Proteomics:Action Items

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Ishtiaq Ahmad

  • Make Warp2d work with MzXML import
  • Implement full IBM toolchain in DAF and run on the grid
  • Research steps needed to implement DAF as looper in Galaxy
  • Implement IBM toolchain in Galaxy
  • Visit AMC and talk about Moteur

Twan America

  • Test warp2d web service

Bas van Breukelen

  • Send labeled orbitrap data to Peter Horvatovich (spiked? pre-analysed?) to test with the IBM toolchain
  • Send worried message to the standard setting committee for MZQuantML on the phased development
  • Send EMC a data set for pathway analysis

George Byelas

  • Test different frameworks using the common JAVA API before August 20.

Carsten Byrman

  • Add analysis tool source code to NBIC Trac
  • Make convertor from APML to R generally available
  • Work on automated collection/summary step after 1000 fold double cross validation
  • Make tools for R-dependency resolution on the grid available to others
  • Get on to the galaxy server

Salvatore Cappadona

  • Get MSInspect for labeled quantification into galaxy

Joost de Groot

  • Make local tools available as command line tools rather than GUI only
  • Implement parsers for more generic data formats
  • Implement MzIdentML

Berend Hoekman

  • Investigate what convertors are needed
  • Install framework on Galaxy

Rob Hooft

  • Set up Proteomics Galaxy tool repository

Peter Horvatovich

  • Complete the tool inventory and chase people to add their information
  • Run IBM toolchain on spiked data from Wageningen
  • Analyse data to be received from Bas

Don de Lange

  • Go to Utrecht Weekly
  • Make Elisabeths tools for mapping to biogrid and visualisation in cytoscape are generally available
  • Analyze Bas' data together with Elizabeth

Pieter Neerincx

  • Install SuperHirn and other dependencies in Galaxy for Berend
  • Tools that are not used/working/installed should be removed from Galaxy
  • Tools in galaxy should be grouped by task force
  • Add APML as data format in Galaxy
  • Check whether workflow editor works on NBIC Galaxy
  • Check whether the admin mail list address for Galaxy listed on the server is still up to date.

Andrew Stubbs

Morris Swertz