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 three years of the award to approximately 1330 delegates. In addition, EI has held the parallel conferences to 350 delegates in summer of 2017 (Genome 10K and Genome Science conferences), supported other events as consultants for programmes and provided logistics including: Inside EI (open day 2019) to over 300 attendees; Doing Science with Colombia 2019 to approximately 100 attendees (held at the Natural History Museum and organised on behalf of BEIS); EI's (internal) KEC training programme across 6 different sessions with up to 45 attendees per session; ELIXIR All-Hands to approximately 40 attendees in 2019 and 60 in 2020; the training events through EI's GCRF GROW to over 200 delegates; a cross-institution workshop as Part of AgriTech week attended by over 65 people; and contributed to sessions and facilitation of the DTP Big Data Science workshop. 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 continues to engage with the Nuffield Research Foundation to offer Nuffield Research Placements to students alongside our Research Experience Placement internships, Year in Industry and other work experience 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 and Metagenomics, which integrate the newest findings, pipelines and tools from Earlham Institute faculty into course material, and for development of new courses as part of this award such as Single Cell RNAseq and Genome Annotation (for delivery in April 2021).
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment,Healthcare,Other

 
Description Meeting with Sir John Kingman to discuss UKRI strategy and the sustainability of Institutes
Geographic Reach National 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
 
Description Membership of BBSRC Transformative technology Panel
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
Impact The transformative technology strategy advisory panel have influence BBSRC policy on data intensive bioscience and big ideas pipeline
 
Description NERC 'Omics Review. I provided advice on the Environmental omics strategy as a memeber of the NERC Environmental omics steering committee
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
Impact The report generated has led to the NERC commissioning of an environmental omics facility to improve the delivery of the NERC strategy and to train the next generation of scientists.
URL http://environmentalomics.org/steering-committee-and-editors/
 
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 ELIXIR-UK: FAIR Data Stewardship training
Amount £79,653 (GBP)
Funding ID MR/V038966/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 02/2021 
End 03/2023
 
Description JIF internship
Amount £81,140 (GBP)
Organisation John Innes Foundation 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2021 
End 03/2025
 
Description John Iness Foundation internship in data-driven plant bioinformatics
Amount £17,500 (GBP)
Organisation John Innes Foundation 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2021 
End 05/2022
 
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
 
Description Unravelling key regulators of thrombopoiesis using a novel RNA based clonal and molecular approaches
Amount £300,000 (GBP)
Funding ID 213731/Z/18/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2019 
End 05/2023
 
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 Collaboration on AI for bioscience with the Alan Turing Institute 
Organisation Alan Turing Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Our team have identified areas of Bioscience research that can be investigates using AI techniques. We have hired fellows supported by this award that will have 12 months training in AI from our collaborative partner
Collaborator Contribution Advice and mentorship in the application of AO
Impact This is a very new award
Start Year 2021
 
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
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 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
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 Sugarcane Research Center
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 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 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 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 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
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 The Carpentries 
Organisation The Carpentries
Country United States 
Sector Charity/Non Profit 
PI Contribution With five members of EI faculty trained as Carpentries trainers, we host at least one Software Carpentry and one Data Carpentry workshop per year. The trainers are able to contribute to the community-developed training materials, which are hosted on the Carpentries website.
Collaborator Contribution The Carpentries website hosts the community-developed training materials, which are under development and improvement based on feedback from users. The Carpentries are also able to list upcoming courses on their website, as well as provide templates for the workshop programme pages and, as part of this, generates links to standardised pre and post-workshop surveys to which we are provided reports.
Impact Software Carpentry and Data Carpentry workshops held and offered to the community, developing researcher skills in data management and programming.
Start Year 2013
 
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 Genomics and Museum collections: Using NGS data from degraded material for conservation, evolutionary and ecological research 
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 Natural history collections are an invaluable source of information. Museum specimens provide a window to the past, and collections of specimens provide a record that can span temporal and geographical ranges of both within and between species diversity. Recent advances in Next-Generation Sequencing (NGS) technologies have provided a means to generate genome-wide datasets from degraded DNA samples. With the purpose of highlight how these advances are transforming the way we can analyse the genomics of museum collections, a one-day seminar was delivered in three Colombian cities (Bogota, Cali and Medellin) on separate dates.

