Presentation at BOSC2012 by S Cain - GMOD in the cloud

1. GMOD in the Cloud
Scott Cain
GMOD Project Coordinator
Ontario Institute for Cancer Research
scott@scottcain.net
BOSC
July 14, 2012

2. Introduction: GMOD is …
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• 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.

3. Who uses GMOD?
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Plus hundreds of others

4. GMOD in the Cloud
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What GMOD in the cloud isn't:
Clouds
Guy getting
blown up
Garry's MOD (aka gmod.com)

5. cloud.gmod.org
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GMOD tools preinstalled:
Tripal Drupal-based web frontend
Chado Generic organism DB schema
GBrowse Venerable genome browser
JBrowse Fast, AJAX genome browser
Sample data Saccharomyces cerevisiae
WebApollo* *Coming soon!
Can be run as a micro machine (albeit slowly)

6. cloud.gmod.org
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AMI
GMOD
Your data
Software and configs

7. WebApollo
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8. A little more on Tripal
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Based on the popular CMS Drupal.
Several modules written to serve as an
interface for Chado:
Controlled Vocabularies
Features
Analyses
Libraries
Stocks
Integrated job management

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13. Potential use case for Cloud GMOD
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Community annotation jamboree:
- Clone GitC image
- Load in computational annotations (MAKER)
- Configure GBrowse, JBrowse, WebApollo
- Unleash the wisdom of the masses (or
trained spider monkeys, or undergrads--
whatever you have)
- When the jamboree is over, dump out as
GFF and shutdown the instance.

14. Why use the cloud?
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Avoid installation related issues (saves you time
and frustration (and me for that matter)!)
Save money (how much, of course, depends)
Availability of common genomic data sets
(several projects already make these available
at AWS)

15. Acknowlegements
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• Funding agencies: NIH, USDA ARS, NSF,
Ontario government
• Lincoln Stein
• Stephen Ficklin and the Tripal group
• Rob Buels, Mitch Skinner and JBrowse
developers
• The rest of the GMOD community--many bug
reports, fixes, users