Metabolic Network Drawing

Question

[Kwet]

Hi all,

As part of a project I have a to draw a large metabolic map. I was wondering what was the most efficient way do a map such as the KEGG ones.

The starting point would be an SBML file, so far I have tried to convert this into a graphical format (dot) and draw the map automatically using GraphViz. It does the job, but the layout is not clear enough. Does anybody know, if there is a tool available to draw metabolic maps ?

Thanks a lot for your help.

Regards

[Chris Evelo]

I think the core difference is he want tos atrt from SBML. The answer will probably also be "Cytoscape" but it might not be trivial to go from SBML to Cytoscape. In fact I would be interested to know best practices for that.

[Pierre Lindenbaum]

Hi Kwet, welcome to Biostar. I think your question is a duplicate of this one . Tell me if I'm wrong and I'll re-open your question :-)

[Michael Schubert]

I agree with Chris that the answer is not simply "Cytoscape" in this case. Please reopen.

[Pierre Lindenbaum]

done :-)

Answer 1

[Michael Schubert]

The standard for graphical representations of a model described in SBML is referred to as SBGN. There's a list of software that is said to support it here.

The 2 software packages I know that are able to render SBML models using SBGN are CellDesigner (used to generate and draw models, can import and export SBML; based on SOSlib that can also be used directly) and BiNoM (a Cytoscape plugin).

Bear in mind that the standard is relatively new and too well supported so far.

Answer 2

[Kwet]

Thank you all for your responses,

@Pierre, this wasn't exactly what I meant but I found very interesting information following your link. I think that would be useful for me as well.

@Michael, thank a lot. I already tried several of the softwares that support SBML and SBGN. (CellDesinger, Cytoscape + sbml plugin, BiNom, SBGN-ed, etc...) more or less successfully. CellDesigner works well, but I found very difficult to rearrange the the layout (for example group the reaction belonging to a same pathway together etc...). Cytoscape works very well too, but it is not for example possible to put reactions/metabolites in a compartement or add new reaction.

My goal would be to draw a clear and well presented map such as : metabolic map

I think that would require a lot of manual work, but even manually, I haven't found a decent way to do it. Any idea ? Thanks a lot for your help.

[Russh]

to add new reactions in cytoscape, can't you just import your new reaction into a fresh network and then take the union of your original network and the new reaction?

It may be possible to localise your reactions by converting sets of nodes into metanodes, ciao, R

[Michael Schubert]

For clarifications, please edit your question instead of posting a new one. For "group the reaction belonging to a same pathway together", it might be a better approach to extract a submodel from the SBML file first and then render it (relatively easy with libSBML).

[Michael Schubert]

Btw, also take a look at the EBI BioModels.net database. It supports automatic generation of submodels.

Answer 3

[Manu Prestat]

Did you take a look to "Pathway tools" ? I'm not sure it manages SBML files but it might be interesting.

Answer 4

[Question]

http://fmm.mbc.nctu.edu.tw/ FMM can reconstruct metabolic pathways form one metabolite to the other one. The different KEGG maps can be connected by our system. Both local and global graphical views of the metabolic pathways were designed.