A total of five speakers were invited (including three members of GROW Colombia), and all of them are experts in applying NGS technologies to analyse genome-wide DNA from degraded samples. Their speciality fields include plant, insect and mammalian paleogenomics as well as human DNA. They outlined the methods involved and discussed a range of questions that can be addressed using ancient DNA datasets, including fields like evolution, ecology and conservation biology. In Bogota (day 1) we also had a discussion panel including local researchers, aiming to contextualise the discussed topics and the opportunities and challenges of this kind of research in Colombia.

The talks were attended by professors, researchers, postgraduate and undergraduate students, museum curators and staff, and some other members of the academic community. They had the opportunity to interact with the speakers and to share ideas and information.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/genomics-and-museum-collections
 
Description 'Strengths and potential of microbial ecology in Colombia' in Bogota 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact 25 participants, more than 50% were principal investigators, from 9 public and private organizations around Colombia attended this workshop in Bogota. The events began with presentations from principal investigators to generate context and inspire future collaborations between institutions. At the end of the day the group participated from a SWOT (strengths, weaknesses, opportunities and threats) analysis in which there was a discussion on the future of microbial ecology in Colombia. A delegate package with a CV summary, research abstract and contact details of attendants was handed to each person to encourage future communication and events.
Year(s) Of Engagement Activity 2019
 
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 5 ways EI is improving global food security 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact 5 ways EI is improving global food security
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/articles/5-ways-earlham-institute-improving-global-food-security
 
Description 600k machine learning collaboration to supercharge data driven science 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact 600k machine learning collaboration to supercharge data driven science
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/newsroom/%C2%A3600k-machine-learning-collaboration-supercharge-data-driven...
 
Description A PhD, is it worth it? Just ask our students 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact A PhD, is it worth it? Just ask our students
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/articles/phd-it-worth-it-just-ask-our-students
 
Description AI 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 Advanced Python for Biologists 
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 Calling upon the expertise of full-time, freelance trainer - Martin Jones (Creator of Python for Biologists) - we were able to host a 5-day workshop teaching advanced Python skills to researchers with a biology background and with a basic knowledge of Python prior to attending. Delegates were able to learn about data structures, explore different approaches (object-oriented, functional) to programming through to benchmarking and unit testing code. Attendees were predominantly from the UK although a small proportion were from overseas. Over 70% of attendees were PostDoctoral researchers demonstrating the advanced nature of the course. 100% of respondents rated the trainer and the overall training event as Very Good or Excellent, and 100% said that they would recommend the course.
Year(s) Of Engagement Activity 2019
URL https://pythonforbiologists.com/advanced-python-for-biologists
 
Description Advanced Python for Biologists 05-16 October 2020 (Virtual) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Calling upon the expertise of full-time, freelance trainer - Martin Jones (Creator of Python for Biologists) - we were able to convert this 5-day face-to-face workshop to an online-only course spread over ten half-day sessions (morning input and hands on exercises) with the afternoons free to concentrated on other duties or further extend skills with the trainer available to answer questions via Slack. Teaching advanced Python skills to researchers with a biology background a basic knowledge of Python prior to attending was essential.

Sessions included: Data Structures; Profiling and Benchmarking; Classes and Objects; Object-oriented Programme design; Functional Programming in Python; Iterators, Comprehensions and Generators; Exception Handling; and Unit Testing.

Attendees were predominantly from the UK(<90%) and in PostDocotral positions (60%) demonstrating the more advanced nature of this course. 100% of delegates: rated the training overall as very good or excellent; the trainer as excellent; and would recommend the course.
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/advanced-python-biologists-2020
 
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 Big Data Science Training for EDESIA Year 1 Cohort 27-28 January 2021 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact An introductory workshop for the first cohort of EDESIA PhD students. This workshop was spread over two days (10:00-15:00), delivered via Zoom and covered the following topics: Research Data Life Cycle; an Introduction to Galaxy including Hands-on session; an Introduction to machine learning; Data Brokering and FAIR data (including demonstration of COPO (Collaborative OPen Omics platform); and an Introduction to Network Biology using Cytoscape, including hands-on exercises.

