[BioC] GeneSpring can call R functions?

[Ramon Diaz-Uriarte]

Dear Ken,

On Wednesday 18 May 2005 20:01, Ken Termiso wrote:
> Hi all,
>
> I was chatting with a friend of mine yesterday who was griping about how
> he's stuck with GeneSpring and how he wishes he could learn R in a
> reasonable amount of time, and he showed me his Genespring layout on his
> computer...
>
> GeneSpring now apparently can call R functions from the command line on a
> windows PC (GeneSpring apparently isn't very stable on anything
> else...LOL). I think I saw one to do an RMA norm of CEL files, and I'm not
> sure what else, but what I'm wondering is whether or not this is actually
> legal? If I'm a software developer, can I just go ahead and write a little
> GUI on top of R and sell it?? This seems like outright thievery to me.

I don't think this, by itself, is a case of writing a GUI on top of R and 
selling it (which might not violate the terms of the license(s) for R 
depending on what you distribute, etc; see Tony Rossini's answer). My 
understanding is that GeneSpring provides the possibility of calling R and 
thus the code you (or anyone else) writes. This functionality, as far as I 
understand, is provided in part by the GeneSpring package, which is part of 
BioC, and is under the GPL.

What they do, according to their docs 
(http://www.silicongenetics.com/Downloads/gs_r_doc.pdf)

is "(...) start an external program and provide this program with the data to 
be analyzed. When the program is finished with its analysis, the results will 
be passed back to GeneSpring, which will present the user with the results in 
the familiar GeneSpring Interface."


Now, in the context of your friend's situation, I think that he might want to 
ponder whether he just wants to learn to use R within GeneSpring or learn to 
use R; he'll need a fully functional R installation anyway. And then, if he 
starts writing code that could be used by others, he might want to consider 
whether he wants to pack/make available that code so that it can be used by 
others regardless of whether or not they use GeneSpring.


Best,

R.



> It's probably safe to say that most of the algorithms in GeneSpring are
> probably ripped straight from open source software, repackaged in a pretty
> GUI, and resold, but it seems that this is a little bit over the line...
>
> just my .02
>
> What do you think?
>
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-- 
Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
(http://ligarto.org/rdiaz/0xE89B3462.asc)




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