Proteomics:Programmers Meeting on 2010-04-16

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Location and time

  • Location: Hojel City Center, gebouw D (5th floor), Graadt van Roggenweg 340, 3531 AH Utrecht
  • Time: 9:00-10:30



Not kept...

Discussion history

Pieter Neerincx

  • Virtual Server for Corra is now running in Groningen. Got access recently, now installing.
  • Wants the Corra/APML to be tested and evaluated before the next proteomics progress meeting
  • Pieter will visit Wageningen
  • Pieter will visit Rotterdam/EMC

Wim Spee

  • Revived ProteoPipeline, a Java library for stream based proteomics data processing. The streaming works only for actions that are taken on a spectrum-by-spectrum basis. The data library is unique and valuable.
  • Wim will talk to Bas about publication of this work
  • Wim will get it into gForge
  • A future action is to make this connect to the existing identification tools

Ishtiaq Ahmad

  • Task server now tested, works well
  • Currently moving hosting from a private machine to the Grid UI. This is causing some problems because the UI has not been used as a web server before, and many access control issues must be resolved.
  • Made a taverna workflow for the 2D alignment
  • Ishtiaq will:
    • Ehance the web page
    • Make sure the application runs reliably on the grid UI
    • Get the taverna workflow into myexperiment with documentation
    • Write a module to get the grid resuts back to the user
    • Solve the registration service limitations
      • Check out Oauth and OpenID
      • Later: different disc quota dependent on the user
    • Add DAF documentation to the Trac for Molgenis

Peter Horvatovich

  • George is testing grid/cloud computing tools.
  • Peter will test these
  • Peter will make contact with Corra originators via his dept head.

Carsten Byrman

  • Existing actions still pending
  • Carsten will publish his workflow
  • Carsten will judge whether APML is suitable for these services
  • APML can not store images. In a discussion this is not deemed to be a problem, because the images are "output only" and do not serve as input to a later stage of the work flow. It is therefore possible to store them separately from the APML data.
  • Carsten will make his tools so that they will take APML input rather than the vendor specific formats.

General action points

  • All groups will evaluate whether APML can store what it needs to store before the next meeting