[Biopython] Representing biological networks was: Re: (no subject)

[Leighton Pritchard]

Hi,

I use Cytoscape and NetworkX, which cope perfectly well - as far as I've pushed them - with GML as a language for data transfer (you might want to get into the habit of using the relabel=True option when using read_gml(), though ;) ).

However, for biological networks, you might also want to look at SBML which, unlike XGMML, is actively maintained and biology-specific, to see if it meets your needs.  Cytoscape handles this format directly, but coverage is still lacking in NetworkX (which would be the appropriate place for this, rather than Biopython, in my opinion).  There is a Python API to libSBML, though.

http://sbml.org/Main_Page

http://sbml.org/Software/libSBML/docs/python-api/

http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats

https://networkx.lanl.gov/trac/ticket/325

Cheers,

L.

On 30 Jan 2012, at Monday, January 30, 11:14, Peter Cock wrote:

On Mon, Jan 30, 2012 at 10:09 AM, Kristian Ullrich
<kristian_ullrich at yahoo.de<mailto: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/
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Dr Leighton Pritchard MRSC
DG31, Plant Pathology Programme, James Hutton Institute (Dundee)
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