[Biopython] (no subject)

[Peter Cock]

On Mon, Jan 30, 2012 at 10:09 AM, Kristian Ullrich
<kristian_ullrich at yahoo.de> wrote:
> Hello Biopython Team,
>
> I am going to work with biological networks, next to the great tool cytoscape
> I want to create networks out of python. To my knowledge there exists
> pygraphviz and networkx which can produce gml and dot output files.
> Cytoscape uses the XGMML Language
> (http://www.cs.rpi.edu/research/groups/pb/punin/public_html/XGMML/).
>
> Is there an easy way of how to use or manipulate existing python xml
> parsers to work with xgmml files or are there plans of the Biopython
> Team to write an XGMML - parser?
>
> Since a lot of biologist work with cytoscape this would be a very useful
> tool to build graphical netowrks.
>
> Thank you in anticipation
>
> Kristian Ullrich

Hi,

XGMML looks much more general than 'just' biology, so I
wonder if XGMML support in NetworkX would a better idea?
I couldn't find an open issue on this on their tracker, but
certainly they sounded positive about this back in 2009,
http://groups.google.com/group/networkx-discuss/browse_thread/thread/fb30306e43414c74

Peter

P.S. There are several Python libraries for using dot
files and GraphViz (which is an excellent library), I
don't recall why but last time I needed to do this I used
pydot - http://code.google.com/p/pydot/