
Year(s) Of Engagement Activity 2018
 
Description Brassica Information Portal Workshop - 15 June 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact The Brassica Information Portal (BIP), a repository for Brassica crop trait data, and for users to provide feedback to guide future development. The concept of the portal is to allow the Brassica community to make their data publicly available and accessible. Efforts with the ELIXIR standards community has meant that data entered into the repository use a controlled vocabulary and standardised data formats, which increases the accessibility and reusability of community data. Following newly implemented features to the BIP, the development team hosted an informal workshop to allow the user community to test and evaluate BIP's different mechanisms for uploading Brassica trait and experimental population data. In this way, feedback from users at the workshop will contribute to future developments of the portal.This was a hands-on workshop where users will learned to submit an experimental plant population, including metadata on the plant background, using a simple Ruby tool. Following this, delegates used the BIP interface to submit trial data, including trial set-up metadata and trait measurements. Delegates also had the opportunity to bring along their own data so that the development team could assist with the upload during the workshop itself.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/brassica-information-portal-workshop
 
Description CPSC PhD course: SYNthetic BIOlogy, From pro- to eukaryotic SYStems (SYNBIOSYS) 
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 Delivered lectures and workshops as part of the University of Copenhagen's CPSC PhD course: SYNthetic BIOlogy, From pro- to eukaryotic SYStems (SYNBIOSYS)
Year(s) Of Engagement Activity 2017
URL http://cpsc.ku.dk/calendar/2017/cpsc-phd-summer-course-2017-synbiosys/
 
Description Covers workshop 
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 Anthony Hall and David Swabrick from the Earlham Institute provided an 'Introduction to Transcriptomics' and as a 'Guide to Annotating Eukaryotic Genomes'. You can download this PDF on the tab to the right.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/cyverse-uk-rnaseq-workshop-2018
 
Description CyVerse Workshop (University of York) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Contributed to a CyVerse UK workshop (20-21 March 2017), delivering a session on RNAseq analysis. Workshop participants were guided in real-time through an established analysis pipeline in a cloud computing environment.
Year(s) Of Engagement Activity 2017
 
Description CyVerseUK RNAseq Workshop 10-12 December 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This workshop brought together trainers from the US and UK to introduce delegates to the tools for RNAseq data analysis. The workshop also included a condensed Data Carpentry workshop (day 1) for delegates focusing on skills in the key tools for RNAseq data analysis for those who had limited or no previous command-line experience and provided an introduction to R. This was a well-attended workshop with 33 delegates, 32 of which also attended the Data Carpentry i.e. the full three-days. This demonstrates that we successfully engaged with our target audience of those who were new to the field with little to no experience in using the command line. Attendees were exclusively PhD students and PostDocs with almost 95% currently residing in the UK. This was a very successful collaborative training event and, as a result, GARNet's community developer has submitted a grant application in which EI is named as a co-organiser and co-developer of a training workshop focused on Single Cell technologies and techniques in plant systems.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/cyverse-uk-rnaseq-workshop-2018
 
Description Data Carpentry 5-6 March 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Of the 13 attendees, 11 were PhD students, the majority of which are based at the University of east Anglia (UEA). Feedback shows that 100% of the attendees would recommend the course and 100% rated the trainers as "very good" or "excellent". An attendee from BBSRC-strategically funded institute Rothamsted, showed interest in engaging with the community to host similar workshops at their own institution.
Year(s) Of Engagement Activity 2016,2017,2019
URL http://www.earlham.ac.uk/data-carpentry-workshop-2019
 
Description Data Carpentry Workshop - 21-22 November 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Data Carpentry's aim is to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. The workshops are are for any life scientist or computational science researcher who has data they want to analyse, and no prior computational experience is required. This hands-on workshop taught basic concepts, skills, and tools for working more effectively with data. Topics included data organisation in spreadsheets, data cleaning, SQL, the command line, and R for data analysis and visualisation, all using examples from biology. Participants bring their own laptops and are encouraged to actively participate. The intention for such workshops is that by the end of the workshop, delegates would have the skills to more effectively manage and analyse data, and that they would be able to apply the tools and approaches directly to their ongoing research. PhD students comprised over 45% of the audience for this workshop and feedback was good with 100% of delegates identifying the trainers as excellent, almost 90% rating the training overall as 'very good' to 'excellent' and 100% saying that they would recommend the course to others.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/data-carpentry-workshop-2017
 
