Ask Pathway Tools logo   Pathway Tools Question & Answer forum for SRI's Pathway Tools

Ask Your Question
0

Construct cellular overview from a sbml model

asked 2017-08-25 11:37:25 -0600

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?

edit retag flag offensive close merge delete

1 Answer

Sort by ยป oldest newest most voted
0

answered 2017-08-26 01:31:13 -0600

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.

edit flag offensive delete link more

Comments

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 -0600 )edit

Your Answer

Please start posting anonymously - your entry will be published after you log in or create a new account.

Add Answer

Question Tools

1 follower

Stats

Asked: 2017-08-25 11:37:25 -0600

Seen: 21 times

Last updated: Aug 26