Difference between revisions of "September 2010 GMOD Meeting"

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m (Monday, 13 September)
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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.ppt|PPT]]
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| [[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.ppt|PPT]]
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| [[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.ppt|PPT]]
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| [[Media:MolGenISXGAPSept2010.pdf|PDF]]
 
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| 14:45
 
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Revision as of 08:36, 23 September 2010

Sept2010MtgLogo300.png
September 2010 GMOD Meeting
13-14 September 2010
Cambridge, UK
{{#icon: GMOD2010Europe300.png|Part of GMOD Europe 2010|200px|GMOD Europe 2010}}

__NOTITLE__

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.


Registration

The GMOD Meeting had a registration fee (£50 early, £65 late) to cover catered lunches, coffee/tea breaks, and other expenses.

Guest Speaker


Jason Swedlow
Professor Jason Swedlow

The Open Microscopy Environment: Open Informatics for Biological Imaging

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 PDF
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 PDF
14:15 MolGenIS and XGAP Morris Swertz PDF
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 PDF
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 PDF
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

BritishSocket.jpg

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

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.