All presentations and hands-on sessions were recorded and shared with the students after the workshop had concluded.
Year(s) Of Engagement Activity 2021
 
Description Big Data Science Workshop for DTP students 21 January 2020 (Virtual) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact As part of the Norwich DTP Year 1 Cohort of students (~40) workshop in Big Data Science, breakout discussion groups were facilitated to allow students to share with their peers their awareness of online training resources providing valuable bioinformatics skills. Further presentations were given by training leads at each of John Innes Centre, University of East Anglia and Earlham Institute to provide signposting to further, free-to-access training materials online, which will be valuable to their skills development over the course of their PhDs.
Year(s) Of Engagement Activity 2021
 
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 COPO Workshop 20 March 2019 
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 Offering hands-on opportunities for researchers to bring along their dataset(s) to experience submitting and retrieval of data using the COPO platform. This was primarily targeted towards plant researchers, but all researchers across the NRP who were intending to submit data to a repository were able to access this workshop.

The majority of the 16 attendees were PostDoctoral researchers and PIs.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/copo-workshop-2019
 
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 1-4 March 2021 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This workshop is designed to teach fundamental data skills and included sessions on: data organisation in spreadsheets, data cleaning with OpenRefine, SQL for data management, R for data analysis and visualisation. This workshop was converted from a 2-day face-to-face event into four, shorter days (10:00-15:00), which are better suited for virtual learning and maintaining concentration.

Around 50% of attendees were PhD students, in line with our target audience and 100% of those providing feedback rated the workshop overall as 'Very Good' or 'Excellent', rated the trainers as 'Very Good' or 'Excellent' and would recommend the workshop.
Year(s) Of Engagement Activity 2021
URL https://www.earlham.ac.uk/data-carpentry-virtual-workshop-2021
 
Description Data Carpentry 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 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 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 Doing Science with Colombia 2019 - Natural History Museum 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact In 2017, an event called Doing Science with Colombia was held at the NHM, as a way to raise awareness of the important milestones that the bilateral science and innovation relationship between the UK and Colombia was achieving. In October 2019, a second edition of this event took place in the same institution. The event programme was focused on issues such as the current state of scientific collaboration, the sustainability of research and innovation projects and the future of bilateral relationship from different perspectives. It also provided space for networking with a range of organisations involved in this bilateral collaboration.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/doing-science-colombia-2019
 
Description EI Innovate 17-19 November 2020 (Virtual) 
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 In its second year, EI Innovate aimed to explore opportunities for collaboration and innovation with external organisations. This year the event was converted to an online only format, spread across three days, with each day focussing on one of the three themes:

1) Disease identification and monitoring - how genomics and bioinformatics are used for disease identification and monitoring, from COVID-19, to AMR to agricultural pathogens.
2) Finding a needle in a haystack - Identifying specific targets in health and disease with long read RNA and single cell sequencing.
3) Accelerating plant breeding with next generation genetics, genomics and epigenetics.

Sharing examples of existing collaborations, this event was a chance to explore new opportunities. Each day was structured with two talks, one from EI faculty and one from an external collaborator, a Q&A panel discussion, facilitated break out discussions and then slots to arrange one-to-one meetings with other participants in the afternoon (event times 09:30-15:30), arranged using the software Meeting Mojo.
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/ei-innovate-2020
 
Description EI Innovate: 13 November 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 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 EI Innovate: a platform for collaboration and new ideas 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact EI Innovate: a platform for collaboration and new ideas
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/articles/ei-innovate-platform-collaboration-and-new-ideas
 
Description 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 GROW Annual Meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The purpose of the GROW Colombia Annual Meeting was for project researchers to share research advances and plan for the upcoming years. The meeting help to strengthen the project's research groups and build capacity among researchers.
Year(s) Of Engagement Activity 2019
URL https://growcolombia.org/capacity-building/
 
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 Inside EI - Open Day 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 One day in May 2019 EI opened its doors to the public and schools from the region. Offering an overview of the Tree of Life with the branches of our tree culminating in posters displaying colourful imagery of our research, visitors were able to talk to researchers about their projects and why the research is important. There were hands on activities providing insight into de novo genome assembly, nanopore sequencing technology, synthetic biology and high performance/cloud computing.

