how to create an sbml file??

[INDRANI RAY]

Is there any good software to make sbml file. I have tried with cell designer, but i could not generate L3V1

[Lucian Smith]

Yes, there are many many software tools that can create and manipulate SBML files--the overall summary is at

http://sbml.org/SBML_Software_Guide

Your only problem is going to be trying to figure out which one to use; which one best fits your own needs.  If you want to also simulate your SBML file after you create it, you might want to go with a simulation package, and if you have unusual parts of your model that you need to make sure work in that environment, you might want to make sure that the tool you're using supports that--the best way I know to make sure of that is to look at the results of the SBML Test Suite:

http://sbml.org/Facilities/Database/Simulator

If you really do only want to create an SBML model, and you like doing so in text, you might try my own tool, Antimony:

http://antimony.sourceforge.net/

or, if you like Antimony but need to do more than just create the model, and you're reasonably comfortable with Python, try Tellurium:

http://tellurium.analogmachine.org/

I'll let other people plug their own tools ;-)

If things are still confusing, feel free to tell us more about what you want to do with your SBML model once you create it, what sorts of features you want it to have, and whether you like GUIs, text UIs, programming environments, etc., and we can probably point you at some reasonable tools to try.  Good luck!

-Lucian Smith

On Wed, Jun 24, 2015 at 10:47 PM, INDRANI RAY <indrani...@gmail.com> wrote:

Is there any good software to make sbml file. I have tried with cell designer, but i could not generate L3V1

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[Chris J. Myers]

You could also try iBioSim especially if you are interested in genetic circuit models.

Http://www.async.ece.utah.edu/iBioSim/

Chris

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[Jason Zwolak]

I'm also having trouble finding tools that support L3V1.  I have seen that Antimony and iBioSim support it.  As well as CoPasi and it seems VCell.

The only tool I have experience with that works and supports L3 is CoPasi.  It definitely works, but I find the user interface to be very obscure.  There is however a good community surrounding this tool, instructional videos, and docs.  I was unable to get VCell to work and I have not tried Antimony or iBioSim.

There is also this tool that I developed called PET: http://mpf.biol.vt.edu/pet/

It does not support L3, but the users of PET really like it ;-)  It supports L2 and it integrates JigCell for model building.  You could also try JigCell by itself if you just want to build the model.  The JigCell UI is pretty straight forward and gives ready access to L2 features.

[Chris J. Myers]

I hope you will give iBioSim a try.  We would be happy to help with that.  We don’t have as large a development team, but we do try to keep the tool as robust as possible with documentation and tutorials.  We support all of L3V1, pass the entire test suite, support several packages including layout, comp, fbc, and arrays.  We think our UI is fairly intuitive though certainly open to suggestions for improvement.  

Chris

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[Andreas Dräger]

Dear Indrani Ray,

CellDesigner can export SBML files in SBML Level 3 format when using it in combination with plugins.

The installation is a little tricky, but if you follow the steps below, CellDesigner will be able to export proper SBML Level 3 Version 1 including Layout extension!

Installation instructions:

1) Locate your CellDesigner installation on your local computer. This can, for instance, be
* /Applications/CellDesigner4.4/ under Mac OS,
* C:\Program Files\CellDesigner4.4\ under Windows, or
* /opt/CellDesigner4.4/ under Linux.

2) Obtain the export plugin here: http://sourceforge.net/projects/jsbml/files/jsbml/1.0/modules/. Just download the file CellDesignerL3ExportPlugin.jar and place it in the plugin folder of your local CellDesigner installation.

3) Download the file http://www.cogsys.cs.uni-tuebingen.de/software/SBMLsqueezer/downloads/jsbml-1.1-a1-incl-libs.jar

4) Replace the file CellDesigner4.4/lib/jsbml-1.0-incl-libs.jar with this newer version. You need to change the name of the newer JSBML version to the older version's name in order to make CellDesigner accept it.

5) You also need to replace the file CellDesigner4.4/exec/celldesigner.jar with the new version that you can download here: http://www.celldesigner.org/~funa/GSoC/.


Now, when you launch CellDesigner, its plugin menu will now provide an entry "SBML Export", which allows you to save arbitrary SBML models to SBML L3 V1 with SBML Layout extension, no matter if you create those files by yourself, open existing models, or modify them with CellDesigner.

I hope this helps!

Cheers
Dr. Andreas Dräger
Bioengineering Dept., Systems Biology Research Group, Office #2506
University of California, San Diego, La Jolla, CA 92093-0412, USA
Phone: +1-858-534-9717, Fax: +1-858-822-3120, twitter: @dr_drae

> Am 25.06.2015 um 07:47 schrieb INDRANI RAY <indrani...@gmail.com>:
>
> Is there any good software to make sbml file. I have tried with cell designer, but i could not generate L3V1
>

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> You received this message because you are subscribed to the Google Groups "sbml-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to sbml-discuss...@googlegroups.com.
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