Download - Providing Bioinformatics Services on Cloud

Christophe Blanchet, Clément Gauthey

Infrastructure Distributed for BiologyIDB-IBCP CNRS FR3302 - LYON - FRANCE

http://idee-b.ibcp.fr

IDB acknowledges co-funding by the European Community's Seventh Framework Programme (INFSO-RI-261552) and the French National Research Agency's Arpege Programme (ANR-10-SEGI-001)

Providing Bioinformatics Serviceson Cloud

C. Blanchet and C. GautheyEGI CF13, Manchester, 9 April 2013

Infrastructure Distributed for Biology - IDB

CNRS-IBCP FR3302, Lyon, FRANCE

EGI CF13, Manchester, 9 April 2013

Bioinformatics Today• Biological data are big data

• 1512 online databases (NAR Database Issue 2013)

• Institut Sanger, UK, 5 PB

• Beijing Genome Institute, China, 4 sites, 10 PB➡ Big data in lot of places

• Analysing such data became difficult• Scale-up of the analyses : gene/protein to complete genome/

proteome, ...

• Lot of different daily-used tools

• That need to be combined in workflows

• Usual interfaces: portals, Web services, federation,...➡ Datacenters with ease of access/use

• Distributed resources• Experimental platforms: NGS, imaging, ...

• Bioinformatics platforms➡ Federation of datacenters

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Sequencing Genomes

source: www.politigenomics.com/next-generation-sequencing-informatics

Complete genome sequencing become a lab commodity with

NGS (cheap and efficient)

source: www.genomesonline.org

http://www.genomesonline.org





Infrastructures in Biology

Lot of toolsand web servicesto treat and vizualize

lot of data


The scene

• Bioinformatics services providers• Is it easy to deploy lot of (incompatible) tools ?

• To make them connected to public databases ?

• To limit transfer of huge data ?

• To provide users with their own computing resources ?

• With their own isolated storage ?

• Scientists• Is it easy to access/use these tools ?

• To adapt to your usage ?

• To get your/other tools deployed on a datacenter ?

• To combine them ?

• To get my own computing/storage resources ?


IDB’s Cloud

• Cloud workbench for Biology• 13 turnkey bioinformatics appliances (as of Apr. 2013)

• Running since Sept. 2011, opened to Biology community

• Lyon, FRANCE

• Powered by• StratusLab

• Compute nodes, Block storage

• +900 cores, +4TB RAM, 36TB vdisks

• Mainly Intel SandyBridge servers with 32c 128GB

• Bigmen servers with 64c 768GB

• VMs from 1 to 64c, 512MB to 760GB RAM

• + Openstack

• Object storage (Swift)

• +200 TB redundant & scalable storage


Driven throught a simple web interface


Integrate Bioinformatics Tools in Cloud

BLAST

GOR4

FastASSearch

Abyss

ClustalW

Bioinformatics

Tools

RayBWA

PhyML RedHat,CentOS

Debian,Ubuntu

Suse

LinuxVirtual machines

Createnew

Appliance

Bioinformatics Marketplace

NGSStructure Galaxy ARIA (…)Sequence

• Appliances are virtual machines• small : few GB, easy to convert in most virtualization formats

• Installed and pre-configured with common bioinformatics tools• e.g. BLAST, Clustalw, ARIA, MEME, HMMer, TopHat, BWA, Samtools, etc.


Bioinformatics Appliances


Select your bioinformatics tools


Run Bioinformatics Cloud InstancesBioinformatics Marketplace

NGSStructure Galaxy ARIA (…)Sequence

IBCP's CloudResources

BLAST,Clustal,

etc.

PaaS

WorkersVM CNS

Shar

ed F

S

launch jobssshIaaS

Master & StorageVM ARIA

Portal

Laun

chIn

stan

ces


Manage your Cloud Instances


UNIPROT

PDB

EMBLPROSITE

Genomes

Public

Data sources

BioinformaticsCloud

BLAST,Clustal,

etc.

PaaS

WorkersVM CNS

Shar

ed F

S

launch jobssshIaaS

Master & StorageVM ARIA

Portal

shared(NFS)

User

Persistent data

pdisk(iSCSI)

Biological Data in CloudUpload your data

Get your results

scp http/S3

scp http/S3


Example: ‘biocompute’ Appliance

• Use your own instance(s)

• With pre-installed standard bioinformatics tools• BLAST, FastA, SSearch,HMM,...

• ClustalW2, Clustal-Omega, Muscle,..

• Bowtie(2), BWA, samtools, ...

• MEME, R, etc.

• Connected to public reference data• Uniprot, EMBL, genomes, PDB, etc.

• Automaticaly shared to the VMs


Example: Galaxy portal for NGS analyses

• Analyse NGS data

• portal Galaxy is widely used in the community

• connected to large public data: sequences and indexes

• large user data (GBs)

• Preserve workflows and results (persistent storage)


Example: Proteomics• Motivation

• Collaboration with a mass spectroscopy platform

• Running out of space on their local resources

• Protein identification• Mass experimental data

• Reference databases : nr, Swiss-Prot

• Reference screening tools:OMSSA, X!Tandem

• User interface• Remote display

• NX

• Reference GUIs

• SearchGUI

• PeptidShaker

source: PeptideShaker site


Conclusion• Provide turnkey bioinformatics appliances

• Standard tools and pipelines

• Interoperability: ready to run on cloud

• Easier to transfer appliances than data (GB vs TB)

• Provide a cloud infrastructure tightly connected to existing bioinformatics infrastructure• Public IDB’s bioinformatics cloud

• Linked to public biological databases

• In collaboration with the French Bioinformatics Institute

• Ease the usage by scientists• Usual bioinformatics gateways

• Persistent and large ubiquitous storage

• Web interface for cloud management


Perspectives• Define good practices to provide academic

community and industry with bioinformatics services!

• French Bioinformatics Institute - IFB• Goals are to provide core bioinformatics resources to the

national and international life science research community in key fields such as genomics, proteomics, systems biology, etc.

• Aims at building a national academic cloud devoted to Bioinformatics, inspired by the model evaluated through the IDB’s cloud.

• European ELIXIR infrastructure• To build a sustainable European infrastructure for biological

information, supporting life science research and its translation

• IFB will be the French representative in ELIXIR.


• Acknowledgment

• StratusLab members

• co-funding by the European Community's Seventh Framework Programme (INFSO-RI-261552) and by the French National Research Agency's Arpege Programme (ANR-10-SEGI-001).

Questions ?


http://www.stratuslab.eu/

http://www.stratuslab.eu/

http://mapreduce.inria.fr/

http://mapreduce.inria.fr/



Download - Providing Bioinformatics Services on Cloud

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