SBML support in the COBRA toolbox

[rmtfleming]

When one clicks on the ? button next to SBML on http://bigg.ucsd.edu/models/Recon3D it shows the following message:

"SBML level 3 (v1) with FBC (v2) This file is fully annotated through MIRIAM and uses version 2 of the FBC package. It is only readable by COBRApy v0.4 and later."

However, SBML level 3 (v1) with FBC (v2), is supported by other modelling software besides COBRApy, e.g., The COBRA Toolbox. Instructions for that are here: https://opencobra.github.io/cobratoolbox/latest/tutorials/tutorialIO.html

We have an issue that it currently takes 15 min to fully load the Recon3D SBML file. It is currently being investigated.

[matthiaskoenig]

I agree. The message is very misleading. There are FBA packages besides COBRA(py) which can work with such files. This is the big advantage of SBML, i.e., that it is interchangable between software, so I would not state "Is is only readable with ..."

On Fri, Mar 9, 2018 at 8:36 AM, Ronan M.T. Fleming <notifications@github.com

wrote:

When one clicks on the ? button next to SBML on http://bigg.ucsd.edu/models/Recon3D it shows the following message:

"SBML level 3 (v1) with FBC (v2) This file is fully annotated through MIRIAM and uses version 2 of the FBC package. It is only readable by COBRApy v0.4 and later."

However, SBML level 3 (v1) with FBC (v2), is supported by other modelling software besides COBRApy, e.g., The COBRA Toolbox. Instructions for that are here: https://opencobra.github.io/cobratoolbox/latest/tutorials/ tutorialIO.html

We have an issue that it currently takes 15 min to fully load the Recon3D SBML file. It is currently being investigated.

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[draeger]

Good catch, @rmtfleming. One could write that a recent software with support for SBML Level 3 and FBC Version 2 is needed. The hint about COBRApy shoud be reformulated to read like an example. How about a text similar to:

SBML level 3 (v1) with FBC (v2) This file is fully annotated through MIRIAM and uses version 2 of the FBC package. Make sure the software you use supports this standard. If using COBRApy, v0.4 and later is required.

[zakandrewking]

Thanks for catching that. The message is pretty old. We will fix asap.

On Fri, Mar 9, 2018 at 12:43 AM Andreas Dräger notifications@github.com wrote:

Good catch, @rmtfleming https://github.com/rmtfleming. One could write that a recent software with support for SBML Level 3 and FBC Version 2 is needed. The hint about COBRApy shoud be reformulated to read like an example. How about a text similar to:

SBML level 3 (v1) with FBC (v2)

This file is fully annotated through MIRIAM and uses version 2 of the FBC package. Make sure the software you use supports this standard. If using COBRApy, v0.4 and later is required.

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[zakandrewking]

OK, I updated it as follows, but I'm happy to keep improving the text:

"This file is fully annotated through MIRIAM and uses version 2 of the FBC package. Make sure the software you use supports this standard. If using COBRApy, v0.4 and later is required. It is also supported by the latest release of the COBRA Toolbox."