What's New with GMOD (Scott Cain)

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

6. Generic, Flexible Schema

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.