Description De Novo Assembly - 13-16 March 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This training course attracted 22 international delegates with approximately one-third PhD students and one-half Post-Doctoral scientists. Taking delegates through from sequencing technology, introduction to k-mers and assembly pipeline parameters 100% of delegates said that they would recommend the course and over 80% rated the trainers as excellent, the remainder as very good. The proof in the accessibility of this course, is that an attendee from our condensed course as part of the Genome 10K and Genome Science 2017 conference, applied and returned to the 2018 full course, demonstrating real value in the knowledge and expertise imparted by the trainers.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/de-novo-assembly-2018
 
Description De Novo Assembly 11-14 February 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Of the 18 attendees, ~78% were researchers based in the UK with the remaining delegates coming from Spain, South Africa and Australia. Two-thirds of the delegates were PhD and PostDocs, other research scientists including those with or wishing to create collaborations or connections with the institute, and one attendee from a company based in the region and who is interested in follow-on support from the group beyond the extent of the course. Significant progress was made through the outline syllabus during this iteration of the course and when compared with previous years. This may be, at least in part, down to the significant effort put in by the lead trainer to produce an online post (GitHub) to introduce some tricky but essential concepts and which was made available as essential pre-reading - "Introduction to k-mers". As a result of the success and delegates' abilities to solve the group working problems during the course, there are plans to create further posts that will introduce other, related concepts.
Year(s) Of Engagement Activity 2017,2018,2019
URL http://www.earlham.ac.uk/de-novo-assembly-2019
 
Description De novo Assembly Training (Genome 10K and Genome Science Conferences) - 1 September 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Organised as one in a series of workshops to encourage and support early career researchers attending the Genome 10K and Genome Science 2017 conferences, this one-day training workshop was a condensed version of our 3.5 day de novo assembly training, followed the formal conference programme closure and ran in parallel with the Genome 10K working groups meetings. This training was oversubscribed and a selection process ensured that the 'best fit' of delegates were given priority places on the course. This intense course immersed a varied delegation in the concepts of assembly whilst giving hands-on opportunities to run assemblies and interpret the metrics to identify good quality data sets and assemblies that were the closest approximation to the original genomes. Over 85% of delegates providing feedback for this course rated the trainers as very good to excellent and said that there was suitable opportunities for discussions amongst trainees and with trainers.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/genome-10k-and-genome-science-conference#Day4-4
 
Description De novo assembly 2018-12 Argentina 
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 De novo assembly training, delivering the same content from the annual EI training. We provided access to the computing resources ad EI. This training was co-founded by CONICET.
Year(s) Of Engagement Activity 2017
 
Description Differential Expression Analysis and Visualisation using Galaxy (Genome 10K and Genome Science 2017) - 1 September 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Organised as part of a series of workshops aimed to encourage and support early careers researchers attending the Genome 10K and Genome Science 2017 conferences, this workshop provided a fantastic introduction both to the Galaxy platform, but also to RNAseq analyses. A lot of material was covered in this one day event, however, the vast majority of delegates believed the balance of detail to be perfect given the duration of this introductory, one-day course.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/genome-10k-and-genome-science-conference#Day4-4
 
Description ELIXIR Workshop for Galaxy training material and skills improvement 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Dr. N. Soranzo, Mr. A. Thanki and Dr. E. Angiolini organised the workshop, which was attended by 16 participants coming from across Europe. During the first day, participants attended a Train-the-Trainer course delivered by Sarah Morgan (EBI, ELIXIR Training Platform). In the following 2 days, participants worked together and in groups on improving and extending the existing training materials for teaching Galaxy. A report is available at https://galaxyproject.eu/posts/2018/06/05/gtn-hackathon/
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/elixir-workshop-galaxy-training-material-and-skills-improvement
 
Description ENWW Masterclass 30 April 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Approximately 30 students (one cohort of third year PhD students) attended an ENWW Masterclass covering short talks on single-cell genomics, machine learning and open data/science, moving to group discussions and pitches of new projects based on the concepts learned.
Year(s) Of Engagement Activity 2018
 
Description European Galaxy Administrator Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The European Galaxy Administrator Workshop was a 5-days course organised by ELIXIR and dedicated to Galaxy server administrators. Participants learned how to install, configure, customize, and extend their own Galaxy servers. Topics included basic and advanced server setup, tool configuration, data managers, authentication and user management, using heterogeneous storage and compute services, Ansible, server monitoring and maintenance.
Year(s) Of Engagement Activity 2018
URL https://www.elixir-europe.org/events/european-galaxy-administrator-workshop
 