In addition to the activities, there were talks and tours of the laboratories, which were fully subscribed.

We were joined by schools from across the region in the morning, and opened our doors to the general public for the afternoon, with a total of over 400 visitors, media coverage (TV and radio) reaching an estimated 500+. The feedback was incredibly positive and we achieved an unbelievably successful set of outcomes. Comparison of pre- and post Open Day attitudes demonstrated that: Participants reported very high increases in understanding of a range of topics, while overwhelmingly agreed that research at EI should be funded by the government. The majority of people left with an increased appreciation of the importance of bioinformatics, genomics, etc. for their every day life, the environment, and more.
Year(s) Of Engagement Activity 2019
URL https://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 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 Introduction to Python for Biologists 08-19 June 2020 (Virtual) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Calling upon the expertise of full-time, freelance trainer - Martin Jones (Creator of Python for Biologists) this course is designed for complete beginners with no prior programming experience. This training course provided theory and hands on experience with basic programming concepts in Python using biological/bioinformatics examples. Topics included: Working with files; lists and loops; conditions; writing functions; regular expressions and dictionaries.

This was the first virtual training course offered by EI and as such includes the use of new technologies and set up for the training team offering remote hosting and support. We canvassed opinions of registrants for the course to determine the best way to deliver the programme virtually. Typically, as a face-to-face course, this would run 09:00-17:00 Monday to Friday, however following our poll, we offered this as ten half day sessions from 09:00-12:30. We hosted the course using the online platform Zoom, with all sessions being recorded. In addition we offered the use of Slack (valuable for sharing code as it can handle the formatting) with dedicated channels and the ability to directly message the trainer. The trainer agreed to be on-hand to answer questions throughout the hands on exercises and during the afternoons when there was no live delivery. Across the two weeks the Slack channel captured a total of ~1000 messages with over 90% of these being direct messages to the trainer.

Furthermore, this was the first time that the trainer had ever delivered training online. As a consequence of the positive experience and support received, the trainer has gone on to teach in various other institutions and has insisted on using precisely the same set up as offered by EI as it worked so seamlessly. He reported feeling confident in converting his lessons to online and thanked the training team at EI for the support to enable him to make this jump.

Attendees were predominantly from the UK although a small proportion (~20%) were from overseas. Over one-third of attendees were PostDoctoral researchers and a further third were PhD students with further attendees across the range of career levels, demonstrating the applicability of developing skills in Python. 100% of respondents rated the trainer and the overall training event as Very Good or Excellent, and 100% said that they would recommend the course.
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/introduction-python-biologists-2020
 
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 Metagenomics: Data Analysis and Interpretation 16-19 September 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 Attended by approximately equal numbers of PhD students to PostDoctoral and Academic researchers (combined), this course provided an overview of metagenomic data analysis, including ample time spent on hands-on activities using example data sets and relevant tools and resources, taking delegates through to production of publication-ready figures. As a newly redeveloped course with new teaching staff, this course still received positive feedback with over 75% recommendation of the course and 70% rating trainers as Very Good or Excellent. There are some lessons learned and the training team are reviewing the course programme and structure, including leadership of the course by an individual research group to address the areas for improvement. Attendees were predominantly from the UK, with some from Europe and one from South America.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/metagenomics-data-analysis-and-interpretation
 
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 News Article (EI website) - Python for biologists: the code of bioinformatics 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The article provided an insight into the importance of Python code for bioinformatics, containing quotes from interviews with the trainer and the delegates, and highlights that, despite the growing need for biologists to be able to code, most Postgraduate students and early career PostDocs are having to learn on the job. This was a very popular article from EI's stories of 2019, with over 1000 views.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/articles/python-biologists-code-bioinformatics
 
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 September 2020 (Virtual) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact In place of our annual single-cell symposium we opted to develop a new programme of speakers for a virtual mini-symposium, hosted via Zoom, to keep our community engaged.

