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 its use in GMOD - suggested by Jonathan Warren

Please also suggest topics for the Satellite Meetings.

Guest Speaker


Jason Swedlow
Professor Jason Swedlow

The Open Microscopy Environment: Open Informatics for Biological Imaging

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

This is nearly final agenda for the meeting. Catered lunches will be provided on both days.

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, PPT
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 Lunch
13:45 GMOD and PSICQUIC Bruno Aranda PDF, PPT
14:15 MolGenIS and XGAP Morris Swertz PDF, PPT
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, PPT
09:45 DAS and its use in GMOD Jonathan Warren PDF, PPT
10:15 InterMine: new Mines and new features Richard Smith PDF, PPT
10:30 Break
11:00 Literature Curation in GMOD Daniel Renfro PDF, PPT
11:30 GO Curation Helen Field PDF, PPT
12:00 BioPivot: Applying Microsoft Live Labs Pivot to Problems in Bioinformatics Steve Taylor PDF, PPT
12:30 Lunch
13:45 CRAWL (Chado RESTful Access Web-service Layer) - a programmatic interface for querying pathogen genomics data Giles Verlarde PDF, PPT
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 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/
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
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 will be held in the Biffen Lecture Theatre, in the Department of Genetics on the University of Cambridge campus.

Wireless

The Biffen Lecture Theatre has 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:

If you are not associated with the University of Cambridge, then we will set up an account for you that should work through 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 has secured a 15-socket extension strip which will be placed on the bench at the front of the room. We'll work out a protocol for sharing this among the meeting's 40+ participants.

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 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

"It's tempting to see bioinformatics as a collection of potential problems. Being at a GMOD meeting helps us see bioinformatics as a collection of potential solutions."
Isabelle Phan, SBRI, and January 2009 GMOD Meeting Participant

Once the meeting is done, please provide feedback!