Kallio Chipster Bosc2008
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  • 1. Chipster – user friendly microarray analysis software
      • Aleksi Kallio
      • CSC – The Finnish IT Center for Science
      • July 19, BOSC 2008
  • 2. Contents
    • Chipster, brief introduction
    • System architecture and design
    • Two paradigm approach
    • Discussion
  • 3. Chipster
    • Goal: Easy access to up-to-date analysis methods (R/Bioconductor)
    • Features
      • Intuitive graphical user interface
      • Comprehensive selection of analysis tools and visualizations
      • Possibility to construct (and share) automatic analysis workflows
      • Support for different array types (Affymetrix, Agilent, Illumina, cDNA)
      • Compatible with Windows, Linux and Mac OS X
      • The graphical client program is easy to install and update
      • Analysis jobs are run on central computing servers
      • Available for local installations, open source.
    • Covered in more detail in
      • Technology Track presentation TT22 on Monday 3:45 pm
      • Poster A13 on Sunday 5:45 pm
  • 4. Technical overview
    • A distributed system implemented with Java and JMS messaging architecture
    • Generic platform and user oriented functional layer on top of that
    • Connected to different external analysis tools
    • Used via graphical user interface
    • User is the king!
  • 5. System architecture ANALYSIS VISUALISATION internet brokers client SSL servers desktop user comp. nodes auth.
  • 6. System architecture web services ANALYSIS VISUALISATION internet brokers client local resources SSL servers desktop user comp. nodes auth.
  • 7. Our development approach
    • User oriented development
      • A lot of effort to keep development team in contact with the rest of the world
      • Agile methodology: release early, release often
      • Communication and espionage needed
    • The minimalist principle: You Are Not Going To Need It
      • Features built only when and if needed
      • Same applies for the development process itself
    • Moving from concrete to abstract, not vice versa
      • What happens when you isolate a programmer from the rest
      • of the world? It starts to write software frameworks.
  • 8. Combining two paradigms
    • Most end user applications are data (document) centric
    • Scientific data analysis calls for workflow orientation
    • Chipster combines the two paradigms
    • Workflow system
      • Workflows are recorded as user analyses the data (“programming by example”) and can be saved as BeanShell scripts for reusing and extending
    • Data management system
      • Manages data transfers and caching in the messaging system
      • Offers an high level API for visualisations
  • 9. Application stack servers messaging data manager task executor selection feature plugins workflows user interface
  • 10. Extending Chipster
    • Own analysis tools can be added (on fly)
      • Currently R, command line and Java supported
    • New type of components can be added to system
    • Web Services interfaces being developed (EMBRACE)
    • All microarray related functionality in an own layer at client side => system can be adapted for other type of data by implementing a new layer
  • 11.
    • Eija Korpelainen
    • Jarno Tuimala
    • Taavi Hupponen
    • Petri Klemelä, Mikko Koski, Janne Käki, Mika Rissanen
    • All the pilot users
    • Department of Computer Science, University of Helsinki
    • Tekes, the Finnish funding agency for technology and innovation
    Acknowledgements
  • 12. For more information
    • Main web page at chipster.csc.fi
    • Code available under GPL at chipster.sourceforge.net
      • In future probably somewhere else than SourceForge
    • Note! User oriented Technology Track presentation on Monday at 3:45 in room 701B
    • Note! Poster A13 on Sunday poster session at 5:45 – 8:30 in hall E
    • We can be contacted via chipster @ csc.fi
  • 13. For discussion
    • How to deal with dependency?
      • In modern bioinformatics software development, you are always depending on others for major parts of your functionality
      • Example: Chipster is depending on R/Bioconductor and some other external analysis tools, and some Web Services
    • How to make dependency related issues easier in future?
      • Web Services? Semantic Web?
      • Grids? Cloud computing? Virtual machines?
      • Common programming languages? Common runtimes?