GMOD in the Cloud Genome Informatics November 3, 2011 Scott Cain GMOD Project Coordinator Ontario...
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Transcript of GMOD in the Cloud Genome Informatics November 3, 2011 Scott Cain GMOD Project Coordinator Ontario...
GMOD in the Cloud
Genome InformaticsNovember 3, 2011
Scott CainGMOD Project CoordinatorOntario Institute for Cancer [email protected]
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 gettingblown up
Garry's MOD (aka gmod.com)
Click to edit the title text formatSeveral GMOD Cloud Projects
Galaxy - Web-based platform for data intensive biomedical research
CloVR - Automated and portable sequence analysis
GBrowse2 - Web-based, scalable genome browser
cloud.gmod.org - Several integrated GMOD tools
http://gmod.org/wiki/Cloud
Click to edit the title text formatGalaxy Cloudman
Get Galaxy without the data or usage limitations.
Combine with Cloud BioLinux to have access to MANY tools.
Create an analysis cluster in minutes. Use autoscaling to get good performance at
low cost.
http://wiki.g2.bx.psu.edu/Admin/Cloud
Click to edit the title text formatDeploying Galaxy cluster on AWS
1.
2.3.
4.
Click to edit the title text formatExercising elasticity with autoscaling
Computation time: 9 Computation time: 9 hrshrs
Fixed cluster size5 nodes Computation cost: $20Computation cost: $20
20 nodes Computation cost: $50Computation cost: $50
Computation time: 6 hrsComputation time: 6 hrs
1 to 16 nodes
Computation time: 6 hrsComputation time: 6 hrs
Dynamic cluster size
Computation cost: $20Computation cost: $20
Click to edit the title text formatCloVR
Cloud Virtual Resource. Automated pipeline for sequence analysis. Uses 2 GMOD tools: Workflow and Ergatis. Use a virtual machine locally to interact with
resources in the cloud.
http://clovr.org/
Click to edit the title text formatCloVR Architecture
Click to edit the title text formatWhy the virtual machine?
Running the pipeline happens on the local machine, while the heavy lifting is done on the cloud/cluster
Click to edit the title text formatGBrowse2
Installed and configured recent release of GBrowse2.
Tools to allow automatically adding rendering servers.
Ability to add standard data sets.
http://gmod.org/wiki/GBrowse
Click to edit the title text formatGBrowse2
Yeast
Fly Worm
Human
Amazon Snapshots
RenderSlaves
Master
GBrowse2 in the Cloud
Click to edit the title text format
Click to edit the title text formatcloud.gmod.org
Tripal Drupal-based web frontend
Chado Generic organism DB schema
GBrowse Venerable genome browser
JBrowse Fast, AJAX genome browser
Sample data Saccharomyces cerevisiae
GMOD tools preinstalled:
Can be run as a micro machine (albeit slowly)
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
Click to edit the title text format
Click to edit the title text format
Click to edit the title text format
Click to edit the title text formatPotential use case for Cloud GMOD
Community annotation:Just add a web-start Apollo and set the security
group to allow it to connect to the database.
When WebApollo is ready, it's even easier: WA is an addon to JBrowse but allows collaborative editing.
Tripal and Drupal allow editing of most data types in Chado, and commenting on pages similar to a blog.
Click to edit the title text formatWhy use the cloud?
Avoid installation related issues (saves you time and frustration!)
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 formatFuture work
Get GBrowse2 AMI public (very soon)
Add Apollo to gmod.cloud.org (relatively soon)
Add WebApollo to gmod.cloud.org (as soon
as it's released)
Click to edit the title text formatConclusion
http://gmod.org/wiki/Cloud for more information on GMOD work in the cloud.
http://cloud.gmod.org/ for a running example of cloud.gmod.org.
http://clovr.org/ for more info on CloVR and to download the client VM.
http://getgalaxy.org/ for more information on getting Cloudman.
Click to edit the title text formatAcknowlegements
• Funding agencies: NIH, USDA ARS, NSF, Ontario Ministry of Economic Development and Innovation • Lincoln Stein, Chris Vandevelde • Enis Afgan and the Galaxy Team• Sam Angiuoli et al at UofM SOM• Stephen Ficklin and the Tripal group• Mitch Skinner and JBrowse developers• The rest of the GMOD community