F02-Cloud-Cloud BioLinux

F02-Cloud-Cloud BioLinux

• 1.
  Cloud BioLinux: opensource, 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 andlarge 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 labsbecome the long tail of sequencing ? amount of sequencing Credit: WikiMedia Commons number of labs
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  “Bioinformatics nation isa 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 viaremote desktop client
• 8.
  What if Iwant 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 snapshotexchange” (Dudley and Butte 2010) capture the state of the computing system and data software execution parameters and “massaged” input datasets
• 10.
  Cloud BioLinux developer'sframework 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'sframework ● 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 inbioinformatics: 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 BradChapman - 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 !