Support of the Microsoft Word add-in for GenePattern

Apr 16, 2014 at 7:43 AM
Hello,

Is there still support for this tool?
If yes, is it possible to make it work with MW 2011.
If yes, is support for Macintosh planned?
If no, is using MW 2007 on windows the only solution to use this tool?
best,
Yohan
May 12, 2014 at 7:43 PM
Hello Yohan,

The add-in is only supported for MW 2007.

What is it that you are trying to do? We may have another tool or suggestion to help you achieve your aims.

Best

-Barbara

Barbara Hill Meyers
Senior Test Engineer
GenePattern Modules Project Manager
Cancer Informatics Development
Broad Institute of MIT and Harvard
http://www.broadinstitute.org/cancer
May 13, 2014 at 6:03 AM
Too bad...
We wanted to use Genepattern in our group as we have a local instance. Basically we try to make our analyses pipelines "reproducible" and "shareable" and I found it really nice that we can directly embed the result of a workflow in a paper like we usually do with R (Sweave or Kintr).

Yohan
May 14, 2014 at 8:46 PM
We too would like to offer something in this vein. Keep an eye on us over the coming months. (You can follow us on Twitter, Facebook, and/or Google+

In the mean time, if you have a pipeline on a server that is accessible to those reading your paper, you can make the pipeline public on that server and then provide a direct link to the pipeline in your paper. Would that help for the time being?

Best

-Barbara
May 15, 2014 at 6:20 AM
Great I will do follow you.

BTW yes, it is the way we would like to use it: "freeze" the pipeline and put the LSID in the paper.


thank you for your help,
Yohan
May 19, 2014 at 8:13 PM
Would you like me to explain how to do this? or do you know how already?

Best

-Barbara
May 20, 2014 at 5:33 AM
Yes, by freezing the pipeline I actually refer to what GenePattern is doing: give one unique URL (with the lsid inside) for the workflow/module you have defined. It register the workflow with all inputs you have and you can run it again or clone it to change some parameters if you want. It is actually very helpful.
It now just missing the part where it can generate dynamic figures from the workflow, but I guess that a Microsoft Word plugin is kind of hard to maintain.

best,
Yohan