1. Cloud BioLinux: open source, fully-customizable
bioinformatics computing on the cloud for the
genomics community and beyond
BOSC 2011 - Vienna, Austria
Ntino Krampis, PhD
Asst. Professor
J. Craig Venter Institute (JCVI)
agbiotec@gmail.com

2. The community is what makes an open source project
Brad Chapman, Tim Booth, Mesude Bicak, Dawn Field, Dan Pass –
core development and planning
Enis Afgan, Pjotr Prins, Stephen Möller -
and all other members of the cloud biolinux community that move it fwd
J. Craig Venter Inst. -
time allowed to work on an open-source project

3. Expensive sequencing and large organizations
Commodity sequencing and small labs
●
large sequencing center, multi-million, broad-impact sequencing projects
● dedicated bioinformatics department, compute clusters
● small-factor, bench-top sequencer available: GS Junior by 454
● sequencing as a standard technique in basic biology and genetics research
● RNAseq and ChiPseq, and each biologist will be tackling a metagenome

4. Will small labs become the long tail of sequencing ?
amount of
sequencing Credit: WikiMedia Commons
number of labs

5. “Bioinformatics nation is a land of city-states” Lincoln Stein
● small labs building small-scale bioinformatics infrastructures
● duplication of effort in compiling and installing software tools
● some groups have no hardware, expertise, or time to install and run software
● NEBC BioLinux ( tinyurl.com/BioLinux-NEBC ) 100+ pre-configured tools
● example: glimmer, hmmer, phylip, rasmol, genespring, clustalw, EMBOSS
how about large-scale sequence datasets ?

6. Cloud BioLinux
pre-configured and on-demand bioinformatics computing on the cloud
●
JCVI cloud computing research
● NEBC BioLinux software repository
+ ● community effort – Hackathon / BOSC 2010 - 11
● Virtual Machine (VM) on Amazon cloud
large-scale computing independently of
=
●
institutional or geographic boundaries
● only need a desktop computer with internet access
cloudbiolinux.org

7. simple for end-users signup at
aws.amazon.com
http://tinyurl.com/cloud-biolinux-tutorial

8. Amazon EC2
→
linux desktop
via remote
desktop client

9. What if I want to
share my
alignments with
a collaborator?
save your data as
a new VM
0.10$ / GB /
month
at 15GB, it costs
1.5$ / month

10. “whole system snapshot exchange” (Dudley and Butte 2010)
capture the state of the computing system and data
software execution parameters and “massaged” input datasets

11. Cloud BioLinux developer's framework
create cloud VM / images with standardized software configurations
● customize Cloud BioLinux based on community requirements
● mix and match software from NEBC or other (DebianMed, Scientific Linux etc.)
● share customized VMs with collaborators, avoiding effort duplication
● deploy Cloud BioLinux on private and local clouds

12. software domains in bioinformatics: nextgen
sequencing, de novo assembly, annotation, phylogeny,
molecular structures, gene expression analysis
github.com/chapmanb/cloudbiolinux

13. Cloud BioLinux developer's framework
● based on python-fabric auto-deployment tool
● software components listed in plain text files
● collaborators use files to share descriptions of cloud VM / images
● start with a bare-bones VM / image
● fabric downloads and installs specified software
tinyurl.com/python-fabric

14. Cloud Biolinux
The future
● groups.google.com/cloudbiolinux and cloudbiolinux.org
● expand community, receive feedback, add more software to the VM
● scalable computing: SGE (Galaxy Cloudman), Hadoop (cloudgene.uibk.ac.at)
● add next-gen sequencing pipelines, NIH funding - adds effort in development
● We just had a 2-day codefest at the MetaLab, http://metalab.at/

15. and before I finish
this talk....

20. Thank you !