Future-Proofing the Sustainability of the MRC High Throughput Sequencing Hub in Scotland

Lead Research Organisation: University of Edinburgh
Department Name: Sch of Biological Sciences

Abstract

The GenePool is the leading next generation genomics facility in Scotland, and one of the largest academic facilities in the UK. The GenePool is funded by the MRC as a High Throughput Sequencing Hub, with specific remit to deliver collaborative access to next generation sequencing and informatics across the MRC science area. This application is for renewal for 24 months of the initial 3-year funding, to bed in the advances made in setting up the MRC Hub, and to move the facility to full cost-recovery. We will focus on delivering first-rate data and analysis on cutting edge science, to a wide range of collaborators both new and established, using the transformative tools of Illumina sequencing and high-throughput computing. We will build upon our MRC Hub and "spokes" model, fostering bioinformatics training and next generation genomics understanding across our target area.
We request core support for promotional and outreach activities, including a new bioinformatics staff member jointly appointed between the Liverpool and Edinburgh MRC Hubs who will organise and deliver advanced training in next generation genomics to PhD students and postdoctoral researchers. We will deliver proactive Next Generation Sequencing Clinics in academic research institutes and departments across Scotland. We will continue to support the Next Generation Bioinformatics User Group meetings, including inviting international speakers and delivering 2-day research workshops on selected technologies. The MRC network of 'spokes' bioinformaticians in institutions across Scotland will be expanded. We will produce promotional materials for distribution to potential collaborators and grant applicants, and use our web site and social media portals to promote the MRC HTS Hub approach to next generation genomics.
We will develop standard operating procedures for new techniques, and to explicitly and rigorously cross-check manufacturers' claims. We have good relationships with the major technology and reagent suppliers and will use these to negotiate early access to new products. We will perform in-house trials of new kits, in direct comparison to existing protocols, and make the results known to our collaborator base. We will work with companies and collaborators to bed in and develop new approaches to the generation of and analysis of next generation sequencing data.
The next generation sequencing revolution is based on two principles: transformative technologies and skilled staff. We have a mature charging model that includes elements of instrument depreciation and staff time, and generate a working surplus (for investment in the facility) each year. We have already transitioned several staff from core grant to cost recovery support. In the period of 24 months of the renewal, we will transition three further core MRC staff posts to full recovery (one bioinformatician and two high-level research technologists). Two new posts will be created to ensure best service to our collaborators, particularly given the vastly increased throughput of the Illumina HiSeq platform. A laboratory manager will ensure fitness-for-purpose of our LIMS installation, manage the wide portfolio of instrumentation (including robotics, qPCR, analytical platforms and other ancillary instrumentation), and provide oversight of the full laboratory workflow process. A business manager will administer the large number of active projects within the facility, in particular dealing with the financial side, managing the LIMS, and keeping collaborators up-to-date with project progress. Both of these new posts are planned to transition rapidly to full cost recovery in two years. Initiation of these posts will free the GenePool Scientific manager (Dr Karim Gharbi) and the Director (Prof Mark Blaxter) to focus on speeding the transformation of researchers' ideas into viable projects, well-analysed studies and high-hitting publications.

Technical Summary

During the first three years of the MRC High Throughput Sequencing Hubs programme, the GenePool invested in training highly-skilled wet-lab and bioinformatics teams and installing leading high-throughput technologies to deliver bespoke genomics collaborations across our science and geographical area. We propose further investment in personnel and in outreach and training to consolidate the Hub at the core of nextgen genomics in our area, to build nextgen genomics analytic capacity across Scotland and the UK, and to transition to a fully cost-recovered financial model.
We will develop a portfolio of training and outreach activities, including a new training post delivering master classes and summer schools in next gen genomics, the very successful Next Generation Bioinformatics User Group meetings and MRC 'spokes' bioinformaticians training. We will deliver proactive NextGen Clinics across Scotland, allowing prospective collaborators to discuss ideas directly with GenePool staff. The training bioinformatics post will be held jointly with our sister MRC Hub in Liverpool, linking the two facilities. We will produce promotional materials, and distribute these, including via our web and social media presences.
We will beta-test and develop standard operating procedures for new applications, including testing of new commercial kits and reagents, and working with collaborators to bed in new ways of using the technology.
We will enhance our collaborators' experience by improving the operation of the facility, appointing a laboratory manager and a business manager. This will streamline the processing of user data, freeing the scientific manager and director to focus on speeding the transformation of researchers' ideas into viable projects, well analysed studies and high-impact publications. At the end of the two year renewal period, the GenePool MRC HTS Hub will be fully transitioned to cost recovery on staff, reagents and equipment renewal.

