Proteomics:Programmers Meeting on 2010-02-24

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Location and date



10:45-11:00 Introduction
11:00-11:30 Organizational questions:
  • platform collaboration
  • infrastructure status
  • summary of the meeting with SARA on 2010-02-23 on DAF installation procedure, access right, available disc space, installation status of dynamic light paths

Update from Twan:

  • presentation of the first workflow designed on the meeting of 2010-02-20 and presentation of the development task required for the implementation
  • APML structure
11:30-12:00 DAF: progress on previous action points
  • current DAF architecture
  • workflow language for DAF
12:00-13:00 DAF: formalization of requirements
13:00-14:00 Lunch break & talks
14:00-16:00 DAF: brainstorming (modularization & code review)
16:00-16:15 Summary & coffee

Discussion history

  • Pieter:
    • The tools in our workflows do not use command line.
    • We need more face-to-face meetings
    • Lack of time due to research work
    • There is no clean API for command-line tools
  • Péter:
    • Some solutions are not generic
  • Pieter:
    • Users want to use Mascot, even it is ugly, just because it produces good results
    • Formats: APML / PeakML (used in RUG) / mzIdentML (official PSi standard)
  • Twan:
    • Have a look how Corra is build.
  • George:
    • Cluster "Hello" application is ready, needs review.
  • Péter:
    • Meeting to integrate application into DAF
  • Pieter:
    • Is working on implementing msconvert as WebService, running msconvert in virtualized environment.
    • Galaxy demo, workflow building in Galaxy

Action points


  • Identify and implement several data converters.
  • Describe a common workflow
  • Publish tools
  • Check APML XSD for missing parts


  • Make some efforts to document Java data conversion library, used in UU.


  • Synchronize API with Ishtiaq


  • Organize next programmer meeting for DAF. Agenda: how to add tools to DAF?
  • Define API for DAF
  • Collect requirements for DAF