September 2010 GMOD Meeting
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September 2010 GMOD Meeting 13-14 September 2010 Cambridge, UK |
{{#icon: GMOD2010Europe300.png|Part of GMOD Europe 2010|200px|GMOD Europe 2010}} |
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The next GMOD community meeting will be held 13-14 September 2010, in Cambridge, UK, as part of GMOD Europe 2010, which also includes Satellite Meetings, an InterMine Workshop, and a BioMart Workshop. The meeting is sponsored and hosted by the Cambridge Computational Biology Institute at the University of Cambridge.
GMOD Meetings are a mix of user and developer presentations, and are a great place to find out what is happening in the project, what's coming up, and what others are doing. See the January 2010 GMOD Meeting page for an idea of what happens at a GMOD meeting.
Registration
Registration is now open. GMOD Europe 2010 has a coordinated registration process for all events. The GMOD Meeting has a registration fee to cover catered lunches, coffee/tea breaks, and other expenses:
- £50 on or before 5 September
- £65 after 5 September
Agenda Proposals
If you have a presentation you want to give, or have a topic that you would like to see covered, please add it here. If you want to second a topic that has already been listed, then add your name to the end of the line. This will give us an idea of interest.
- Project Overview and Update - Scott Cain
- Help Desk Update - Dave Clements
- Publication Annotation Tools in GMOD - suggested by Dave C., Daniel Renfro
- Next Generation Sequencing in GMOD - suggested by Dave C.
- Workflow tools in GMOD - suggested by Dave C.
- GMOD RPC API demo/update --Jogoodma 20:05, 16 July 2010 (UTC)
- Discussion of lessons to be learned from the Apache Software Foundation --Jogoodma 20:05, 16 July 2010 (UTC)
- GBrowse and JBrowse - what's the plan? -- Erick Antezana and Dave Clements
- Implementing GBrowse from scratch: suggestions from the GBrowse users community. - suggested by Christelle Robert
- GBrowse integration within a Java/JSP-based web application: pitfalls to avoid / best strategies. - suggested by Christelle Robert
- Integration of GBrowse within Drupal content management system: guidelines. - suggested by Christelle Robert
- DAS and it's use in GMOD - suggested by Jonathan Warren
Please also suggest topics for the Satellite Meetings.
Guest Speaker
The Open Microscopy Environment: Open Informatics for Biological Imaging
- Professor, Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee
- Principal Investigator, Open Microscopy Environment (OME)
The meeting's special guest speaker will be Prof Jason Swedlow, who will discuss his work with with the Open Microscopy Environment (OME), an open international consortium that develops and releases data specifications and management tools for biological imaging. OME metadata enables image sharing, analysis, and integration with other data types. This topic is of particular value to the GMOD community as many GMOD members expand into phenotypes, gene expression, fate mapping, natural diversity, and other image-intensive questions. The arrival of high-throughput imaging platforms also makes this timely, as high throughput imaging has the potential to transform these areas, but only if biologists have the tools and standards to manage and integrate these images. OME is a leading way to address these issues.
Dr Swedlow is a Professor at the Wellcome Trust Centre for Gene Regulation and Expression and the University of Dundee. He is also a past organizer of the Genome Informatics meeting. Jason's research focuses on mechanisms and regulation of chromosome segregation during mitotic cell division.
Agenda
The detailed agenda will be posted shortly before the meeting. Catered lunches will be provided on both days.
Confirmed speakers/topics
- Jason Swedlow (University of Dundee), The Open Microscopy Environment: Open Informatics for Biological Imaging
- Scott Cain (Ontario Institute for Cancer Research), Advances in Chado, GBrowse and other GMOD applications
- Morris Swertz (University Medical Center Groningen), MolGenIS and XGAP
- Bruno Aranda (European Bioinformatics Institute), GMOD and PSICQUIC
- Josh Goodman (FlyBase, Indiana University), GMOD RPC (aka REST API)
- David Beare (Sanger), Cosmic GBrowse
- Jonathan Warren (Sanger), DAS and it's use in GMOD
- Richard Smith (Cambridge), InterMine: new Mines and new features
Monday, 13 September
Note: I am still working on this schedule--don't take any times as gospel. Scott 15:12, 3 September 2010 (UTC)
| Time | Topic | Presenter(s) | Links |
|---|---|---|---|
| 09:15 | Introductions | Scott Cain | |
| 10:00 | The State of GMOD | Scott Cain | |
| 10:30 | Break | ||
| 10:45 | Update from the Help Desk | Dave Clements | |
| 11:15 | Keynote: The Open Microscopy Environment: Open Informatics for Biological Imaging | Jason Swedlow | |
| 12:00 | Lunch | ||
| 13:15 | |||
| 13:45 | |||
| 14:15 | |||
| 14:45 | Break | ||
| 15:00 | |||
| 15:30 | |||
| 16:15 |
Tuesday, 14 September
| Time | Topic | Presenter(s) | Links |
|---|
Wednesday & Thursday, 15-16 September
GMOD Europe 2010 continues after the GMOD meeting, starting with the Satellite Meetings and the InterMine Workshop, and finishing with the BioMart Workshop. See GMOD Europe 2010 for a complete schedule.