Single-cell technologies are now widely used but continue to develop rapidly - in this mini-symposium we focussed on the "next generation" of tools to study living systems at cellular resolution, including: Long-read/Isoform sequencing; Multi-omic analysis; Proteomics; Spatial transcriptomics.

Year on year, our annual symposium has been a great platform for discussion between researchers in diverse fields (microbial, plant, biomedical) focussing on the applications of new technologies.

We made this event free to register in order to ascertain the interest in the community and to monitor attendance rates. We were delighted with 244 registrations and, despite the free registration we observed a 60% turn-out rate. This is in comparison to the typical 70-80 attendees we have for the face-to-face version of this symposium. In addition, the attendees, who would typically predominantly be from Norwich Research Park for face-to-face events, were from a much wider geographic range with 25% from Norwich Research Park, one-third National and almost 45% International (from 25 countries outside of the UK), spreading awareness of EI and our Single Cell expertise.
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/virtual-single-cell-symposium-future-single-cell-analysis
 
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 16-17 October 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 With approximately 70 attendees, the third Norwich Single-Cell Symposium featured speakers covering topics as diverse and neuronal development, embryonic reprogramming in humans, tapetal development in plants and splicing variation in hematopoietic stem cells, as well as a keynote lecture from Professor Sir Mel Greaves working in cancer. Delegates and sponsors enjoyed the variety of topics and opportunities for engagement through the lunch time exhibition, poster and networking sessions. Attendees were predominantly Postdoctoral researchers and industry representatives (including attendees who did not sponsor), with several group leaders and PhD students also in attendance. The training team collected live feedback using a powerpoint-based software, which proved useful in determining overall opinions (over half of the attendees provided feedback using their mobile devices). This feedback indicated a desire to repeat the symposium in 12 months, with approximately 90% of respondents in agreement with the length of the symposium, plus an overall rating of of keynote speaker and invited speakers as 4.7 and 4.5 out of 5.0, respectively, plus networking with delegates and engaging with sponsors as 4.2 and 3.9, respectively.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/single-cell-symposium-2019
 
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 Nuffield Research Experience Placements Summer 2020 (Virtual) 
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 Schools
Results and Impact Nuffield reported a dramatic loss of placements due to the COVID-19 pandemic and the need to move these placements online. Earlham Institute were able to host 6 students, 5 to completion, through a four week research programme. Students worked in pairs, with each pair being assigned a different supervisor and organism to study, however, the cohort was combined in twice-weekly meetings to go over the tools and resources that were relevant to each project on a weekly basis so that they could see the data analysis approaches were similar across the different projects, and in a final presentation to all of the project supervisors and the training team at the end of their placement.

The presentations at completion of the placements demonstrated just how much the students had each learned and achieved in such a short time, despite the difficulties in having to host these placements entirely remotely.
Year(s) Of Engagement Activity 2020
 
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 - 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 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 Science and development media engagement training planing 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Engaged with Cabi (SciDev.Net) and Loughborough University to deliver a Science and Media Engament training with the purpose of bring together and enhancing the scientific communication skills of scientists and journalists.
Year(s) Of Engagement Activity 2019
 
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 Signalling Networks: From Data to Modelling 1-5 April 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 Providing an introductory overview of tools and resources to investigate signalling pathways and networks, delegates received hands-on experience in how to reconstruct, analyse and visualise networks, plus how to develop models of signalling events. The course was well received with 100% recommendation of the course from feedback respondents and 100% rating the trainers as Very Good or Excellent.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/signalling-networks-data-modelling
 
Description Single-Cell RNAseq 19-22 October 2020 (Virtual) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Aimed at researchers who were in the experimental planning stages of a Single-Cell genomics project, the course required no previous experience in bioinformatics approaches with the najority of hands-on analysis delivered through the web-based, user-friendly interface - Galaxy.

