Loading metabolic model in Cytoscape with cy3sbml

[sarat...@gmail.com]

Hi everyone!

Is there any app to load metabolic models (large ones like Recon2 or HMR) in cytoscape?

I tried loading the metabolic model of adipocyte derived from HMR (biomodels ID: MODEL1402200001) using cy3sbml but I don't see anything being displayed under the 'base' network. However, I was able to 'create view' for the network under the section 'all'. What am I missing here?

Also, a trivial question, what is the difference between the networks in these sections - all, base and kinetic?

Thank you in advance.

Best,

Chaitra

[Scooter Morris]

Hi Chaitra,
   Looks to me like the base network simply hasn't been laid out.  Try running a force-directed layout and see what you get.  As far as the differences between the networks, I would suggest checking out the talk Matthias gave at COMBINE: http://co.mbine.org/events/COMBINE_2016/agenda?q=system/files/Koenig_COMBINE_cy3sbml.pdf but basically the "full" network is everything in the SBML, the kinetic network is only the part of the SBML that contain kinetics and the base networks are species, reactions, and gene associations.

-- scooter

[Matthias König]

Hi Chaitra,
like scooter said, the different networks contain different subsets of information.
The base network is mainly the stoichiometric network of the SBML with some additional GeneAssociations (if these are defined in the SBML fbc extension) and regulatory interactions. The kinetic and all network also contain information about the kinetics in the computational models.
With the large genome-scale metabolic networks like Recon2 no initial layout is generated (because this takes quit long). You can just apply the layout manually. That is basically why you see one single node (all nodes are over each other without any initial layout).

I am working on an upcoming release of cy3sbml and will include this information in a tutorial. Currently the information about usage is quit sparse, but if you have questions just ask.

Best Matthias

[Chaitra]

Thank you Scooter and Matthias for your replies! 

I understand the differences between base/kinetics now.

I figured that, by default, all nodes were laid onto each other, hence the one big red square which was visible. 

So I filtered a few reactions into and applied the forced directed layout (~160 nodes) as you suggested. The network definitely looks much better now, I can see the individual nodes and edges. However, part of the network is still a hairball. I manually have to reposition the nodes in order to visualise how every reactant is being used up.

Is there a solution to reduce this kind of manual work? I ask because I have to work with about 20 such subnetworks and that would mean a lot of manual repositioning.

Thank you for your help.

Best,

Chaitra

[Scooter Morris]

Hi Chaitra,
    I think what I would do is to bring up the settings dialog for the force directed layout and adjust the default spring length.  That should allow you to move things apart.  You can also use the Node Layout tools and adjust the scale.  That effectively spreads things out.

-- scooter

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