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. Expensive sequencing and large organizations
Commodity sequencing and small labs
●
large sequencing center, multi-million, broad-impact sequencing projects
● dedicated bioinformatics department, large Sun Grid Engine cluster
● 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

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

4. “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 labs 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 ?

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

6. Cloud BioLinux
simple for end-users
signup at
aws.amazon.com
then
aws.amazon.com/console
and
http://tinyurl.com/cloud-biolinux-tutorial

7. Amazon EC2
→
linux desktop
via remote
desktop client

8. 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

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

10. 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

11. 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 open.eucalyptus.com

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

13. Cloud Biolinux
The future
● expand community, receive feedback, add more software to the VM
● groups.google.com/cloudbiolinux and cloudbiolinux.org
● add data analysis pipelines that are used by sequencing centers
● actively seeking funding to put major effort in development
● 2011 ISMB/BOSC in Vienna, Austria, http://metalab.at/
●

14. Acknowledgments & Credits
Brad Chapman - development of the fabric scripts and community organizer
Tim Booth, Mesude Bicak, Dawn Field, Bela Tiwari – BioLinux 6.0
J. Craig Venter Inst. - time allowed to work on an open-source project
D. Gomez, E. Navarro, J. Shao, I. Singh – JCVI technology innovation
Deepak Singh and AWS - education grant supporting ISMB / BOSC workshop
Members of the Cloud Biolinux community – precious development time
Thank you !