Proteomics:Programmers Meeting on 2011-02-18
Location and time
- Location: Hojel City Center, building D (5th floor), Graadt van Roggenweg 340, 3531 AH Utrecht
- Date: Friday February 18th, 2011
- Time: 9:00-10:30
- Carsten Byrman (AMC)
- George Byelas (UMCG)
- Henk van den Toorn (UU)
- Ishtiaq Ahmad (RUG)
- Michael van Vliet (LU, from the Metabolomics task force)
- Péter Horvatovich (RUG, via Skype)
- Rob Hooft (NBIC)
- Freek de Bruijn (NBIC)
- Presentation from George on MOLGENIS
- Action points and status updates
- Next meeting
Presentation from George on MOLGENIS
George held a presentation on MOLGENIS (see File:Programmers-Meeting-on-2011-02-18-George-Byelas-MOLGENIS.pdf for the slides). There were discussions of interesting topics, like how to handle a variable number of output files and how to give external tools access to data on a cluster.
Action points and status updates
- Carsten came to say goodbye. He had a temporary contract with AMC and although there was still one year left, he decided to accept a new challenge with a technical consulting company. Keywords: water management, open source software and located in Utrecht (biking distance). AMC is making plans for continuing the work with the remaining funding.
- He has transferred knowledge to collegues, wiki, etc.
- He has also sent some example code on how to call the AMC tools in Galaxy to Elizabeth (EMC).
- Thanks for the great collaboration, Carsten!
- Elizabeth received data from Javier Munoz (UU) to test MS PRUNA.
- Peter suggests to combine msCompare and OMSSA in Galaxy. Pieter (UU) is planning to look at this later.
Wim (update by Henk):
- Wim is working on software for quantative analysis of overlapping isotopes. The aim is being able to predict overlaps and do a correction for this.
Pieter (update by Henk):
- Pieter is mainly busy with phosphorylation site motifs. He is using the MEME suite and TOMTOM tool to search for motifs. Pieter plans to add support for proteins.
- He is analyzing Trichoplax with proteogenomics tools.
- Ishtiaq is integrating msCompare in DAF, which requires OpenMS. It is a lot of hassle to recompile it for a different Linux distribution.
- He is also planning to work on adding more checks for input files for the DAF web service.
Berend (update by Peter):
- 2D LCMS is almost added to msCompare.
- Light paths will be installed in AMC (it turned out to be impossible in Wageningen).
Friday March 18th 9:00-10:30 will be our next programmer's meeting.