Description Flexible Talent Mobility Account Launch Workshop - 21 March 2018 
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 This workshop brought together ten (10) industry representatives from seven (7) different companies, ranging from Information Technology/Hardware, to transnational consumer goods companies, breeders and Research and Development companies with some of our project leaders to discuss potential areas for collaboration and skills transfer. We have since awarded seed funding to initiate pilot projects engaging EI faculty with companies in attendance for this workshop. In addition a number of NDAs are under development.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/flexible-talent-mobility-account-and-workshop
 
Description Flow Cytometry Workshop 26 February 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This training was a one-day lecture/theory-based workshop aimed at those who have access to Flow Cytometers and were in the planning stages of a project which would require their use. The two trainers were external experts - Dr Rachael Walker, running the Babraham Institute facility; Dr Derek Davies, running the facility and training/outreach associated at the Crick Institute. Aimed at beginners in the early planning stages of their experiments, the 21 attendees comprised mainly PhD students (~38%) and PostDocs (~28.5%) with other facility/service providers also in attendance. Feedback is still be collected and reviewed at the time of reporting.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/flow-cytometry-training
 
Description GCC2017 - Conda and Containers for Tool Dependencies - A Developer's Perspective 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This training workshop was part of the Galaxy Community Conference 2017 (GCC2017, https://gcc2017.sched.com ) and was aimed at people with some experience developing tools and deployers who need to manage complex sets of dependencies for tools.

Galaxy tools define the applications and other dependencies they require to run using their requirements section. This training session covered the elements of the requirements section and how Galaxy can be configured to utilize these.

The current best practice for resolving these dependencies is using Conda and Bioconda, and so a substantial amount of time will be spent on these topics. We went through the process of creating, testing, and publishing a Bioconda package. We worked through an example of connecting these packages to Galaxy.

We also discussed how the Biocontainers project constructs Docker containers from Bioconda packages and how to emulate this process for local testing before publication. Finally, we reviewed approaches to leveraging these containers from Galaxy to run jobs within containers.
Year(s) Of Engagement Activity 2017
URL https://gcc2017.sched.com/event/9mzb/conda-and-containers-for-tool-dependencies-a-developers-perspec...
 
Description GCC2017 - Writing & Publishing Galaxy Tools 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This training workshop was part of the Galaxy Community Conference 2017 (GCC2017, https://gcc2017.sched.com ). This session walked developers and bioinformaticians through the process of taking a working script or application and turning it into a Galaxy tool. It also covered the basics of using Planemo, a command-line utility to assist in building and publishing Galaxy tools. We investigated wrapping, common parameters, tool linting, best practices, loading tools into Galaxy, citations, and publishing tools to Github and the Galaxy Tool Shed. Common tips and tricks were discussed, as well as insights from experienced tool developers.
Year(s) Of Engagement Activity 2017
URL https://gcc2017.sched.com/event/9mzP/writing-publishing-galaxy-tools
 
Description Genome Technologies and Innovation Workshop - 31 October 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Organised in conjunction with UEA, having attracted funding from Research England, this workshop and symposium attracted 58 people from across the Norwich Research Park, including a number of small companies (e.g. Tropic Biosciences and Food Forensics), plus larger, multi-national companies involved in genome and related technologies. It showcased the wide-ranging expertise of researchers across the park as well as the facilties and equipment, plus announcing winners of a pilot project award, funded jointly by 10X Genomics and Illumina to access the institute's facilities.

The final session of the workshop was a closed session exploring potential engagement with both small and large enterprises with genomics and related technologies.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/genome-technologies-and-innovation-workshop
 
Description Hosting a PhD student from CIMMYT (Mexico) for training 
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 The Hall lab group hosted a Phd student supervised by Dr Matthew Reynolds (CIMMYT) and Dr John Faulkes (University of Nottingham) for training in crop genetics.

Over a period of 3 days we introduced her to concepts surrounding phenotype - genotype association analysis culminating in the successful application of GWAS to her data.

This lead to a very well recieved poster presentation at the Plant and Animal Genomes conference in 2019:

https://pag.confex.com/pag/xxvii/meetingapp.cgi/Paper/33006

Strategies for achieving genetic gains in yield potential must combine enhanced above-ground dry matter as well partitioning to the grain (harvest index). The present study aligned with NIFA-IWYP (International Wheat Yield Partnership) project N-IWYP700* aimed to identify grain partitioning traits that help maximize grain yield in high biomass backgrounds.
A High Biomass Association Panel (HiBAP) comprised of 150 spring wheat elite genotypes was phenotyped in 2015-16 and 2016-17 at CIMMYT experimental station Norman E. Borlaug located in NW Mexico. Physiological traits measured included biomass, plant length (height, spike, awns, peduncle, internode 2 & 3), organ DM partitioning (spike, leaf lamina, true stem and leaf sheath) and fruiting efficiency (# of grain set per unit spike dry weight) at anthesis (GS65) + 7 days and at harvest, biomass, grain yield, yield components and harvest index was measured. BLUEs (Best Linear Unbiased Estimators) from the cross-year analysis and molecular markers generated using the 35K Wheat Breeders Axiom array were used to carry out a genome-wide association study (GWAS).

