Difference between revisions of "September 2010 GMOD Meeting"
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| Update from the [[GMOD Help Desk|Help Desk]] | | Update from the [[GMOD Help Desk|Help Desk]] | ||
| [[User:Clements|Dave Clements]] | | [[User:Clements|Dave Clements]] | ||
− | | [[Media:HelpDeskSept2010.pdf|PDF]], [ | + | | [[Media:HelpDeskSept2010.pdf|PDF]], [ftp://ftp.gmod.org/pub/gmod/Meetings/2010/GMODSeptember/HelpDeskSept2010.ppt PPT] |
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| GMOD and [http://psicquic.googlecode.com PSICQUIC] | | GMOD and [http://psicquic.googlecode.com PSICQUIC] | ||
| [[User:Baranda|Bruno Aranda]] | | [[User:Baranda|Bruno Aranda]] | ||
− | | [[Media:PSICQUICSept2010.pdf|PDF | + | | [[Media:PSICQUICSept2010.pdf|PDF]] |
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| 14:15 | | 14:15 | ||
| [[MolGenIS]] and [http://www.xgap.org XGAP] | | [[MolGenIS]] and [http://www.xgap.org XGAP] | ||
| Morris Swertz | | Morris Swertz | ||
− | | [[Media:MolGenISXGAPSept2010.pdf|PDF | + | | [[Media:MolGenISXGAPSept2010.pdf|PDF]] |
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| 14:45 | | 14:45 |
Revision as of 08:36, 23 September 2010
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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This GMOD community meeting was held 13-14 September 2010, in Cambridge, UK, as part of GMOD Europe 2010, which also included Satellite Meetings, an InterMine Workshop, and a BioMart Workshop. The meeting was 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. The January 2010 GMOD Meeting was the previous event. The next meeting is likely to be held in spring 2011.
Contents
Registration
The GMOD Meeting had a registration fee (£50 early, £65 late) to cover catered lunches, coffee/tea breaks, and other expenses.
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 guest speaker was Prof Jason Swedlow, who discussed 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.
Dr Swedlow is a Professor at the Wellcome Trust Centre for Gene Regulation and Expression and the University of Dundee. Jason's research focuses on mechanisms and regulation of chromosome segregation during mitotic cell division.
Agenda
If you are a speaker please either upload your slides, or send them to Dave Clements and he will upload them for you.
Monday, 13 September
Time | Topic | Presenter(s) | Links |
---|---|---|---|
09:15 | Introductions | Scott Cain | |
10:00 | The State of GMOD | Scott Cain | |
10:30 | Break | ||
11:00 | Update from the Help Desk | Dave Clements | PDF, PPT |
11:30 | Keynote: The Open Microscopy Environment: Open Informatics for Biological Imaging | Jason Swedlow | PDF, PPT |
12:30 | Catered Lunch | ||
13:45 | GMOD and PSICQUIC | Bruno Aranda | |
14:15 | MolGenIS and XGAP | Morris Swertz | |
14:45 | The Chado Natural Diversity Module | Bob MacCallum | PDF, PPT, gdoc |
15:15 | Break | ||
15:45 | Cosmic GBrowse | David Beare | PDF, PPT |
16:15 | ISGA and WebGBrowse | Chris Hemmerich | PDF, PPT |
Tuesday, 14 September
Time | Topic | Presenter(s) | Links |
---|---|---|---|
09:15 | GMOD RPC (aka REST API) | Josh Goodman | |
09:45 | DAS and its use in GMOD | Jonathan Warren | PDF, PPT |
10:15 | InterMine: new Mines and new features | Richard Smith | PDF, PPT |
10:40 | Break | ||
11:00 | Literature Curation in GMOD | Daniel Renfro | PDF, PPT |
11:30 | GO Curation | Helen Field | PDF, KEY |
12:00 | BioPivot: Applying Microsoft Live Labs Pivot to Problems in Bioinformatics | Steve Taylor | PDF, PPT |
12:30 | Catered Lunch | ||
13:45 | CRAWL (Chado RESTful Access Web-service Layer) - a programmatic interface for querying pathogen genomics data | Giles Verlarde | |
14:15 | Lessons the GMOD community can glean from the Apache Software Foundation | ||
14:45 | Lightning talks | ||
15:15 | Break |
Wednesday & Thursday, 15-16 September
GMOD Europe 2010 continued 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.
Presentations
Summaries of presentations will be posted here over the coming weeks.
Participants
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/ |
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/ |
Jason Swedlow | Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, The Open Microscopy Environment (OME) | http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html, http://www.openmicroscopy.org/ |
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 | http://buell-lab.plantbiology.msu.edu, http://solanaceae.plantbiology.msu.edu, http://potatogenome.net |
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 | http://www.ebi.ac.uk/intact, http://psicquic.googlecode.com |
Mahmut Uludag | European Bioinformatics Institute | |
Giles Velarde | The Sanger Centre | http://www.genedb.org, http://www.sanger.ac.uk |
Andy Jenkinson | European Bioinformatics Institute | |
Kevin Howe | Wellcome Trust Sanger Institute |
Logistics
This meeting was held in the Biffen Lecture Theatre, in the Department of Genetics on the University of Cambridge campus.
Wireless
Thanks to Ian Clark, the Biffen Lecture Theatre had wireless. From the Cambridge website:
Members of the University of Cambridge can either use their Raven login to connect to Lapwing or they can configure their computer to use Eduroam. Visitors from institutions participating in the Eduroam initiative can also use Eduroam, but should obtain instructions from their home institution.
Visitors who cannot use Eduroam for any reason can obtain a time-limited Lapwing ticket by asking their contact in Genetics to mail the following information to the CO:
Accounts were setup for all attendees for the duration of GMOD Europe 2010.
Power
The Biffen Lecture Theatre has wireless, but it does not have power outlets throughout the room.
To help us through the days, Gos Micklem secured a 15-socket extension strip which was placed at the back of the room. Please come to the meeting fully charged.
Transportation and Lodging
See the Transportation and Lodging sections on the GMOD Europe 2010 pages for details.
Sponsor: Cambridge Computational Biology Institute
The September 2010 GMOD Meeting was 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 Miclem, Shelley Lawson, and Richard Smith for hosting the event. We could not have done this without their support, effort and time.
Feedback
Please provide your feedback! We will use it to guide future GMOD events.