GMOD in the Cloud

GMOD in the Cloud

Genome Informatics

November 3, 2011

Scott Cain

GMOD Project Coordinator

Ontario Institute for Cancer Research

scott@scottcain.net

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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.

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Who uses GMOD?

Plus hundreds of others

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GMOD in the Cloud

What GMOD in the cloud isn't:


Clouds

Guy getting

blown up

Garry's MOD (aka gmod.com)

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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

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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

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Deploying Galaxy cluster on AWS

1.

2.

3.

4.

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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

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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/

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CloVR Architecture

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Why the virtual machine?

Running the pipeline happens on the local machine,

while the heavy lifting is done on the cloud/cluster

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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


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GBrowse2

Yeast

Fly

Worm

Human

Amazon Snapshots

Render

Slaves

Master

GBrowse2 in the Cloud

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cloud.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)

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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

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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.

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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)

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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)

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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.




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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