Novel marker-trait associations for the grain partitioning traits were identified mainly in chromosomes 5B and 6A; resulting in 13 at anthesis (e.g. LamPI, spike length) and 9 at harvest (e.g. HI, FE_GSP). More detailed results will be presented and their potential application in breeding programs in marker-assisted selection discussed.
Year(s) Of Engagement Activity 2018
URL https://pag.confex.com/pag/xxvii/meetingapp.cgi/Paper/33006
 
Description Introduction to Multiomics Data Integration 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Tamas Korcsmaros delivered a talk on the nature of different data types, and provided a training on Cytoscape
Year(s) Of Engagement Activity 2009,2018
URL https://www.ebi.ac.uk/training/events/2018/introduction-multiomics-data-integration-0
 
Description 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 Meiosis and Beyond - 5-6 March 2018 
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 A mini symposium bringing together researchers from a wide variety of fields united by one common theme - meiosis (before, during and after). Delegates and presenters working on a variety of organisms from plants to birds to nematodes came together to hear some of the latest research using new and emerging technologies and approaches in the field of meiosis. Beyond the mini symposium the group gathered for discussions including challenges they face in common with one another, technology that could help to answer their biological questions and to roadmap where they were as a research cohort.

The group are working on a paper summarising the current state and challenges and a subset have taken discussions from the workshop to successfully apply for funding to support new and emerging ideas.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/meiosis-and-beyond
 
Description Molecular Training Workshop for African Scientists, University of Cambridge 
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 Lectures deleivered as part of a two week training evint for agricultural research scientists, academics and PhD students from across Africa. This was followed by discussion and follow-up questions by email.
Year(s) Of Engagement Activity 2018
URL http://www.jrbiotekfoundation.org/cambridge-lab-training-2018/
 
Description Monogram Grain Conference 2019 
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 of GWAS of 150 spring wheat lines associating agronomic, yield and biomass related traits to SNP markers for use in the CIMMYT (Mexico) pre-preeding marker trait assisted breeding program. This work is now published here: https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.13052 and was carried out as part of the International Wheat Yield Partnership to provide essential marker trait associations to wheat breeders at CIMMT for tracking high biomass and radiation use efficiency, both which are thought to be a current bottleneck in genetic gains in their populations.

The poster was well received and gained a lot of attention during the poster session. A link made during this yielded an on going collaboration with scientists at Rothamsted Research (Mathew Paul).
Year(s) Of Engagement Activity 2018
URL http://www.monogram.ac.uk/MgNW2018.php
 
Description Norwich Biomakers 
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 Norwich Biomakers brings together an interdisciplinary network of people from across NorwichCity and the Norwich Science Park that share an interest in the cross-over of biology with design, technology, engineering, electronics and software. This group meets monthly at a variety of local spaces for events including talks, training in the use of technologies and to work on projects.
Year(s) Of Engagement Activity 2017,2018,2019
URL https://www.meetup.com/Norwich-Biomakers/
 
Description Norwich Single Cell Symposium 16-17 May 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The symposium was predominantly aimed at researchers across the region and attracted some 77 people with international speakers plus sponsors to discuss the latest development and challenges in the field. Offering sponsorship opportunities meant additional support for costs for the symposium but also a high degree of engagement from these sponsor companies, who were interested in our applications of Single Cell Technologies.
Year(s) Of Engagement Activity 2017,2018
URL http://www.earlham.ac.uk/norwich-single-cell-symposium-2018
 
Description Norwich Single-Cell Symposium - 8 May 2017 
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 With the developments in single-cell genomics technologies, particularly in the broadening of applications, we organised this symposium to bring together researchers who were curious about single-cell genomics with external speakers engaged in advanced single-cell research as well as highlighting the single-cell capabilities available at Earlham Institute. The idea was that this would provide an informal platform to catalyse future development and application of single-cell genomics across the region. The one-day symposium covered single-cell genomics topics in the following areas: technology development, developmental biology, health and disease, plant science and data analysis. The inaugural event had over 90 registrations, including a small number of industry representatives who had the option to sponsor and exhibit at the meeting. Feedback received suggested that the symposium offered a great diversity of topics in an informal and friendly setting. Many respondents providing feedback commented upon the high standard of presentations and enjoyable networking opportunities citing that they would like to see a repeat symposium the following year and that the meeting should be a little longer, with more networking.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/norwich-single-cell-symposium
 
