Two potential directions this BoF could follow depending on who (if anyone) is interested in attending - this could take the form of an tutorial/advertisement session or more of a planning session.
If there are attendees who are not currently supporting proteomics with their Galaxy installations but would like to, this could be more of tutorial session - we could discuss various options currently available - ProtK, Galaxy-P tools, Adapt, NBIC, what it takes to get them up and running, current challenges, etc....
If the attendees are more or exclusively current developers using Galaxy for proteomics we could skip right to discussing what our plans are for the next year, strategize how to spur adoption and papers, develop documentation/best practices, etc....
When and Where
The Proteomics BoF has been tentatively scheduled for lunch on tuesday in the cantina
Who is Participating
If you are interested, please add your name below and/or send an email to John Chilton <jmchilton AT gmail DOT com>.
- John Chilton
- Ira Cooke
- Gianmauro Cuccuru
Send them to John Chilton <jmchilton AT gmail DOT com>.
BoF participants introduced themselves and gave some statement about their interest in Proteomics and Galaxy. Partipants had interests along a spectrum from primarily software development to primarily biology. A common reason for interest in using Galaxy for Proteomics was an interest in combining Proteomics with other "omics" such as Genomics, Metabolomics and Transcriptomics.
Resources for Proteomics
There was a strong feeling that Proteomics needed a presence on the Galaxy wiki. As a start to this John Chilton created two new pages;
A proteomics use cases page to help tool developers focus their efforts and new users to learn about what tools exist and what common proteomics workflows are covered by galaxy.
Both users and tool developers were encouraged to use the galaxy-proteomics mailing list for discussion.
John Chilton discussed galaxy-p and described its relationship to the main galaxy distribution
Pieter Lukasse gave a demonstration of his X!Tandem tool including a spectrum viewer
We highlighted the need for Proteomics specific visualisations in galaxy. Several participants are using or have developed such tools but they are not easily distributable.