Opened 14 years ago
Closed 14 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 )
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 14 years ago by
| Description: | modified (diff) |
|---|---|
| Type: | defect → task |
comment:2 Changed 14 years ago by
comment:3 Changed 14 years ago by
| Resolution: | → duplicate |
|---|---|
| Status: | new → closed |
Moved to BASE plug-ins site: http://baseplugins.thep.lu.se/wiki/net.sf.basedb.genepattern
Note: See
TracTickets for help on using
tickets.
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...