1. GMOD in the Cloud Genome Informatics November 3, 2011 Scott Cain GMOD Project Coordinator Ontario Institute for Cancer Research scott@scottcain.net

2. Click to edit the title text format Introduction: 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.

3. Click to edit the title text format Who uses GMOD? Plus hundreds of others

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

5. Click to edit the title text format Several 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

6. Click to edit the title text format Galaxy 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

7. Click to edit the title text format Deploying Galaxy cluster on AWS 1. 2. 3. 4.

8. Click to edit the title text format Exercising elasticity with autoscaling Computation time: 9 hrs Fixed cluster size 5 nodes Computation cost: $20 20 nodes Computation cost: $50 Computation time: 6 hrs 1 to 16 nodes Computation time: 6 hrs Dynamic cluster size Computation cost: $20

9. Click to edit the title text format CloVR 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/

10. Click to edit the title text format CloVR Architecture

11. Click to edit the title text format Why the virtual machine? Running the pipeline happens on the local machine, while the heavy lifting is done on the cloud/cluster

12. Click to edit the title text format GBrowse2 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

13. Click to edit the title text format GBrowse2 Yeast FlyWorm Human Amazon Snapshots Render Slaves Master GBrowse2 in the Cloud

14. Click to edit the title text format

15. cloud.gmod.org Tripal Drupal-based web frontend ChadoGeneric organism DB schema GBrowseVenerable genome browser JBrowseFast, AJAX genome browser Sample dataSaccharomyces cerevisiae GMOD tools preinstalled: Can be run as a micro machine (albeit slowly)

16. Click to edit the title text format A 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

17. Click to edit the title text format

21. Potential 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.

22. Click to edit the title text format Why 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)

23. Click to edit the title text format Future 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)

24. Click to edit the title text format Conclusion 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.

25. Click to edit the title text format Acknowlegements 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