Planned Impact

Investment by MRC in the GenePool will have a wide and significant range of impacts on academic research, biotechnological and healthcare industries, and clinical research, leading to impacts on clinical practice and policy. We will also have impacts on public understanding of science, and genomics in particular, and individual impact as we develop the skills of highly-motivated young researchers.
The direct impacts of the investment will be in enabling the collaborating research community to access and exploit next generation genomics. By leveraging investments by MRC, NERC, SULSA, the Darwin Trust and the University of Edinburgh the GenePool can deliver cutting edge science across the spectrum of genomic biology.
Impacts will be both institutional and individual. For institutions, access to the GenePool means that sorely-restricted funds can be effectively invested in complementary activities (other high-throughput analytical technologies, or staff and expertise in bioinformatics, for example). Collaborating institutions can rely on GenePool staying abreast of new developments and supporting their research portfolios in a directed and effective manner. For individual researchers, from senior principal investigators to postdoctoral students, access to the GenePool means they can focus on ground breaking biological and clinical research, leaving the details (and heavy lifting) of the genomics data generation and analysis to the Facility.
We have a record in supporting all researchers, no matter what the stage of their careers, and in particular in assisting genomics novices in understanding the platforms and the data, developing research ideas and being successful in grant and fellowship applications. These successes in turn mean that the research institutions and individuals are more successful in attracting additional investment and funding, and progressing their careers. Our proposed programme of master classes and summer schools will allow individuals at early stages in their careers to learn skills in next generation genomics, and prepare themselves for effective future research careers.
On our staff we have a cadre of young scientists who are, as is necessary in this fast moving field, learning on the job. The skills they are developing (in project management and collaborative science as well as in next generation sequencing or bioinformatics) will stand them in good stead in developing their research careers.
Our collaborative user base extends from university, to NHS clinical research and independent research institute staff. While most our collaborators are based in Scotland, there is a significant group from the remainder of the UK, and some from Europe and other countries. These include multinational collaborations investigating human disease (especially parasitic disease) and projects addressing pressing issues of food security in developing and emerging economies. On the commercial side, we collaborate closely in an academic setting with several research groupings, delivering academic genomics service to further specific commercial goals.
Collaborative research with clinical researchers may lead to changes in clinical practice and policy, either at the level of surveillance and screening (the development of tests for genetic or epigenetic changes associated with a particular disease) or in treatment (when a potentially causative genomic signature is identified and a possible treatment path developed). We will work closely with researchers in developing directed assays (such as targeted resequencing platforms, including for smaller-throughput technologies such as IonTorrent) that can be deployed in a clinical situation.
We will promote the work of the GenePool, and next generation genomics in general, to the wider scientific and general public through our website, through directed promotional materials and through presentations at open days and other forums within the University and elsewhere.

Publications

10 25 50
 
Title The genome of Caenorhabditis elegans 
Description The work is the complete genome of C. elegans printed in hardbound volumes, with each chromosome occupying two volumes, 12 volumes in all. The covers of the volumes tesselate to form a picture of the nematode, and the spinse align to make a picture of the nematode. The mitochondrial genome is supplied as an "erratum sheet". 
Type Of Art Artwork 
Year Produced 2014 
Impact The work has been on long term loan and is permanently exhibited in the Summerhall Arts Complex, Edinburgh, as part of a permanent exhibition curated by ASCUS. 
 
Title Transmissions exhibition 
Description The Blaxter lab collaborated closely wth artists-in-residence (see http://www.ascus.org.uk/ciie-micro-residency-artists-announced/) in the Centre for immunity Infection and Evolution to inspire and be part of the final exhibition "Transmissions". Mark Blaxter appears in the film work produced by Anne Milne, and the work of the lab inspired Jo hodges and Robbie Coleman to produce a piece dedicated to the lab. 
Type Of Art Artwork 
Year Produced 2014 
Impact 'Transmissions' was showcased to the general public within a group exhibition 'Parallel Perspectives' in Summerhall as part of the Edinburgh International Science Festival 2015 art programme, How The Light Gets In . This exhibition of work susequently travelled LifeSpace, Dundee, returning to Edinburgh to showcase at the Tent Gallery, Edinburgh College of Art. 
URL http://www.ascus.org.uk/ciie-micro-residency-2/
 
