e afgan - zero to a bioinformatics analysis platform in four minutes

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Zero to a Bioinformatics Analysis Platform in Four Minutes Enis Afgan , Brad Chapman, Konstantinos Krampis, James Taylor BOSC 2012 Long Beach, CA

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Presentation at BOSC2012 by E Afgan - Zero to a bioinformatics analysis platform in four minutes

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Page 1: E Afgan - Zero to a bioinformatics analysis platform in four minutes

Zero to a Bioinformatics Analysis Platform in Four Minutes

Enis Afgan, Brad Chapman, Konstantinos Krampis, James Taylor

BOSC 2012 Long Beach, CA

Page 2: E Afgan - Zero to a bioinformatics analysis platform in four minutes

Australian National Research Cloud

Provide computational infrastructure to support researchers needs

Compute and Storage

(~25,000 cores + ? PB)

Page 3: E Afgan - Zero to a bioinformatics analysis platform in four minutes

What’s required for genomics? •  Compute

•  Storage

•  Data resources o  Ensembl, dbSNP, etc

•  Tools

•  Visualisation

•  Protocols

•  Expertise

•  Community!

✔ ✔

Page 4: E Afgan - Zero to a bioinformatics analysis platform in four minutes

Genomics Virtual Lab

Page 5: E Afgan - Zero to a bioinformatics analysis platform in four minutes

Compute + Storage = IaaS

Page 6: E Afgan - Zero to a bioinformatics analysis platform in four minutes

shell vs. IDE

We want it now

Page 7: E Afgan - Zero to a bioinformatics analysis platform in four minutes

What’s required for genomics? •  Compute

•  Storage

•  Data resources o  Ensembl, dbSNP, etc

•  Tools

•  Visualisation

•  Protocols

•  Expertise

•  Community!

Page 8: E Afgan - Zero to a bioinformatics analysis platform in four minutes

Galaxy

BioCloudCentral.org

CloudBioLinux

CloudMan y

y

y

y

Page 9: E Afgan - Zero to a bioinformatics analysis platform in four minutes

Playing together •  CloudBioLinux

o  Quickly build-your-own tool suite / ready to roll o  Graphical & command line access

•  CloudMan o  Create a scalable and shareable processing platform

•  Galaxy o  Do exploratory analysis

•  BioCloudCentral.org o  Get started easily

Page 10: E Afgan - Zero to a bioinformatics analysis platform in four minutes
Page 11: E Afgan - Zero to a bioinformatics analysis platform in four minutes

•  Bundle infrastructure with an analysis tool suite, quickly o  Validate our approach o  Easier to maintain and replicate

•  Expose it all via at a variety of interfaces o  Support meta-analysis workflow

•  Move forward o  Add new features o  Start using it

Page 12: E Afgan - Zero to a bioinformatics analysis platform in four minutes

And one new thing…

blend

o  A python library for interacting with Galaxy’s API o  And CloudMan o  And BioCloudCentral

Page 13: E Afgan - Zero to a bioinformatics analysis platform in four minutes

Request compute infrastructure

Manipulate compute infrastructure

Upload data and run analyses

Test

Docs and examples

Distribute

Automate repetitive tasks

Page 14: E Afgan - Zero to a bioinformatics analysis platform in four minutes

Docs and examples included http://blend.readthedocs.org/

Page 15: E Afgan - Zero to a bioinformatics analysis platform in four minutes

Playing together •  CloudBioLinux

o  Build-your-own tool suite / ready to roll o  Graphical & command line access

•  CloudMan o  Create a scalable and shareable processing platform

•  BioCloudCentral.org o  Get started easily

•  Galaxy o  Do exploratory analysis

•  Blend library o  Automate repetitive tasks: analysis AND infrastructure

Page 16: E Afgan - Zero to a bioinformatics analysis platform in four minutes

Questions? cloudbiolinux.org usecloudman.org usegalaxy.org biocloudcentral.org blend.readthedocs.org Visit the poster session (poster #10)