E Afgan - Zero to a bioinformatics analysis platform in four minutes
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This document discusses how to quickly set up a bioinformatics analysis platform in four minutes using various open source tools. It introduces CloudBioLinux for building custom tool suites, CloudMan for creating scalable processing platforms, Galaxy for exploratory analysis, and BioCloudCentral for getting started easily. A new Python library called Blend is also introduced for automating repetitive tasks related to analysis and infrastructure manipulation using the APIs of these tools.
E Afgan - Zero to a bioinformatics analysis platform in four minutes
- 1. Zero to a Bioinformatics Analysis Platform in Four Minutes Enis Afgan, Brad Chapman, Konstantinos Krampis, James Taylor BOSC 2012 Long Beach, CA
- 2. Australian National Research Cloud Provide computational infrastructure to support researchers needs Compute and Storage (~25,000 cores + ? PB)
- 3. What’s required for genomics? ✔ • Compute ✔ • Storage • Data resources o Ensembl, dbSNP, etc • Tools • Visualisation • Protocols • Expertise • Community!
- 5. Compute + Storage = IaaS
- 6. shell vs. IDE We want it now
- 7. What’s required for genomics? • Compute • Storage • Data resources o Ensembl, dbSNP, etc • Tools • Visualisation • Protocols • Expertise • Community!
- 8. Galaxy y y CloudMan CloudBioLinux y y BioCloudCentral.org
- 9. 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
- 11. • 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
- 12. And one new thing… blend o A python library for interacting with Galaxy’s API o And CloudMan o And BioCloudCentral
- 13. Request compute infrastructure Manipulate compute infrastructure Upload data and run analyses Docs and examples Test Automate repetitive tasks Distribute
- 15. 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
- 16. Questions? cloudbiolinux.org usecloudman.org usegalaxy.org biocloudcentral.org blend.readthedocs.org Visit the poster session (poster #10)