Description BBSRC Project Grant (Genome Databasing)
Amount £671,655 (GBP)
Funding ID BB/K020161/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2013 
End 11/2016
 
Description BBSRC Project Grant (Ruff)
Amount £176,281 (GBP)
Funding ID Bb/J018791/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2013 
End 09/2015
 
Description BBSRC project grant (Striga)
Amount £43,647 (GBP)
Funding ID BB/J011703/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2013 
End 12/2015
 
Description BBSRC/DFID Project Grant (Ash Dieback)
Amount £162,746 (GBP)
Funding ID NORNEX 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2014 
End 04/2015
 
Description European Commission FP6 (Filariasis)
Amount £120,500 (GBP)
Organisation Sixth Framework Programme (FP6) 
Sector Public
Country European Union (EU)
Start 08/2010 
End 08/2013
 
Description NERC Project grant (Genome evolution)
Amount £469,000 (GBP)
Funding ID NE/J011355/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 09/2012 
End 09/2015
 
Description SynTax
Amount £26,587 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 05/2012 
End 05/2013
 
Description SynTax
Amount £19,775 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 05/2012 
End 05/2013
 
Description TSB (Atlantic salmon SNP chip)
Amount £323,669 (GBP)
Funding ID 100965 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 07/2011 
End 07/2014
 
Description Wellcome Trust (RNASeq)
Amount £169,000 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2009 
End 08/2012
 
Title 2012 Installation of MiSeq platforms 
Description Following the successful installation and two Illumina HiSeq platforms in 2010, The GenePool installed two Illumina MiSeq instruments in 2012 to support small scale, quick turnaround projects. 
Type Of Material Improvements to research infrastructure 
Year Produced 2012 
Provided To Others? Yes  
Impact The MiSeq installation has been an immediate success with many R&D projects completed in weeks rather than months, and an expanding user base taking advantage of the quick turnaround time, high quality data. 
URL http://genomics.ed.ac.uk
 
Title 2013 Computational infrastructure upgrades 
Description The facility now runs a secure, powerful computer cluster running SGE, with several hundred cores and 2 terabytes (Tb) of RAM. The University of Edinburgh's HECTOR supercomputer and the Edinburgh Compute and Data Facilities (ECDF), a parallel compute cluster with over 3000 cores and several Tb of RAM, provide additional infrastructure. We have an advanced data store (with many hundreds of Tb of capacity) based on highly resilient technology to assure availability and security of data. 
Type Of Material Improvements to research infrastructure 
Provided To Others? No  
Impact The increase in the computational resources has increased our resilience and security, and allows the facility to take on ever larger projects. 
URL http://genomics.ed.ac.uk
 
Title 2013 Installation of four Beckman liquid handling robotic platforms 
Description The Beckman liquid handling robots are state-of-the art instruments for processing samples from purified nucleic acid to quantitated libraries ready for sequencing. 
Type Of Material Improvements to research infrastructure 
Provided To Others? No  
Impact The Beckman robotics platforms allow the facility to process large numbers of routine genomic and RNA samples efficiently and accurately, releasing skilled staff to deal with more difficult or bespoke projects. 
URL http://genomics.ed.ac.uk
 
Title 2013 Installation of six HiSeq 2500 instruments 
Description The facility has replaced its older HiSeq2000 instruments with the 2500 version. These offer higher throughput, faster turnaround, better quality data and improved reliability. 
Type Of Material Improvements to research infrastructure 
Provided To Others? No  
Impact Installation of the additional HiSeq2500 instruments across the two sites of the Edinburgh Genomics entity has made us the biggest in the UK (in data generation capacity) outside the Sanger Instiutute. The increased number of instruments, and changed ways of working with them allow us to respond rapidly to collaborator requests. 
URL http://genomics.ed.ac.uk
 
Title 2013 Installation of three MiSeq instruments 
Description The MiSeq is a key technology for both improving the flow of samples in the facility (it is used for sample/library QC) and delivering very rapid turnaround on critical samples (<24 hrs). 
Type Of Material Improvements to research infrastructure 
Provided To Others? No  
Impact The acquisition of three MiSeq has made the service offered more robust, and has allowed the facility to deliver to ever shorter timescales. in addition the increased read lengths of this instrument deliver to some key needs in the field. 
URL http://genomics.ed.ac.uk
 
