Proteomics:Programmers Meeting on 2010-04-16
Location and time
- Location: Hojel City Center, gebouw D (5th floor), Graadt van Roggenweg 340, 3531 AH Utrecht
- Time: 9:00-10:30
- Rob Hooft (NBIC)
- Carsten Byrman (AMC)
- Ishtiaq Ahmad (RUG)
- Peter Horvatovich (RUG)
- Pieter Neerincx (UU)
- Wim Spee (UU)
- Kees van Bochove (NBIC and TNO)
- Marco Roos
- 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
- 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
- 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
- George is testing grid/cloud computing tools.
- Peter will test these
- Peter will make contact with Corra originators via his dept head.
- 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