The course provided an introduction to single-cell genomics for researchers who are new to bioinformatics and covered: assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variations at the single-cell level. It consisted of a mixture of conceptual and methodological lectures and hands-on sessions, including best practices and tips as learned first-hand by Earlham Institute's faculty.

The course was converted from a 5-day course that was previously split 3 days of lab work and 2 days of bioinformatics into a bioinformatics only course, spread over 4, shorter days (10:00-15:00) and involved a number of new teaching faculty.

The majority of attendees were national and outside of the Norwich Research park, and from academia (88%). They rated the training overall as very good or excellent (100%) and the trainers very good or excellent (100%), with 100% saying that they would recommend the course.

Despite the virtual nature of the course, there were plenty of opportunities to to discuss matters with both trainers and discuss with other delegates and there were many requests during our introductory delegate 'flash' presentations where individuals wished to reach out to each other for longer-term collaborations and/or to discuss new techniques/approaches that were presented.
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/single-cell-rnaseq-2020
 
Description 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 18-21 January 2021 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This workshop is designed to help scientists become more productive by teaching them basic computing skills like program design, version control, testing and task automation.

Following discussions with trainers and review of the feedback from the first online iteration of this workshop in June 2020, the programme was redeveloped to run over the course of four, shorter days (10:00-15:00). This allowed for the short tutorials to continue as before, but with more time allowed for the hands-on practical exercises with which they alternated.

Lessons included: using the shell to do more in less time; automating tasks and pipelines; writing structured programs; using Git to manage and share information; how (and how much) to test programs. In particular, there was more time to spend on the breakout groups for the Git collaboration lessons, and for Python tutorials.

Attendees were predominantly UK residents (88%) and all were from academic institutions, with the majority from our local community across the Norwich Research Park (94%). 100% of delegates rated the course as very good or excellent and agreed or strongly agreed that trainers were knowledgeable and approachable.
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/software-carpentry-virtual-workshop-2021
 
Description Software Carpentry 30 June-02 July 2020 (Virtual) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This workshop is designed to help scientists become more productive by teaching them basic computing skills like program design, version control, testing and task automation. In this three-day bootcamp, short tutorials will alternate with hands-on practical exercises. Lessons included: using the shell to do more in less time; automating tasks and pipelines; writing structured programs; using Git to manage and share information; how (and how much) to test programs.

Usually this syllabus is taught over two days, for this online only iteration we opted to run this as a three-day programme with shorter days (10:00-15:00).

Attendees were all UK residents and from academic institutions, with the majority from our local community across the Norwich Research Park. 100% of delegates rated the course as very good or excellent and agreed or strongly agreed that trainers were knowledgeable and approachable.
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/software-carpentry-2020
 
Description Software Carpentry Workshop - 10-11 October 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact The intention of this workshop is to help scientists become more efficient in data analysis through teaching basic computing skills such as programme design, version control, testing and task automation. The two-day workshop alternates short tutorials with hands-on practical exercises to reinforce concepts and best practice. This course is aimed at researchers in the life science and computational science disciplines and across all research stages. Delegates learned how to: use the shell to do more in less time, automate tasks and pipelines, write structured programmes, using Git to manage and share information, plus how and to what extent to test programmes. 100% of delegates rated the event overall as very good to excellent, 100% rated the trainers as very good to excellent and 100% said that they would recommend the course.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/software-carpentry-workshop-october-2017
 
Description Software Carpentry Workshop - 26-27 April 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact The intention of this workshop is to help scientists become more efficient in data analysis through teaching basic computing skills such as programme design, version control, testing and task automation. The two-day workshop alternates short tutorials with hands-on practical exercises to reinforce concepts and best practice. This course is aimed at researchers in the life science and computational science disciplines and across all research stages. Delegates learned how to: use the shell to do more in less time, automate tasks and pipelines, write structured programmes, using Git to manage and share information, plus how and to what extent to test programmes. Almost 50% of delegates in attendance were PhD students, in accordance with our target audience. Around 90% of delegates rated the training overall as very good top excellent, and 100% stated that they would recommend the course to others.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/software-carpentry-workshop-2017
 