Title Compute Infrastructure 2011 
Description The vast increase in data production from the facility required a significant upgrade in our informatics capacity. To this end we have upgraded our network within the facility, installed a 72 Tbyte high-availability data store, brought online several high-end compute clusters, and developed routines for use of the University of Edinburgh's grid computing environment ECDF. 
Type Of Material Improvements to research infrastructure 
Year Produced 2009 
Provided To Others? Yes  
Impact The improved compute infrastructure has allowed GenePool to keep abreast of increased data volumes, and offer more advanced bioinformatic support to collaborators. 
URL http://genomics.ed.ac.uk
 
Title HiSeq2500 
Description The HiSeq2500 is a key next generation sequencing platform that we have installed and offer to a wide range of research teams throughout the UK. While our roster of instruments is changed to suit requirements, we have had up to 5 HiSeq2500 instruments in the facility. 
Type Of Material Technology assay or reagent 
Year Produced 2014 
Provided To Others? Yes  
Impact The HiSeq2500 has generated data that underpin more than 300 papers published to date. 
URL http://genomics.ed.ac.uk
 
Title HiSeq4000 
Description The HiSeq4000 is a key next generation sequencing platform that we have installed and offer to a wide range of research teams throughout the UK. While our roster of instruments is changed to suit requirements, we currently have one HiSeq4000 instrument in the facility. 
Type Of Material Technology assay or reagent 
Year Produced 2015 
Provided To Others? Yes  
Impact The HiSeq4000 offers cheap, high quality sequence data for genome sequencing and resequencing, RNASeq and many other applications. 
URL http://genomics.ed.ac.uk
 
Title HiSeqX 
Description The HiSeqX is a key next generation sequencing platform that we have installed and offer to a wide range of research teams throughout the UK. While our roster of instruments is changed to suit requirements, we currently have 6 HiSeqX instruments in the facility. 
Type Of Material Technology assay or reagent 
Year Produced 2015 
Provided To Others? Yes  
Impact The HiSeqX allows the facility to sequence human and other genomes at very low per-base costs, promoting genetical and genomic research across the RC spectrum. 
URL http://genomics.ed.ac.uk
 
Title Installation of HiSeq2000 and associated robotics 2010 
Description The GenePool recieved delivery of an illumina HiSeq 2000in 2010. A second HiSeq 2000 was delivered in late 2010. Since then we have worked closely with Illumina UK to troubleshoot these instruments and move them from preproduction to production. The increased data production capacity of these instruments has required installation of robotic platforms for shearing, library preparatiion and presequencing amplification, and high-throughput QC/QA instrumentation. 
Type Of Material Improvements to research infrastructure 
Year Produced 2010 
Provided To Others? Yes  
Impact The improved QC/QA procedures made possible by the improved instrumentation has ensured timely delivery of data at high resilience. The robotics platforms have allowed us to take on larger projects and to make best use of the huge data production capacities of the HiSeqs. The HiSeqs are in production, generating 40 Gbase/day. 
URL http://genomics.ed.ac.uk
 
Title Installation of NovaSeq6000 
Description Edinburgh genomics installed the Illumina NovaSeq600 sequencer to replace its ageing HiSeq instruments. The NovaSeq is Illumina's latest platform, and offers higher, scalable throughput at lower cost. The NovaSeq was installed and operational within 1 month of delivery and has been used to service a wide range of UKRI-funded projects. 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact The NovaSeq offers improved sequencing throughput at lower per base cost to users. 
URL http://www.genomics.ed.ac.uk
 
Title Installation of PromethION sequencer in Edinburgh genomics 
Description In early 2019, Edinburgh Genomics installed a PromethION sequencer, the latest long read sequencer from Oxford Nanopore. The sequencer has been tested on control and real world samples through an early adopter programme, and is now ready for open access use by the UK science community. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? Yes  
Impact The PromethION install is in its early days, but has already engendered a lot of interest in the community. 
URL http://www.genomics.ed.ac.uk
 
Title Installation of a second HiSeq 2000 
Description Second instrument purchased to meet demand for Illumina sequencing technology 
Type Of Material Improvements to research infrastructure 
Year Produced 2011 
Provided To Others? Yes  
Impact The installation of a second instrument effectively doubled the GenePool's sequencing capacity, allowing us to expand our user base and reduce turnaround times for all users 
URL http://genomics.ed.ac.uk
 