Description Octoseq Workshop 18-19 December 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Project leaders and researchers engaged in the grant came together to report on the development of the project plus a short training activity relating to the grant output - a browser developed to explore the data. 14 people attended.
Year(s) Of Engagement Activity 2018
 
Description Oral Presentation The Rank Prize meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The meeting was run as an invitational meeting run by the "The Rank Prize Fund" and was named "The shape of wheat to come". The meeting was attended by 30 early career scientists and around 20 more seasoned scientists with the aim of introduction of early career scientists to long established members of the wheat community (including breeding companies). A participant was invited from the most influential groups studying wheat mainly from the UK and France. Each participant was required to
A brief description below:

The Trustees' Advisory Committee on Nutrition is arranging a series of symposia on topics that are of current interest. In 2018 we intend to organise a mini-symposium on The Shape of Wheat to Come which will be held at The Wordsworth Hotel, Grasmere, Cumbria, England, from 19th to 22nd March 2018.

The aim of the meeting is to provide a forum in which leading scientists and young research workers can meet and interact, in order to stimulate discussion and to advance the development of the subject. Attendance is by invitation only and will be limited to about 30 participants. The main speakers will have about 40 minutes for their talk and related discussion and the young scientists will be allocated 20 minutes to give an account of their work. The value of these symposia lies in their small, fully interactive nature, not only during the presentations and discussion, but at other times over meals, in the hotel bar and during recreational periods.
Year(s) Of Engagement Activity 2018
 
Description Oral presentation at conference: Training on Durum Wheat Genomics and Breeding, University of Bologna, Italy 
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 Oral presentation at training conference to educate and train breeders, farmers and students in bioinformatic techniques for the analysis of wheat genomics data
Year(s) Of Engagement Activity 2017
URL http://www.wheatinitiative.org/events/durum-ewg-workshop-bioinformatics-advance-wheat-breeding
 
Description Oral presentation at the Wheat and Barley Legacy for breeding improvement annual meeting at the University of Haifa, Israel 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Attended and presented work at the Wheat and Barley Legacy for breeding improvement annual meeting at the University of Haifa, Israel. This built links with researchers in Italy, France and Israel for future collaboration and sparked their interest in epigenetic research.
Year(s) Of Engagement Activity 2017
 
Description Oral presentation: Agilent User group meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact I presented my work analysing the methylation of wheat to many of the users of Agilent technology in the UK since I implemented Agilent technology for the study. Many PI's and postdoctoral researchers were present and were interested in how they could use this methodology for their own analyses.
Year(s) Of Engagement Activity 2018
URL https://www.chem.agilent.com/edm/2017/06/Uk_Seminar_2017/Documents/GenUGM/Agenda_GUGM.pdf
 
Description Organising and hosting: Genome 10K and Genome Science Parallel Conferences 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Earlham Institute hosted two conferences in parallel - The biannual Genome 10K conference and the annual Genome Science meeting from 29 August - 1 September 2017 (http://www.earlham.ac.uk/genome-10k-and-genome-science-conference). The conference attracted over 350 delegates, including sponsors and local council representatives in addition to the target attendees of PhD students, Postdocs and PIs from around the World. We received fantastic support from Greater Norwich Partnership, which comprises several local councils, including fantastic opportunities to showcase the city as well as entertain delegates with an exclusive tour of the castle. A joint press release was made with the councils, which was picked up by local media, resulting in a news article, and a lengthy (~15 minute) in-studio interview with our Director of Science, Federica Di Palma, raising awareness of the institute, our research and the wider goals of projects associated to the conference e.g. Genome 10K Project. Feedback from the delegates was fantastic with many delegates providing verbal feedback at the conference itself, including praise around gender balance of speakers, logistics and organisation of the conference, catering and entertainment. As part of our commitment to supporting early career researchers, we offered, at no additional registration cost, limited spaces on training and careers development workshops (de novo assembly course, RNAseq using Galaxy course, science communication workshop, CV skills workshops, and a session on career paths). Delegates enjoyed the location of the conference, for many it was their first visit to the area, and hosting these two conferences not only raised the profile of the institute and it's location, but also the fantastic research that we are engaged in, and elicited promises of return visits through anticipated collaborations, plus an appreciation for our skills in wider activities such as training and events.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/genome-10k-and-genome-science-conference-2017-gallery
 
