Re: [Tellurium discuss] Digest for tellurium-discuss@googlegroups.com - 5 updates in 1 topic

[Jalil Nourisa]

Thank you very much, Lucian,

That’s what I was looking for.

Best

On 26. Mar 2021, at 10:35, telluriu...@googlegroups.com wrote:

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• How to extend a SBML model - 5 Updates

How to extend a SBML model

Jalil Nourisa <jalil....@gmail.com>: Mar 25 09:51PM Hi, In my simulation, I have a SBML file of a previous model that I need to extend in certain ways. I wonder, is such a thing possible in Tellurium, and if yes, can you pls give me a hint how to do it? Best Jalil Nourisa

Herbert M Sauro <hsa...@uw.edu>: Mar 25 03:04PM -0700 If you have an existing model I would convert the SBML into Antimony format and then edit that. Antimony will give you a list of reactions, species,rate laws etc, Any changes you make can be converted back to SBML, or loaded straight into the tellurium simulator.   For example, if you have an SBML file or a string containing some SBML you can do:   import tellurium as te   r = te.loadSBMLModel (string or file name of SBML model)   To get the Antimony you can use   antStr = r.getAntimony ()   You can print out the antStr and copy the string to a new editor window.   What I generally do is if you're using the Windows spyder distribution of tellurium, there is an import sbml option in the file menu and that will convert the SBML to antimony and drop it in the editor windows.   Herbert     On Thu, Mar 25, 2021 at 2:54 PM Jalil Nourisa <jalil....@gmail.com> wrote:     -- Herbert Sauro, Professor University of Washington, Bioengineering 206-685-2119, www.sys-bio.org hsa...@uw.edu Books: http://books.analogmachine.org/

Lucian Smith <luciano...@gmail.com>: Mar 25 03:09PM -0700 It's also possible to use the functions like 'addReaction' or 'addSpecies' in roadrunner, i.e.:   r = tellurium.loada(antimonyStr) r.addSpecies("S1", "c", 3.0)   would add species S1 in compartment c.   There are similar functions for deleting elements, too.   https://libroadrunner.readthedocs.io/en/stable/api_reference.html?highlight=addreaction#RoadRunner.RoadRunner.addReaction   -Lucian

Jalil Nourisa <jalil....@gmail.com>: Mar 25 11:06PM Thank you very much, Herbert, I was more looking for a clean way of doing that without opening the SBML model. But, this would do the job. Best

Herbert M Sauro <hsa...@uw.edu>: Mar 25 07:16PM -0700 See Lucian reply, I’d forgotten we have a new api to manipulate a model directly.   Herbert   On Thu, Mar 25, 2021 at 4:07 PM Jalil Nourisa <jalil....@gmail.com> wrote:     > On 25. Mar 2021, at 22:04, Herbert M Sauro <hsa...@uw.edu> wrote:   > antStr = r.getAntimony ()   > -- Herbert Sauro, Professor University of Washington, Bioengineering 206-685-2119, www.sys-bio.org hsa...@uw.edu Books: http://books.analogmachine.org/

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