Title RAD Seq 
Description RAD seq is a new method for genotyping by sequencing. Edinburgh Genomics pioneered its use in the UK ecological and evolutionary genomics community, and continues to develop it. In 2014 Edinburgh Genomics signed the first European licence with KeyGene, holder of paptents in the RAD/GBS area, giving the facility security to deliver the technology in including new variations that improve throughput and accuracy. The facility has also developed software toolkits for RAD analyses and run RAD workshops and meetings.. 
Type Of Material Technology assay or reagent 
Year Produced 2009 
Provided To Others? Yes  
Impact RAD sequencing is now a tool of choice across biosciences. In particular it is excellent for discovering variants in new genomes, and then building high throughput assay tools. This has been made concrete in the development of a SNP assay chip for salmon with our industrial partners LandCatch. 
URL http://genomics.ed.ac.uk
 
Description Edinburgh Genomics 
Organisation ARK-Genomics
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution We have formally merged the two genomics facilities in Edinburgh to form Edinburgh genomics. By judicious forward investment in technology and staff we are now the largest academic sequencing facility in the UK after the Sanger Institute.
Collaborator Contribution We joined the infrastructure and staff of the GenePool with that of ARK-Genomics, a BBSRC core funded facility in the Roslin Institute.
Impact Increased capacity; Improved service delivery
Start Year 2013
 
Description Heliconius genome consortium 
Organisation University of Cambridge
Department Department of Zoology
Country United Kingdom 
Sector Academic/University 
PI Contribution Offering genomic sequencing and reseaquencing technologies; close involvement in experimental design.
Collaborator Contribution Joining the consortium has allowed GenePool to develop custom targeted resequencing technologies, and associated bioinformatics skiils, and made us much more visible across this area of science
Impact The Heliconius melpomene genome has been assembled and annotated. A manuscript describing this work is submitted for publication. On the basis of the GenePool's involvement in this consortium we have coordinated a ladybird genome consortium with 6 partner laboratories, and currently have 2 genomes in sequencing.
Start Year 2010
 
Description MRC hub-spokes network 
Organisation Medical Research Council (MRC)
Department MRC Human Genetics Unit
Country United Kingdom 
Sector Academic/University 
PI Contribution Training and support for spokes bioinformaticians at collaborating institutions
Collaborator Contribution Training workshops, collaborative projects
Impact Training workshops, collaborative projects with GenePool
Start Year 2009
 
Description MRC hub-spokes network 
Organisation University of Aberdeen
Department Institute of Medical Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Training and support for spokes bioinformaticians at collaborating institutions
Collaborator Contribution Training workshops, collaborative projects
Impact Training workshops, collaborative projects with GenePool
Start Year 2009
 
Description MRC hub-spokes network 
Organisation University of Dundee
Country United Kingdom 
Sector Academic/University 
PI Contribution Training and support for spokes bioinformaticians at collaborating institutions
Collaborator Contribution Training workshops, collaborative projects
Impact Training workshops, collaborative projects with GenePool
Start Year 2009
 
Description MRC hub-spokes network 
Organisation University of Edinburgh
Department The Roslin Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Training and support for spokes bioinformaticians at collaborating institutions
Collaborator Contribution Training workshops, collaborative projects
Impact Training workshops, collaborative projects with GenePool
Start Year 2009
 
Description MRC hub-spokes network 
Organisation University of Glasgow
Department Polyomics Facility
Country United Kingdom 
Sector Academic/University 
PI Contribution Training and support for spokes bioinformaticians at collaborating institutions
Collaborator Contribution Training workshops, collaborative projects
Impact Training workshops, collaborative projects with GenePool
Start Year 2009
 
Description MRC/BBSRC Genome Centre Network 
Organisation Earlham Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Organisation of networking meetings and training workshops
Collaborator Contribution Organisation of networking meetings and training workshops
Impact Networking, exchange of best practices, development of collaborative projects and joint proposals, training workshops for facility staff
Start Year 2010
 
Description MRC/BBSRC Genome Centre Network 
Organisation University of Cambridge
Department Eastern Sequence and Informatics Hub (EASIH)
Country United Kingdom 
Sector Academic/University 
PI Contribution Organisation of networking meetings and training workshops
Collaborator Contribution Organisation of networking meetings and training workshops
Impact Networking, exchange of best practices, development of collaborative projects and joint proposals, training workshops for facility staff
Start Year 2010
 