Description Paul Bailey talk at PAG at Cyverse workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact As more genomes are sequenced it is becoming apparent that gene duplication and deletion are important drivers in evolution, with rapidly expanding gene families often a signature of their role in an organism's adaptation to the environment. To identify these events, we are building a gene family analysis toolkit which will be deployed on the Cyverse cloud infrastructure for use by the scientific community. Central to its purpose will be the ability to distinguish evolutionary relationships between genes within gene families for currently and newly sequenced species, both at the intra- and inter-species level.
As a pilot study, we are using a collection of landrace bread wheats (the Watkins collection) which have been sequenced by exome capture to explore the diversity of the large Nucleotide Binding Leucine Rich Repeat (NLR) family of plant resistance genes in the collection. Illumina read data from each wheat line have been assembled using various tools. The resulting contigs have been aligned to their corresponding subgroups within the NLR family. Looking at subgroups that are expanded relative to other monocot species, we can demonstrate that further novel gene duplication events have occurred in specific lines of the Watkins collection. The next step will be to understand whether specific genes in the family are under positive selection and therefore which genes have particular functional significance. The assembly and downstream procedures will be placed into a Docker container for use on Cyverse as a tool for exploring the diversity of any gene family in any species with sequence data.
Year(s) Of Engagement Activity 2018
URL https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/29841
 
Description Plant and Animal genomes conference 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Attendance to plant and animal genomes conference 2019- including 2 x poster presentations. One poster contained work carried out and reported in a recent publication ( 10.1111/pbi.13052). This poster recieved a lot of attention and we were approached multiple times by scientists working in wheat barley and rice along with making contact with a member of the breeding community (KWS) who was interested in the marker trait associations (MTAs) we had discovered and presented in the poster. The second poster featured collaborative work we have carried out with Dr John Faulkes from the University of Nottingham, which also gain wide interest as it denotes the first identifiaction of markers relating to various stem and spike partitioning indices.

These presentations also have lead to further discussions with scientists from NIAB about the use of a capture probe set we have designed as part of Designing Future Wheat ISP and our International Wheat Yield partnership grant.
Year(s) Of Engagement Activity 2019
URL https://www.intlpag.org/2019/
 
Description Population Variation Genetics Training Course - 22-26 May 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Aimed at researchers who were in the planning or data-production stages of a Genotype-By-Sequencing project, this course aimed to familiarise delegates with the molecular and analytical aspects of the genetic screening method Genotype-By-Sequencing (GBS). The course focused on the UNIX skills that are necessary to handle GBS data, as well as how to clean and demultiplex Illumina sequences. Delegates had hands-on experience with the computational pipeline 'Stacks' which was designed for the analysis of such data. They were able to analyse RAD-seq data de novo to perform a population analysis without the aid of a reference genome using Stacks and structure, as well as from an organism with a reference genome to generate Fst measures and identify signatures of selection. 100% of the delegates providing feedback rated the training overall as very good to excellent and would recommend the course to others. Delegates reported a general development of knowledge and understanding of STACKS, useful for the application to their research.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/population-variation-genetics#Programme-2
 
Description Poster presentation at international conference: Binding sites within long non-coding RNAs discriminate between RNA- and transcription-mediated mechanism 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The poster presented at the Genome 10K / Genome Science conference was selected on abstract submission. The poster was presented in front of industry participants, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Tomasz Wrzesinski, Wilfried Haerty and of the Earlham Institute
Year(s) Of Engagement Activity 2017
 
Description Poster presentation at international conference: Discovery and visualisation of homologous genes and gene families using Galaxy 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The poster presented at the Genome 10K / Genome Science conference was selected on abstract submission. The poster was presented in front of industry participants, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Anil Thanki, Nicola Soranzo, Wilfried Haerty, Robert Davey and of the Earlham Institute
Year(s) Of Engagement Activity 2017
 
Description Research Cyberinfrastructure Colombia Workshop 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The workshop involved a multidisciplinary team of Colombian and international experts to understand user needs and available resources, discuss innovative solutions, and design a strategy to grow research capacity for the high-throughput computational analysis of biological data in Colombia.
This workshop was an opportunity for intensive discussions to uncover innovative solutions, identify critical partners and produce a realistic strategy and open vision for the creation of C3Biodiversidad (Consorcio Colombiano de Ciberinfraestructura) in Colombia.
Year(s) Of Engagement Activity 2018
URL http://www.bridgecolombia.org/c3-biodiversidad/
 
Description 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 Stewarded the Innovation Hub at the Royal Norfolk Show. The Innovation Hub aims to showcase agricultural related technologies and developments and communicate them to the general public, farmers and growers. This two day event attracted around 80,000 visitors from around the county and across the UK.
Year(s) Of Engagement Activity 2017
 