Description Software carpentry workshop 21-22 January 2020 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact With an overview of basic program design, version control, testing and automation, this workshop is designed to provide delegates with little or no prior programming experience and to teach how to improve efficiency using the command line, automation of tasks and how to manage and share your own code and information using Git. Aimed at early career researchers it is no surprise that almost all of the attendees were undergraduate students, postgraduate students or Postdoctoral scientists and almost 75% of these were from the local area (Norwich Research Park). Respondents to feedback surveys indicated that the trainers were knowledgeable and easy to interact with, with 100% rating as in 'Agree' or 'Strongly Agree'
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/software-carpentry-2020
 
Description 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 Successful communications 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 This virtual traininig course amined at providing tools and techniques to develop communication skills so that the participants could create and leave a positive lasting impression. In total 12 participants from the GROW project and BRODGE network attended the training. Some of the topics that were addressed were: 1) assertiveness, 2) passive, assertive and aggressive behaviours, 3) importance of non-verbal communication, 4)inner thinking affects the way we communicate, 5) effective listening, 6) effective questioning, 7) constructive feedback, 8) dealing with challenging communication situations and 9) developing strategies to improve written communication. As an output GROW and BRIDGE iindividual memebers have developed action plans to take back to the workplace and start to implement.
Year(s) Of Engagement Activity 2020
 
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 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 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 Time management 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 This training course on Time manegement involved 12 participats from the GROW project and BRIDGE network, including postdocs, Co-Is, research assistants and the management team. This training course aimed at helping participants to develop their skills in time management to achieve more effective results in less time. This was a practical course that introduced proven techniques for mastering time. The approach involved discussion to introduce the concepts of time management and practical exercises and syndicate work to develop personal skills. As output partcioants have reported to use the tools to imporve their performance on GROW activities.
Year(s) Of Engagement Activity 2020
 
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 Training workshop. Methods and tools for biodiversity and ecosystems services valuation and management. The invisible numbers behind ecosystem services. 
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 objective was to provide the basic knowledge to evaluate and value the ecosystem services and Colombian biodiversity, which are the objectives of different laws and policies. The workshop gave knowledge and experience on: • practical tools that allow to increase knowledge about the economic and social value of nature, and that allow to communicate these values.
• Relate to methodologies that allow the implementation of the ecosystem approach for decision making.
• Construction of scenarios that support the evaluation of different policies
• Incorporation of ecosystems and their services within the formulation and evaluation of projects, programs and policies, to improve decision making.
• Identify the opportunities and risks that exist from the dependence of some businesses on ecosystems and their services.
• Be able to apply these tools as part of the preparation of business plans.
• Apply the methodologies learned for the evaluation of impacts and strategic planning.
• Identify and evaluate trade-offs in ecosystem services by implementing different projects or policies (changes in land use).
• Know the application case of the presented methods.
In total 40 participants from public, private and NGO's were trained on economic valuation tools.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/valuation-biodiversity-ecosystems
 
Description UK CBCB: an ELIXIR for cross-disciplinary collaboration in bioinformatics 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact UK CBCB: an ELIXIR for cross-disciplinary collaboration in bioinformatics
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/articles/uk-cbcb-elixir-cross-disciplinary-collaboration-bioinformatics
 
Description UK-Conference of Bioinformatics and Computational Biology (UK-CBCB) 29-30 September 2020 (Virtual) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This was the inaugural UK Conference of Bioinformatics and Computational Biology (UK-CBCB), organised in conjunction with ELIXIR -UK. The conference was designed to bring together biologists, bioinformaticians, computer scientists, software engineers and data scientists across the life sciences to share innovations, applications and best practice in their fields. Applicable to bioinformatics researchers working on core services or in research teams as well as computer scientists or bioinformaticians developing tools or maintaining data resources.

Converting this to an online format, we reduced the number of presentations, namely by including only invited speakers for this iteration, and ran this as a shorter two-day programme of talks.