Description MRC/BBSRC Genome Centre Network 
Organisation University of Liverpool
Department Liverpool Centre for Genomic Research
Country United Kingdom 
Sector Academic/University 
PI Contribution Organisation of networking meetings and training workshops
Collaborator Contribution Organisation of networking meetings and training workshops
Impact Networking, exchange of best practices, development of collaborative projects and joint proposals, training workshops for facility staff
Start Year 2010
 
Description MRC/BBSRC Genome Centre Network 
Organisation University of Oxford
Department Oxford Genomics Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution Organisation of networking meetings and training workshops
Collaborator Contribution Organisation of networking meetings and training workshops
Impact Networking, exchange of best practices, development of collaborative projects and joint proposals, training workshops for facility staff
Start Year 2010
 
Description Marine Alliance for Science & Technology for Scotland 
Organisation National Oceanography Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution Experimental support: assistance with understanding technology and experimental design; Delivery of sequencing service; Horizon scanning consultation to SAMS collaborators
Collaborator Contribution The MASTS collaboration is coordinating marine science in Scotland, and has recommended GenePool as its sequencing provider
Impact Several projects running in GenePool; participation in SAMS genomics workshop.
Start Year 2010
 
Description The Caenorhabditis Genomes Project 
Organisation Columbia University
Country United States 
Sector Academic/University 
PI Contribution We are sequencing assembling and annotating the genomes of the remaining unsequenced species in the genus Caenorhabditis.
Collaborator Contribution Marie-Anne Felix and laboratory have paid for some of the sequencing and provided DNA and RNA samples. Peter Sarkies and laboratory have paid for sequencing small RBNA samples. Erich Schwarz and collaborators have provided PacBio data. Asher Cutter has supported the project with dedicated staff time.
Impact Genome sequences of three species have been deposited in public databases and distributed widely.
Start Year 2012
 
Description The Caenorhabditis Genomes Project 
Organisation Imperial College London
Department Imperial College Trust
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution We are sequencing assembling and annotating the genomes of the remaining unsequenced species in the genus Caenorhabditis.
Collaborator Contribution Marie-Anne Felix and laboratory have paid for some of the sequencing and provided DNA and RNA samples. Peter Sarkies and laboratory have paid for sequencing small RBNA samples. Erich Schwarz and collaborators have provided PacBio data. Asher Cutter has supported the project with dedicated staff time.
Impact Genome sequences of three species have been deposited in public databases and distributed widely.
Start Year 2012
 
Description The Caenorhabditis Genomes Project 
Organisation University of Toronto
Country Canada 
Sector Academic/University 
PI Contribution We are sequencing assembling and annotating the genomes of the remaining unsequenced species in the genus Caenorhabditis.
Collaborator Contribution Marie-Anne Felix and laboratory have paid for some of the sequencing and provided DNA and RNA samples. Peter Sarkies and laboratory have paid for sequencing small RBNA samples. Erich Schwarz and collaborators have provided PacBio data. Asher Cutter has supported the project with dedicated staff time.
Impact Genome sequences of three species have been deposited in public databases and distributed widely.
Start Year 2012
 
Description The Caenorhabditis Genomes Project 
Organisation École Normale Supérieure, Paris
Country France 
Sector Academic/University 
PI Contribution We are sequencing assembling and annotating the genomes of the remaining unsequenced species in the genus Caenorhabditis.
Collaborator Contribution Marie-Anne Felix and laboratory have paid for some of the sequencing and provided DNA and RNA samples. Peter Sarkies and laboratory have paid for sequencing small RBNA samples. Erich Schwarz and collaborators have provided PacBio data. Asher Cutter has supported the project with dedicated staff time.
Impact Genome sequences of three species have been deposited in public databases and distributed widely.
Start Year 2012
 
Description 2018 Edinburgh genomics Training Workshops 
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 Edinburgh Genomics delivered a rich portfolio of training courses in 2018, ranging from a one day Interoduction to Linux (delivered three times) through to an intensive "spring school" in Bioinformatics for Genomics (one week). The courses were delivered in Edinburgh, and had from 12 to 50 participants. The participants came from across the UK HEI sector, including undergraduates, postgraduates and postdoctoral researchers, and also attracted overseas attendants (mainly from other European countries). The training strand is funded from student fees and from BBSRC and NERC dedicated sources. The training strand employs a full time Training Manager who both administers the scheme and develops and delivers courses.
Year(s) Of Engagement Activity 2018
 