Description 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 Stewarded the Innovation Hub at the Royal Norfolk Show. The Innovation Hub aims to showcase agricultural related technologies and developments and communicate them to the general public, farmers and growers. This two day event attracted around 80,000 visitors from around the county and across the UK.
Year(s) Of Engagement Activity 2017
 
Description Science Communication Workshop (Genome 10K and Genome Science 2017 Conference) - 29 August 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This workshop was one of several organised with the intention of encouraging and supporting early career researchers attending the Genome 10K and Genome Science 2017 conferences. Recognising the increasing importance of explaining scientific research to the general public and stakeholders, we provided an informal workshop to explore the complex nature of communicating ideas to a wide audience. The main focus was on the language that we use to communicate our research, with attendees asked to provide a scientific abstract about their research, rewrite it using simplified language based on feedback from other researchers in the room, and then rethink and rewrite their abstract using the one-thousand most common words in English. Delegates reported knowing before the workshop that some of their concepts and research could be difficult for non-experts to understand, but only after attending the workshop did they fully appreciate the discrepancy. Of survey respondents, 85% said that the workshop had changed their approach for communicating their work and 100% said that they would like to see this sort of training as a regular feature in the workplace.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/science-communication-workshop
 
Description Scientific Advances in Agriculture 5 November 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Industry/Business
Results and Impact An evening workshop organised as part of AgriTech week, this event dissemination was supported by AgriTech East. 29 people attended the evening including EI faculty, local farmers, agronomists and other related-businesses. The programme for the evening, included demonstrations with discussions as small group rotations covering: Genome Technologies in Agriculture; Can In-field AI/Robotics improve crop yield; How could Synthetic Biology impact Agriculture; What could Genomics do for Crop Advancement. Delegates were also given ample opportunity to see the facilities and ask many questions through the tours of: Genomic Pipelines Laboratory; DNA Foundry Laboratory; and Data Centre. Email requests were made to follow up on initial discussions from this workshop and to put EI experts in touch with other overseas researchers wishing to implement a similar framework.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/scientific-advances-agriculture
 
Description Single-cell RNAseq Training Course Delivered 3-7 Dec 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This was the first iteration of this course, demonstrating EI's both introducing Single Cell Genomics and demonstrating EI's capability. It covered several aspects such as: the experimental design, cell sorting and processing for production of quality samples for sequencing, in the three-days of laboratory hands-on sessions; generation of sequencing data, assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variants at the single cell level in the following two-days of theory and computational hands-on sessions. A total of twelve (12) delegates attended this course, with ten (10) attending the full five days. Also included was a short half-day session with practical elements on single molecule FISH, delivered by EI faculty, and an overview of 10X Genomics' data analysis platform, presented by one of their Field Application Specialists.

Delegates were predominantly UK-based (~83%) and PostDocs (two-thirds), with a couple of attendees responsible for similar laboratory facilities in their home institutions. All attendees rated the trainers as "Very Good" to "Excellent", and a survey of the ten laboratory sessions attendees suggested that, having followed the course, many hoped to engage with a Single-Cell RNAseq service for their research (53% very likely and 40% likely), with 53% wishing to provide cells.

Following the unprecedented success of delegates producing high quality data to analyse, course organisers wish to review the programme. The proposal for the second iteration is to run the course as 3 or 4 days in the laboratory, with sequencing running over a weekend, and then extending the bioinformatics from 2 days to 4 days, running this on the following week.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/single-cell-rnaseq-training-course
 
Description Software Carpentry Workshop - 10-11 October 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact The intention of this workshop is to help scientists become more efficient in data analysis through teaching basic computing skills such as programme design, version control, testing and task automation. The two-day workshop alternates short tutorials with hands-on practical exercises to reinforce concepts and best practice. This course is aimed at researchers in the life science and computational science disciplines and across all research stages. Delegates learned how to: use the shell to do more in less time, automate tasks and pipelines, write structured programmes, using Git to manage and share information, plus how and to what extent to test programmes. 100% of delegates rated the event overall as very good to excellent, 100% rated the trainers as very good to excellent and 100% said that they would recommend the course.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/software-carpentry-workshop-october-2017
 
