G07-Misc-Gmod
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The document provides updates on the GMOD project, including new developments to the Chado schema, Tripal toolkit, GBrowse genome browser, and efforts to deploy GMOD tools on cloud platforms. Key updates include a new natural diversity Chado module, improved features in Tripal 0.3b like loaders and custom templates, new user account options in GBrowse2, and work to provide pre-configured GMOD server images on Amazon Web Services. The document acknowledges funding sources and contributors to ongoing work.
G07-Misc-Gmod
- 1. Project Update BOSC 2011 Scott Cain GMOD Project Coordinator Ontario Institute for Cancer Research scott@scottcain.net
- 2. What Is GMOD? • A set of interoperable open-source software components for visualizing, annotating, and managing biological data. • An active community of developers and users asking diverse questions, and facing common challenges, with their biological data.
- 4. What's New • Chado Natural Diversity Module • Tripal • GBrowse2 • GMOD in the Cloud
- 5. Natural Diversity Chado Module
- 7. Use case: insecticide resistance assay
- 8. Use case: mosquito field collection
- 9. Use case: rice growth condition
- 10. Tripal: a construction toolkit for online biological databases Relational Database Web Content Management • Drupal GMOD Chado • Requires little or no programming Community supported • Users can change content directly Well documented • Well documented and supported Integrates with a suite of tools • Very Popular
- 11. Tripal: a construction toolkit for online biological databases • Benefits – Reduced IT costs (less programming) – Faster time to release – Active development (released v0.3b in June) – Support: Mailing list, online tutorials, responsive developers – Already used by multiple genome databases – Use of Chado allows for use of other GMOD tools • Maker: automatic genome curation • Apollo: manual curation • GBrowse: genome visualization – Use of Drupal allows for incorporation of non-biological content • Forums, RSS feeds, community pages, • Site stake-holders can add / update content without waiting on programmers
- 12. Tripal: a construction toolkit for online biological databases
- 13. Tripal: what’s new? • The following functionality is new with v0.3b • Chado Installer • OBO, GFF, GAF and FASTA file loaders • Formalized API for customizing templates and future module development • Integration with Drupal Panels and Views to allow for non-programmatic customizations and data mining • Currently under development • Chado bulk loader for loading of any tab delimited data • Additional support for chado tables, such as the Natural Diversity tables, publications, contact, etc.
- 14. GBrowse2 • Very widely installed genome browser (hundreds of installed instances) • Perl/Apache based • Support for multiple database backends
- 15. New in GBrowse2 (Since last BOSC) • User accounts: • OpenID • Plugable authentication support (with example LDAP plugin) • "Details multiplier" for smooth side scrolling • iPad support • Debian package • REST API • User defined "favorite tracks"
- 16. GMOD on the Cloud • Still in its infancy • Goal: really easy set up of servers for "naive" and/or time crunched users • Platform: AWS • Micro AMI to allow new users to experiment without spending much (any) money (my first month's bill: $0.65)
- 17. GMOD on the Cloud • Available now: GBrowse2 • Coming soon: mountable stores with standard datasets (code in git now) • Also coming soon: AMI with Chado, GBrowse2, Tripal
- 18. More GMOD Resources • Community meeting: October 12-13 in Toronto, Canada. • Web page: http://gmod.org/ • Many mailing lists; help@gmod.org • Workshops: • PAG, January, San Diego, California, 1day • NESCent, Summer '12, Durham, NC, 5 days
- 19. Acknowledgments NatDiv Tripal GBrowse2 Dave Clements Stephen Ficklin Lincoln Stein Scott Cain Meg Staton Chris Vandevelde Sook Jung Chun-Huai Cheng Sonu Lall Dorrie Main Laceyanne Sanderson Tony deCatanzaro Stephen Ficklin Dorrie Main Robert Buels Bob MacCallum Peter Ruzanov Seth Redmond Naama Menda Funding Rob Buels GMOD is supported by a specific Genevieve DeClerk cooperative agreement from the USDA Agricultural Research Service, and by NIH Maren Friesen grants co-funded from the National Yuri Bendana Human Genome Research Institute and Pantelis Topalis the National Institute of General Medical Sciences. Additionally, GBrowse Emmanuel Dialynas development is supported by the Ontario Ministry of Research and Innovation.