In contrast to the Single Cell Symposium, we opted here for a nominal registration fee of £10 and this saw our attendance rates from those registered reach 90%.

Sessions included: Data Management; Metagenomics and Microbial Genomics; Computational Proteomics and Metabolomics; Bridging Genotype to Phenotype; Structutral Bioinformatics; and Single Cell Genomics. These sessions saw an even spread of attendees with similar numbers across all sessions.

Three themes emerged from the conference:
Theme 1: FAIR data
Theme 2: COVID-19 response
Theme 3: AI and Machine Learning

Attendees were predominantly national (non-Norwich Research Park) (60%) with some international (~20%) and from academia (88%) with the remainder (12%) from industry.
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/uk-conference-bioinformatics-and-computational-biology-2020
 
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 Website Article: An accessible single-cell RNA seq bioinformatics training suite using Galaxy 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Detailed the development of a workflow and related training materials via the user-friendly Galaxy interface to support biologists with no prior experience in command line. This was used as part of the training course in Single-Cell RNAseq bioinformatics earlier in the year. The workflow remains freely accessible and demonstrates the longer-term impact through continued availability of our training materials and courses developed through NC4.
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/articles/accessible-single-cell-rna-sequencing-bioinformatics-training-usi...
 
Description Website Article: Is this the future of science conferences? 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Outlining the experience of both the training team and faculty members in the conversion to online, virtual training events, conferences and similar. Detailing the positives of going virtual (reducing carbon footprint, widening participation, shorter and more focussed programmes tailored to a more realistic attention span, inclusive networking, availability of recordings for playback and enhanced recollection) versus the down-sides (presenting to the void, ability to become distracted, lacking the social side and food, more time sat in front of a screen, technical issues)
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/articles/future-science-conferences-if-we-are-serious-about-climate-action...
 
Description Website article on Inside EI Open Day 
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 covering the EI Open Day 2019.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/inside-ei-public-engagement-science-impact
 
Description Website article: Eye, Robot (30/09/2019) 
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 Article about robots and imaging.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/articles/eye-robot
 
Description Website article: We're ten years old; 21/09/2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Website article highlighting contributions of EI, including work delivered through the NC4. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/articles/ten-years-leading-decoding-complex-genomes
 
Description Website article: Why do a Year in Industry? 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact Web article outlining the experience of two year ins industry students undertaking a placement between September 2019 and August 2020. Focus on the research and transferrable skills, in particular the benefits of bioinformatics, that they were able to develop through their placements and how this is impacting the next steps in their careers. Demonstrates the supportive and engaging environment offered whilst learning valuable skills at EI.
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/articles/why-do-year-industry
 
Description Why statistics is important in a world of big data 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Why statistics is important in a world of big data
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/articles/why-statistics-important-world-big-data
 
Description Year in Industry 2019/20 
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.
Year(s) Of Engagement Activity 2011,2012,2013,2015,2016,2018
URL http://www.earlham.ac.uk/year-industry
 
Description Year in Industry 2020/21 
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 started their placements virtually, undertaking a short rotation period within the first three weeks at the institute. During this time students were able to join faculty group weekly lab meetings, including an overview by the group leader to understand the groups' research interests and how they are connected, plus to listen to the individual providing their project update that week, and discuss potential projects on offer. They were also able to spend time with a Genomics Pipelines team leader going through protocols and other relevant introductory materials, plus guided discussions to review this information. Additionally they undertook various science communication tasks with the Communications team, sculpting news articles based on EI's research due for imminent publication, plus a presentation on the same subject intended for a lay audience.

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(s). The students are carrying out their research projects until approximately the end of June, when they will then concentrate on their project dissertation. One student is entirely focussed on bioinformatics work and the other has a combination of lab work to implement a new protocol for automation in conjunction with Genomics Pipelines whilst also carrying out the data analysis.
Year(s) Of Engagement Activity 2011,2012,2013,2014,2016,2018,2019
URL https://www.earlham.ac.uk/year-industry
 
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 2011,2012,2013,2015,2016,2018
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