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Construct cellular overview from a sbml model

asked 2017-08-25 11:37:25 -0500

mikeaalv gravatar image

I am using 21.0 on mac. I know how to construct cellular overview from Pathologic, but not sure from SBML file. I can import SBML file. Is there any method to construct a cellular overview from SBML file?

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answered 2017-08-26 01:31:13 -0500

Suzanne Paley gravatar image

I believe the answer is no. Section 5.2 of the User Guide gives you step-by-step instructions for how to create a PGDB using an SBML file as the data source. Once you do the Merge Reactions step, you will have a PGDB that contains compounds and reactions, but no pathways. Without any pathways, you will not be able to generate a useful cellular overview diagram. I was going to suggest you just run the PathoLogic Rescore Pathways command on your PGDB, but I believe that since your PGDB won't have any enzymes associated with any reactions, no pathways will be predicted, so that won't help. I'll put in a query to the dev team to see if there is any way around that.

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Yeah. Pathologic didn't work as well. For the SBML import, my sbml file actually contains enzymes, though it is not imported anyway. It would be reasonable if enzymes could be imported as well. Even I import SBML on a constructed PGDB, it seems just increase reaction number and others no change.

mikeaalv gravatar imagemikeaalv ( 2017-08-26 09:26:35 -0500 )edit

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Asked: 2017-08-25 11:37:25 -0500

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Last updated: Aug 26 '17