Matthias,

I want to echo Eleanor's enthusiasm. We would like to include the modifications you and others have made into the code base. As soon as the current release is completed, we will turn our attention to bringing in your changes and will look at some of the others you suggest.

If you have ideas about developing an API beyond the gaggle approach, we would appreciate hearing them since the best API is one that people outside our development group can use easily.

JQ


Eleanor Howe wrote:
Hi Matthias, 

Thanks for your interest in the MeV project. Right now there isn't a
formalized way to integrate the community's contributions to the source
base. I'd love to take a closer look at the work you've done and see how
we could add it into our source. We are always happy when people decide
they like MeV enough to try adding something to it. Is there a place where
I can find more details about the patch you have made? 

We're in the home stretch of putting together a new release right now, so
we're about to make a whole bunch of commits to the repository. Because of
that I'd like to wait a little while before adding a bunch of new code.
But I'd be more than happy to look into doing so after MeV v4.1 comes out.

Thank you for pointing out these other projects that support new data
sources for MeV! I'll have a look at those and see if I can identify
common elements that we could integrate into our base code. As far as our
own interoperability efforts, we are currently working on implementing the
Gaggle API (http://gaggle.systemsbiology.net/docs/) in MeV. That
implementation may be included in the MeV 4.1 release. 

Putting a link to the Sourceforge site onto tm4.org is an excellent idea,
and we should have thought of it earlier. I'll make sure that gets done.

Again, thanks so much for your interest and your work on MeV.

Eleanor Howe
Dana-Farber Cancer Institute


On Sat, 13 Oct 2007, Matthias Berth wrote:

  
Hello,


we have made several changes to TMeV in order to adapt it to the needs 
of Delta2D [1] our software for 2D gel image analysis. We have, for example:

- used expression profiles from our spot data as input

- made it possible to propagate the selection of expression profiles 
back to our program

- patched the analysis procedure such that newly generated analysis 
branches are opened immediately

- removed some code duplications

We'd like to contribute our changes to the main code base. What would be
the process for this?

I have found other projects that maintain patches to use other data sources:

- The Generation Challenge Program (GCP) if the International Rice 
Research Institute [2] [3]

- BASE - BioArray Software Environment [4] [5]

- Signae (uses BASE) [6]

So using external data sources would be an interesting avenue for 
further development, e.g. by defining an API.

We'd be glad to contribute to this and to the TMeV package in general. 
Please let me know how we can get involved.


best regards

Matthias Berth
CTO, DECODON GmbH
www.decodon.com


PS: It was somewhat hard for me to find the sourceforge project page, 
http://sourceforge.net/projects/mev-tm4/ how about putting a link to it 
on http://www.tm4.org/mev.html ?


[1] Delta2D - http://www.decodon.com/Solutions/Delta2D.html
[2] GCP software https://cropforge.org/projects/pantheon/
[3] TMeV patches from the GCP 
https://cropforge.org/plugins/scmsvn/viewcvs.php/Osiris/projects/TMEV/?rev=9239&root=pantheon&sortby=rev#dirlist
[4] BASE - http://base.thep.lu.se/
[5] BASE - patches to TMeV: http://trac.thep.lu.se/trac/basehacks/wiki/MeV
[6] Signae TMeV  http://www.sigenae.org/index.php?id=88


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