NERC Biomolecular Analysis Facility - Edinburgh
Lead Research Organisation:
British Geological Survey
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Organisations
- British Geological Survey (Lead Research Organisation)
- Natural Environment Research Council (Collaboration)
- UNIVERSITY OF CAMBRIDGE (Collaboration)
- UNIVERSITY OF OXFORD (Collaboration)
- UNIVERSITY OF EDINBURGH (Collaboration)
- ARK-Genomics (Collaboration)
- UNIVERSITY OF ABERDEEN (Collaboration)
- NATIONAL OCEANOGRAPHY CENTRE (Collaboration)
- UNIVERSITY OF GLASGOW (Collaboration)
- Medical Research Council (MRC) (Collaboration)
- UNIVERSITY OF LIVERPOOL (Collaboration)
- UNIVERSITY OF DUNDEE (Collaboration)
- EARLHAM INSTITUTE (Collaboration)
Publications
Baxter SW
(2011)
Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism.
in PloS one
Becher H
(2014)
Endogenous pararetrovirus sequences associated with 24 nt small RNAs at the centromeres of Fritillaria imperialis L. (Liliaceae), a species with a giant genome.
in The Plant journal : for cell and molecular biology
Bergero R
(2015)
Gene loss from a plant sex chromosome system.
in Current biology : CB
Bergero R
(2019)
Arms races with mitochondrial genome soft sweeps in a gynodioecious plant, Plantago lanceolata.
in Molecular ecology
Bergero R
(2011)
Preservation of the Y transcriptome in a 10-million-year-old plant sex chromosome system.
in Current biology : CB
Bianconi ME
(2020)
Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species.
in Proceedings. Biological sciences
BIHARI P
(2011)
Western Palaearctic phylogeography of an inquiline oak gall wasp, Synergus umbraculus PHYLOGEOGRAPHY OF AN INQUILINE GALL WASP
in Biological Journal of the Linnean Society
Blackmore T
(2015)
Genetic-geographic correlation revealed across a broad European ecotypic sample of perennial ryegrass (Lolium perenne) using array-based SNP genotyping.
in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Blaxter M
(2015)
The evolution of parasitism in Nematoda.
in Parasitology
| 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 | NERC NBAF is a service delivery project and thus there are no science-based project-specific deliverables. We support a wide (and growing) range of cutting edge environmental bioscience projects. Our delivery however underpins a wide range of NERC science. Within the project we focus on (a) high quality support for collaborators, (b) high quality data delivery and (c) high quality analysis delivery. |
| Exploitation Route | Our policy is to place data in the public domain as soon as is possible in collaboration with users. We embed newly developed technologies and procedures in the facility so that they can be accessed by others. We leverage the investment by NERC to attract addtional external, matching funding. |
| Sectors | Aerospace Defence and Marine Agriculture Food and Drink Environment Culture Heritage Museums and Collections |
| URL | http://nbaf.nerc.ac.uk |
| Description | The NERC NBAF project continues to have wide impact across the NERC portfolio, with hundreds of users and tens of publications per node each year. |
| First Year Of Impact | 2006 |
| Sector | Agriculture, Food and Drink,Environment,Culture, Heritage, Museums and Collections |
| Impact Types | Cultural |
| 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 | Daphne Jackson Trust Fellowship |
| Amount | £80,457 (GBP) |
| Organisation | University of Surrey |
| Department | Daphne Jackson Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 08/2011 |
| End | 08/2014 |
| Description | EU EPIAF/Scoot |
| Amount | £115,000 (GBP) |
| Funding ID | 242131 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 08/2010 |
| End | 08/2014 |
| 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 | 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 |
| 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 | 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 | NERC NBAF |
| Organisation | Natural Environment Research Council |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | We are a funded node of the NERC Biomolecular Analysis Facility. This collaboration involves three other University facilities. |
| Collaborator Contribution | We are charged with delivering research support, sequencing and bioinformatics to NERC funded researchers. |
| Impact | The collaboration is multi-disciplinary, involving genetics, genomics, bioinformatics, nmetabolomics and transcriptomics. The outputs include dozens of research papers and several collaborative grants. |
| Start Year | 2006 |
| Title | AfterParty transcriptome analysis tool |