Description Software Carpentry Workshop - 26-27 April 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact The intention of this workshop is to help scientists become more efficient in data analysis through teaching basic computing skills such as programme design, version control, testing and task automation. The two-day workshop alternates short tutorials with hands-on practical exercises to reinforce concepts and best practice. This course is aimed at researchers in the life science and computational science disciplines and across all research stages. Delegates learned how to: use the shell to do more in less time, automate tasks and pipelines, write structured programmes, using Git to manage and share information, plus how and to what extent to test programmes. Almost 50% of delegates in attendance were PhD students, in accordance with our target audience. Around 90% of delegates rated the training overall as very good top excellent, and 100% stated that they would recommend the course to others.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/software-carpentry-workshop-2017
 
Description Software carpentry workshop 22-23 January 2019 
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 Just under half of the 17 attendees were PhD students. The majority of these were students primarily based at University of east Anglia (UEA), and who registered as the result of new connections with training and skills development personnel within the Biology faculties. Movement and loss of personnel at UEA had left a gap in the training programme and following discussions with EI faculty who put them in touch with the training team, we were able to offer a reserved number of spaces at a reduced rate to fulfil these requirements. Uptake for this course was very good and the training team are looking to strengthen these links going forward. Feedback collected shows that, of the total respondents: 100% would recommend the course; 100% rated trainers and 100% rated training materials as "Very Good" or "Excellent".
Year(s) Of Engagement Activity 2016,2017,2019
URL http://www.earlham.ac.uk/software-carpentry-workshop-january-2019
 
Description Synthetic biology session and discussion panel at the London Festival of Genomics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Chaired a session on synthetic biology session and participated in a panel discussion at the London Festival of Genomics, 2017. This brought the synthetic biology to a new audience of industry, investors and the general public. There was a lengthy discussion with the general public, investors and industry representatives from diverse fields (e.g. computing and engineering) about the ethics and potential of biological engineering at the panel discussion and also following the workshop.
Year(s) Of Engagement Activity 2017
URL http://www.festivalofgenomicslondon.com/full-agenda
 
Description Talk and discussion with Elsoms seeds 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact The talk was to breeders and crop scientist work at Elsoms seed, The aim was to raise awareness of the work that Design future wheat and my group were doing. This lead to a letter of support for our BBSRC grant and a line of communication with their wheat and brassica breeders.
Year(s) Of Engagement Activity 2018
 
Description Techology Day at 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 7500 members of the general public attended Nature Day at Norwich Science Festival. A number of activities were available to engage the general public with the work of the institute. A number of talks/presentations were scheduled also.
Year(s) Of Engagement Activity 2018
 
Description The Essex Synthetic Biology School (ESBS), University of Essex, UK : 
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 Presented lectures on "Engineering Plant Genomes for Farming and Pharming" and "Sharing Biology in the Information Age: Perceived Threats of Dematerialisation and Open Data". These were followed by discussions on the use of biotechnologies in agricultures and a debate on access and benefit sharing of genetic resources. Participants reported changes in their views on the common practices used to share information relating to genetic resources as well as physical resources.
Year(s) Of Engagement Activity 2018
URL https://esbs.essex.ac.uk
 
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 Training course delivery: BecA-ILRI Hub 
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 Myself and Laura Jayne Gardiner were approached to deliver a 1 week training session at the BecA-ILRI Hub, Nairobi, Kenya. The course was a 3 month training program ran by the Alliance for Accelerated Crop Improvement in Africa. Our contribution to the program was training in the background of NGS technologies and their use in crop development along with teaching applied bioinformatics fundamentals to the group of students. The students on the course were from >15 countries in Africa and returned to their host institutes with a fantastic base knowledge of bioinformatics which they will apply for crop/livestock improvement throughout Africa.
Year(s) Of Engagement Activity 2018
URL https://acaciaafrica.org/bioinformatics-community-practice/members-and-management/
 
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 - 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 Year in Industry Programme 2018/19 
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 Undergraduate students
Results and Impact The institute supported two Year in Industry students from mid-September with a stipend and whose expected end date is the end of August (11.5 months). Students undertook a short rotation period within the first three weeks at the institute, shadowing staff in the Genomics Pipelines teams to understand sample processing, including working with our Project management team to understand derivation of quotes and tracking of samples, then with laboratory staff through library construction and loading the sequencers. During this time students met with various potential project supervisors to discuss project ideas. Once they had chosen a project the students were able to write their project proposal and refine this through further discussions with the project supervisor. The students are carrying out their research project until approximately the end of June, when they will then concentrate on their project dissertation.
The institute has also also hosted a third, unpaid intern, who started mid-September, but whose project placement is due to complete at the end of July. The student is undertaking a pre-defined research project, but still followed the other students on rotation to gain a good understanding of the institute's operational set up and core strategic programmes.
Year(s) Of Engagement Activity 2011,2012,2013,2015,2016
URL http://www.earlham.ac.uk/year-industry
 
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