[BioC] DEGraph graph format?

[laurent jacob]

Hi Oliver,

2012/6/10 Oliver Ruebenacker <curoli at gmail.com>:

>  Can you explain some more why you choose not to use Rredland? It
> seems almost certainly relevant for the design of a BioPAX package.
> Did the issue have to do with separating the actual reaction network
> from other types of information?

If I remember well, I wasn't sure how to reconstruct the network
structure form Rredland output, in particular how to recover the edges
from the parsed BioPAX statements. It's not that the parsing done by
Rredland was problematic, it's more that additional work (which seemed
non-trivial to me at the time) was required to convert the output to
graph objects.

Are you planning to develop a bioconductor package or an independent
Java parser? If you plan on using Java, you may want to look at what
the mskcc people did for their Cytoscape plugin, which I used for my
own package: http://cbio.mskcc.org/cytoscape/plugins/biopax/

Best,

Laurent

-- 
Laurent Jacob
Department of Statistics
UC Berkeley
http://cbio.ensmp.fr/~ljacob