GMOD

August 2009 GMOD Meeting

August 2009 GMOD Meeting 6-7 August, 2009 Oxford UK Part of GMOD Europe 2009, five days of GMOD including a GMOD Summer School

This GMOD Community Meeting was held 6-7 August, 2009, in Oxford UK. The meeting was a part of GMOD Europe 2009, a week long event that also included a GMOD Summer School. This is the first time a GMOD meeting has been held in Europe.

As with previous GMOD meetings, this meeting had a mixture of project talks, component talks, and user talks. The agenda was driven by attendee suggestions. The two previous meetings were the January 2009 and July 2008 meetings. GMOD meetings are an excellent way to meet GMOD developers and users, and to learn (and affect) what’s coming in the project.

Contents

• 1 Schedule
• 2 Presentations
  • 2.1 GMOD Project Talks
    • 2.1.1 HHMI Science Education Alliance
    • 2.1.2 What’s new
    • 2.1.3 GMOD Summer School
    • 2.1.4 Outreach
    • 2.1.5 GMOD Community Surveys
    • 2.1.6 Upcoming GMOD Hackathon ?
  • 2.2 Linked Data for GMOD Databases
    • 2.2.1 OpenFlyData
    • 2.2.2 Open-BioMed
    • 2.2.3 RDF & SPARQL: Benefits & Risks
  • 2.3 GMOD in the Trenches
    • 2.3.1 GBrowse at CBRG
    • 2.3.2 Extending GBrowse
    • 2.3.3 Make Existing GBrowse More Useful to External Developers
  • 2.4 A DBIx Class layer for Chado
  • 2.5 GMOD Biological Object Layer
    • 2.5.1 GBOL Architecture
    • 2.5.2 Biological Layer Configuration
    • 2.5.3 Future Developments
  • 2.6 A Restful interface for MODs
  • 2.7 Quest for Standard: Sequence alignment/map format (SAM) and SAMtools
    • 2.7.1 Quest for Standards
    • 2.7.2 SAM Format
    • 2.7.3 BAM Format
    • 2.7.4 APIs, Implementations and Supported Platforms
    • 2.7.5 Displaying Alignments
  • 2.8 Visualising NGS Data in GBrowse 2
  • 2.9 GBrowse: Lessons Learned and Statement of Interest
    • 2.9.1 History and Current GBrowse Infrastructure
    • 2.9.2 Statement of Interest: Requirements and Needs
      • 2.9.2.1 GBrowse Database Adaptors
      • 2.9.2.2 GBrowse User Interaction
      • 2.9.2.3 GBrowse Configuration Files
      • 2.9.2.4 Metadata Web Services
    • 2.9.3 Conclusion / Discussion
  • 2.10 JBrowse
  • 2.11 GBrowse_syn
    • 2.11.1 Other GMOD Synteny Viewers
    • 2.11.2 GBrowse_syn
    • 2.11.3 Where do I get data for GBrowse_syn?
    • 2.11.4 Using GBrowse_syn
    • 2.11.5 Future Developments
  • 2.12 GBrowse.org
  • 2.13 DAS update
    • 2.13.1 DAS 1.6E
    • 2.13.2 DAS Registry
    • 2.13.3 Current and Future Work
    • 2.13.4 Some Implementations
  • 2.14 InterMine update
    • 2.14.1 Mines4Mods
  • 2.15 Show and Tell, Discussion
• 3 Agenda Suggestions
• 4 Location
• 5 Lodging
• 6 Cost and Registration
• 7 Mailing List
• 8 Sponsor
• 9 Attendees
• 10 Feedback
• 11 Next Meeting: January 2010 in San Diego California

Schedule

Heng Li

Wellcome Trust Sanger Institute

Dr Heng Li of the Sanger Institute was the special guest speaker. Heng discussed his recent work on SAMtools, a set of file formats and scripts for efficiently storing and accessing next generation sequence data. Heng is a developer on several projects focused on next generation sequencing, including SAMtools, BWA, and MAQ.

Date	Time	Session	Link(s)
Thursday 6 August	8:30-12:00	Last half day of 2009 GMOD Summer School - Europe
	13:30-14:30	Scott Cain - Introductions and the State of GMOD	Prezi, PPT, PDF, Summary
	14:30-15:00	Dave Clements - [Semantic web](Category%253ASemantic_web "Category%253ASemantic web") - [JBrowse](Category%253AJBrowse "Category%253AJBrowse") ## Navigation menu ### Navigation - [GMOD Home](Main_Page) - [Software](GMOD_Components) - [Categories / Tags](Categories) ### Documentation - [Overview](Overview) - [FAQs](Category%253AFAQ) - [HOWTOs](Category%253AHOWTO) - [Glossary](Glossary) ### Community - [GMOD News](GMOD_News) - [Training / Outreach](Training_and_Outreach) - [Support](Support) - [GMOD Promotion](GMOD_Promotion) - [Meetings](Meetings) - [Calendar](Calendar) ### Tools - Browse properties - Last updated at 19:37 on 4 September 2013. - Content is available under a GNU Free Documentation License unless otherwise noted.