| Description | Background Next-generation DNA sequencing technologies have made it possible to generate transcriptome data for novel organisms quickly and cheaply, to the extent that the effort required to annotate and publish a new transcriptome is greater than the effort required to sequence it. Often, following publication, details of the annotation effort are only available in summary form, hindering subsequent exploitation of the data. To promote best-practice in annotation and to ensure that data remain accessible, we have written afterParty, a web application that allows users to assemble, annotate and publish novel transcriptomes using only a web browser. Results afterParty is a robust web application that implements best-practice transcriptome assembly, annotation, browsing, searching, and visualization. Users can turn a collection of reads (from Roche 454 chemistry) or assembled contigs (from any sequencing chemistry, including Illumina Solexa RNA-Seq) into a searchable, browsable transcriptome resource and quickly make it publicly available. Contigs are functionally annotated based on similarity to known sequences and protein domains. Once assembled and annotated, transcriptomes derived from multiple species or libraries can be compared and searched. afterParty datasets can either be created using the existing afterParty server, or using local instances that can be easily built using a virtual machine. afterParty includes powerful visualization tools for transcriptome dataset exploration and uses a flexible annotation architecture which will allow additional types of annotation to be added in the future. Conclusions afterParty's main use case scenario is one in which a working biologist has generated a large volume of transcribed sequence data and wishes to turn it into a useful resource that has some durability. By reducing the effort, bioinformatics skills, and computational resources needed to annotate and publish a transcriptome, afterParty will facilitate the annotation and sharing of sequence data that would otherwise remain unavailable. A typical metazoan transcriptome containing several tens of thousands of contigs can be annotated in a few minutes of interactive time and a few days of computational time. |
| Type Of Technology | Software |
| Year Produced | 2013 |
| Open Source License? | Yes |
| Impact | AfterParty now has a community of users worldwide. |
| URL | http://afterparty.bio.ed.ac.uk |
| Title | Badger genome exploration environment |
| Description | Summary: High quality draft genomes are now easy to generate, as sequencing and assembly costs have dropped dramatically. However, building a user friendly, searchable website and database for a new annotated genome data is not straight forward. Here we present Badger, a lightweight and easy-to-install genome exploration environment designed for next generation, non-model organism genomes. Availability: Badger is released under the GPL and is available at http://badger.bio.ed.ac.uk/. We show two working examples: (1) a test dataset included with the source code and (2) a collection of four filarial nematode genomes. |
| Type Of Technology | Software |
| Year Produced | 2013 |
| Open Source License? | Yes |
| Impact | Badger has been used extensively by the Blaxter lab and others to present genome data to the world. |
| URL | http://badger.bio.ed.ac.uk |
| Title | TAGC-plots and Blobsplorer tools for genomics |
| Description | Generating the raw data for a de novo genome assembly project for a target eukaryotic species is relatively easy. This democratisation of access to large-scale data has allowed many research teams to plan to assemble the genomes of non-model organisms. These new genome targets are very different from the traditional, inbred, laboratory reared model organisms. They are often small, and cannot be isolated free of their environment - whether ingested food, the surrounding host organism of parasites, or commensal and symbiotic organisms attached to or within the individuals sampled. Preparation of pure DNA originating from a single species can be technically impossible, but assembly of mixed-organism DNA can be difficult, as most genome assemblers perform poorly when faced with multiple genomes in different stoichiometries. This class of problem is common in metagenomic datasets that deliberately try to capture all the genomes present in an environment, but replicon assembly is not often the goal of such programmes. Here we present an approach to extracting from mixed DNA sequence data subsets that correspond to single species' genomes and thus improving genome assembly. We use both numerical (proportion of GC bases and read coverage) and biological (best-matching sequence in annotated databases) indicators to aid partitioning of draft assembly contigs, and the reads that contribute to those contigs, into distinct bins that can then be subjected to rigorous, optimised assembly. We also present a tool, blobsplorer, that aids exploration and selection of subsets from GC/coverage/taxonomy annotated datasets. Partitioning the data in this way "rescues" poorly assembled genomes, and reveals unexpected symbionts and commensals in eukaryotic genome projects. The TAGC-plot pipeline script is available from http://github.com/blaxterlab/blobology, and the Blobsplorer tool from https://github.com/mojones/blobsplorer. |
| Type Of Technology | Software |
| Year Produced | 2013 |
| Open Source License? | Yes |
| Impact | Blobsplorer/TAGC plots are now in wide use in genomics. The toolkit has been featured in several courses and publications. |
| URL | http://github.com/blaxterlab/blobology |
| 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 | Bioinformatics Training Workshops, Buenos Aires and LaPlata, 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 | We preseented two week-long workshops under the auspices of CONICET and the University of La Plata, on bioinformatics tools for next generation genomics, inlcuding Blobtools, GenomeHubs and retated topics. |
| 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 |