Visualizing reaction set as a network

[Deepa Maheshvare]

Hello Everyone,

I would like to visualize a set of reactions in the form of a network/pathway.I have the set of reactions in SBML format.Is it possible to view this as a pathway map on cytoscape?

Thanks a  lot for your time and kind consideration.

Deepa

[Scooter Morris]

Hi Deepa,
   Certainly!  I would suggest starting with reading the SBML in directly.  You can use the built-in SBML reader, or cy3sbml, which is much more advanced.

-- scooter

[Deepa Maheshvare]

Hi Scooter,

Thank you so much for your kind response.I have a set of ~20 reactions.The rate law expression of each reaction is in a separate SBML file.Before I load in cytoscape,should I merge all the individual SBML files into a single file?

Or, can I import all the SBML files into cytoscape and later define the sequence in which the reactions occur ?

Thanks again,

Deepa

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[Scooter Morris]

On 07/06/2017 09:27 AM, Deepa Maheshvare wrote:

Hi Scooter,

Thank you so much for your kind response.I have a set of ~20 reactions.The rate law expression of each reaction is in a separate SBML file.Before I load in cytoscape,should I merge all the individual SBML files into a single file?

Or, can I import all the SBML files into cytoscape and later define the sequence in which the reactions occur ?

Thanks again,

Deepa

Hi Deepa,
    To be honest, I'm not sure.  My suggestion would be to take a look at the app documentation to see how it works.  My guess is that you are going to need to merge the files, but I have no idea if that is, in fact, the case.

-- scooter

On Thu, Jul 6, 2017 at 9:19 PM, Scooter Morris <sco...@cgl.ucsf.edu> wrote:

Hi Deepa,
   Certainly!  I would suggest starting with reading the SBML in directly.  You can use the built-in SBML reader, or cy3sbml, which is much more advanced.

-- scooter

On Wednesday, July 5, 2017 at 11:39:55 PM UTC-7, Deepa Maheshvare wrote:

Hello Everyone,

I would like to visualize a set of reactions in the form of a network/pathway.I have the set of reactions in SBML format.Is it possible to view this as a pathway map on cytoscape?

Thanks a  lot for your time and kind consideration.

Deepa

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