GMOD in the Cloud

BOSC July 14, 2012

Scott Cain GMOD Project Coordinator Ontario Institute for Cancer Research scott@scottcain.net

Click to edit the title text formatIntroduction: GMOD is …

• 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.

Click to edit the title text formatWho uses GMOD?

Plus hundreds of others

Click to edit the title text formatGMOD in the Cloud

What GMOD in the cloud isn't:

Clouds

Guy getting blown up

Garry's MOD (aka gmod.com)

Click to edit the title text formatcloud.gmod.org

Tripal Drupal-based web frontendChado Generic organism DB schema

GBrowse Venerable genome browserJBrowse Fast, AJAX genome browser

Sample data Saccharomyces cerevisiaeWebApollo* *Coming soon!

GMOD tools preinstalled:

Can be run as a micro machine (albeit slowly)

Click to edit the title text formatcloud.gmod.org

AMI

GMOD Software

Your data and configs

Click to edit the title text formatWebApollo

Click to edit the title text formatA little more on Tripal

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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Click to edit the title text formatPotential use case for Cloud GMOD

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.

Click to edit the title text formatWhy use the cloud?

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)

Click to edit the title text formatAcknowlegements

• 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