Opened 13 years ago

Closed 13 years ago

#1301 closed task (duplicate)

BASE and GenePattern

Reported by: Jari Häkkinen Owned by: everyone
Priority: major Milestone:
Component: core Version:
Keywords: Cc:

Description (last modified by Jari Häkkinen)

GenePattern, http://www.broad.mit.edu/cancer/software/genepattern/, would allow BASE users to create and execute pre-defined work flows.

We should examine the feasibility of using GenePattern and how easy it is to add new analysis modules to GenePattern.

There may be work done on this already. Jari should check this.

Change History (3)

comment:1 Changed 13 years ago by Jari Häkkinen

Description: modified (diff)
Type: defecttask

comment:2 Changed 13 years ago by Nicklas Nordborg

We had a quick look at this today... and it doesn't seem to be all that complicated. GenePattern seems to be well documented and we could find Java code examples of how to invoke analysis modules on a GenePattern` server and how to send and receive input/output files.

The server software can be downloaded and it should work on most operating systems.

If there is interest in this I suggest that we create a "GenePattern plug-in package" and that we start to implement a front-end (=plug-in) for a one or two of the modules. I don't know which module to pick though...

comment:3 Changed 13 years ago by Nicklas Nordborg

Resolution: duplicate
Status: newclosed
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