Re: Biopax sbml conversion

[Nicolas Rodriguez]

Hi Andrew,

There is indeed a biopax2sbml converter in sbfc. Unfortunately, we did not produce a package/release that contain it.

So I could either create a quick package for you to test it, waiting for a new release that should happen in the next few months.

Or you can also try to setup SBFC your self, following the instructions here: http://sbfc.sourceforge.net/mediawiki/index.php/Installation_and_Configuration_for_SBFC_core

In either cases, you should be able use the biopax2sbml converter, in particular, you can use the GUI to do that. You can start the GUI with the script sbfConverterGUI.sh or sbfConverterGUI.bat.

Let me know if you manage to setup and don't hesitate to report any problems you find with the converter.
Thanks,
Nico

On 17/04/18 15:17, Andrew J. Stout wrote:

Dear Mr. Rodriguez,

My name is Andrew Stout, and I am a PhD student at Tufts University in the US. I am currently working on transferring some metabolic models from pathway tools to cobra, and am having trouble in my conversions. Through pathway tools, I have both an SBML that is relatively incomplete / qualitatitve, as well as BioPAX (level 2 and level 3) files. As the SBML I have from pathway tools is incomplete, I was hoping to transfer the biopax file into a separate SBML to then make it readable by the cobra toolbox. I have spoken with Dr. Draeger, and he pointed me in your direction. Specifically, I have tried exploring the SBFC, which Dr. Draeger seems to imply can convert a biopax to an sbml, but am having trouble finding this option. Could you please point me in the right direction (if this is possible)?

Thank you,

Andrew Stout

New Harvest Research Fellow

Biomedical Engineering PhD student

The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT Registered Charity No. 1053902.

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