Description Blaxter group presentations and outreach 2015 
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 Mark Blaxter and research team communication and outreach 2015

Globodera genomics and blobtools software
25/02/2015 JHI Postgraduate Student Competition 2015 James Hutton Institute, Aberdeen, UK A tale of Two Peaks: Analysing Genomic Data from Potato Cyst Nematodes Talk
26/03/2015 JHI Cell and Molecular Sciences (CMS) seminar James Hutton Institute, Invergowrie, Dundee, UK Frustration and happiness : (De)-constructing parasite genomes Talk
16/06/2015 JHI Dundee effector consortium (DEC) meeting 2015 Birnam Arts and Conference Centre, Birnam, UK Variation within the Globodera pallida species complex: preliminary results Talk
03/09/2015 Molecular and Cellular Biology of Helminth Parasites IX Bratsera Hotel, Hydra, Greece Inter- and intra-specific analyses of the effector complement in potato cyst nematodes Poster
18/09/2015 UoE Postgraduate Poster Day University of Edinburgh, Edinburgh, UK Inter- and intra-specific analyses of the effector complement in potato cyst nematodes Poster
26/09/2015 Edinburgh University Doors Open Day University of Edinburgh, Edinburgh, UK Potato Cyst Nematodes (PCN) - Nematode parasites of potatoes Poster
30/11/2015 NextGenBug University of Edinburgh, Edinburgh, UK Blobtools: Blobology 2.0 Talk
01/12/2015 UK pollinator genomics meeting Roslin Institute, Edinburgh, UK Bees and Blobs Talk

LepBase
06/03/2015 EMARES Cambridge, UK The Bicyclus Genome Project Talk
06/03/2015 EMARES Cambridge, UK An introduction to Lepbase Talk
17/06/2015 Arthropod Genomics Manhattan, Kansas, USA Lepbase - A multi genome database for the Lepidoptera Poster
24/07/2015 10th Heliconius Meeting Gamboa, Panama Lepbase - A multi genome database for the Lepidoptera (API demonstration) Workshop
24/07/2015 10th Heliconius Meeting Panama Lepbase - A multi genome database for the Lepidoptera Poster
26/07/2015 10th Heliconius Meeting Panama Lepbase Workshop Talk
04/09/2015 Edinburgh Bioinformatics Edinburgh, UK Lepbase - A multi genome database for the Lepidoptera Talk
26/09/2015 Open Doors Day "Make a butterfly" interactive exhibition
26/09/2015 Edinburgh University Doors Open Day Edinburgh, UK Lepbase Multiple Sequence Alignments game Poster+Game
28/10/2015 NextgenBUG Dundee, UK Lepbase - an Ensembl (and more) for the Lepidoptera Talk

Nematode genomics
24.06.2015 20th International C. elegans Meeting Los Angeles USA A new evolutionary framework for the phylum Nematoda: a case study of HOX cluster evolution Poster
24.06.2015 20th International C. elegans Meeting Los Angeles USA Caenorhabditis Genomes Project Workshop (organiser and chair) Talk
24.06.2015 20th International C. elegans Meeting Los Angeles USA Current status of the CGP in Edinburgh Talk

Meloidogyne genomics
10-14 August 2015 ESEB Lausanne-Switzerland Genomic consequences of hybridization and the loss of meiotic recombination in Root-knot nematodes poster
15-18 December 2015 PopGroup Edinburgh-UK Genomic consequences of hybridization and the loss of meiotic recombination in Root-knot nematodes talk
23 February 2016 NextGenBug Edinburgh-UK Genomics of Root-knot nematodes talk
Year(s) Of Engagement Activity 2015
 
Description Press releases and website 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact We have engaged actively with the University press office to promote press coverage of our research outcomes, particularly major publications (which have had coverage in national and international newspapers) and in blogs and other online media. We have also promoted major new initiatives such as additional core funding of the Edinburgh genomics facility.

Increased visibility of Edinburgh Genomics within the community; requests for comment by funders and government on matters pertaining to genomics.
Year(s) Of Engagement Activity 2009,2010,2011,2012,2013,2014,2015,2016