Participants
This list is tentative. We expect many additions and a few deletions between now and the start of the meeting.
| Participant | Affilliation(s) | URL |
|---|---|---|
| Scott Cain | OICR | http://gmod.org/ |
| Dave Clements | NESCent, GMOD | http://nescent.org http://gmod.org |
| Josh Goodman | FlyBase - Indiana University | http://flybase.org |
| Richard Smith | Cambridge University | http://www.intermine.org |
| Anup Mahurkar | Institute for Genome Sciences University of Maryland School of Medicine | |
| joan pontius | SAIC-NCI-FREDERICK Laboratory of Genomic Diversity | http://lgd.abcc.ncifcrf.gov/cgi-bin/gbrowse/cat/ |
| Anh-Thu Tieu | Helmholtz Zentrum München | http://www.helmholtz-muenchen.de |
| Christelle Robert | The Roslin Institute The University of Edinburgh | |
| Matthew Eldridge | Cancer Research UK - Cambridge Research Institute | |
| Fengyuan Hu | Department of Genetics, University of Cambridge | |
| Daniel Renfro | EcoliWiki, SubtilisWiki, Hu lab - Texas A&M University | EcoliWiki, SubtilisWiki, GONUTS |
| Ellen Adlem | Cambridge University Cambridge Institue of Medical Research | http://www.t1dbase.org |
| Kerstin Koch | KWS Saat AG Bioinformatics Grimsehlstr. | |
| Oliver Burren | Cambridge University | http://www.t1dbase.org |
| Chris Jiggins | University of Cambridge | http://heliconius.zoo.cam.ac.uk/ |
| Dave Beare | Cancer Genome Project, Wellcome Trust Sanger Institute | http://www.sanger.ac.uk/research/projects/cancergenome.html |
| seth redmond | Imperial College / Vectorbase | |
| Chris Hemmerich | http://cgb.indiana.edu | |
| Emmanuel Quevillon | Institut Pasteur | http://www.pasteur.fr/ip/easysite/go/03b-00000m-0q8/recherche/logiciels-et-banques-de-donnees |
| Bob MacCallum | VectorBase Imperial College London | http://www.vectorbase.org |
| Ewan Mollison | Tun Abdul Razak Research Centre, Hertford | http://www.tarrc.co.uk |
| Jen Harrow | Wellcome Trust Sanger Institute | |
| Gos Micklem | University of Cambridge | http://www.sysbiol.cam.ac.uk/index.php?page=dr-gos-micklem |
| Malcolm Hinsley | Wellcome Trust Sanger Institute | |
| Gemma Barson | Wellcome Trust Sanger Institute | http://www.sanger.ac.uk/ |
| Brett Whitty | Michigan State University | |
| Morris Swertz | Genomics Coordination Center, University Medical Center Groningen EMBL - European Bioinformatics Institute | http://www.molgenis.org |
| Jerven Bolleman | UniProt Swiss-Prot | |
| Alex Kalderimis | InterMine, Cambridge University | http://www.intermine.org, http://www.flymine.org |
| Oksana Riba Grognuz | Swiss Institute of Bioinformatics (SIB) Department of Ecology and Evolution, University of Lausanne | |
| Dr Helen Imogen Field | FlyBase Dept Genetics University of Cambridge | http://www.gen.cam.ac.uk/research/flybase.html |
| Kim Rutherford | Cambridge Systems Biology Centre | http://www.pombase.org/ |
| Robert Wilson | National Institute for Medical Research, London | |
| Gerd Anders | Public research institute: Max-Delbrueck-Centrum Berlin (MDC), Researcher and database developer | http://www.mdc-berlin.de/en/research/core_facilities/cf_massspectromety_bimsb/teammember/index.html http://www.mdc-berlin.de/en/research/core_facilities/cf_bioinformatic/teammember/index.html |
| Joeri van der Velde | University of Groningen, GBIC UMGC, dept. of Genetics Genomics Coordination Center | |
| Jonathan Warren | The Sanger Institute | http://www.dasregistry.org |
| Stephen Taylor | CBRG, Oxford University | http://www.cbrg.ox.ac.uk/ |
| Bruno Aranda | EMBL-EBI | |
| Mahmut Uludag | European Bioinformatics Institute |
Logistics
See the Transportation and Lodging sections on the GMOD Europe 2010 pages for details.
Sponsor: Cambridge Computational Biology Institute
The September 2010 GMOD Meeting is sponsored by the Cambridge Computational Biology Institute, which is hosting the meeting and is also the home of InterMine. The CCBI is "set up to bring together the unique strengths of Cambridge in medicine, biology, mathematics and the physical sciences. Its aim is to create a centre of excellence in research and teaching and to promote collaborations both within the Cambridge area and beyond."
Please thank Gos, Richard, and Shelley for hosting the event. We could not have done this without their support, effort and time.
Feedback
We will solicit feedback from meeting participants at the end of the meeting, and post it here once we have it.
Feedback on previous meetings (January 2010, August 2009, January 2009, and 2008 and before) has been very positive.
