visualisation

[CuypersBart]

I am trying to make a visualization of a metabolic network using COBRApy and escher (as they suggest in the COBRApy manual). I have an sbml file with all the reactions in my organism.

I already generated my own escher HTML file using following code:

model = cobra.io.read_sbml_model('E:/e.coli.sbml') modeljson = cobra.io.json.to_json(model) b = Builder(map_json=modeljson) b.save_html('E:/e.coli.html') Opening the html file in my browser(s) just results in an empty screen, although the file itself is not empty.

Does anyone have an idea how I could solve this, or get to the bottom of the problem?

The b.display_in_browser(), also does not work (gives a grey empty screen)

Thanks,

Bart

[zakandrewking]

Hi Bart. The trouble here is that you are passing the model data to the Builder as map data. If you are interested in viewing maps of E. coli metabolism, you have to specify a map in addition to a model.

Which version of Escher are you using, so I can help you with this? (import escher; print escher.__version__)

[CuypersBart]

Hey Zachary,

I’m using version 1.0.0b3.

Actually I have my own reactions and metabolites in a CobraPy model and would like to build a map of it (and later visualize fluxes).

How can I build my own map? Can I do this using escher?

Thank you,

Bart

From: Zachary King [mailto:notifications@github.com] Sent: maandag 3 november 2014 17:49 To: zakandrewking/escher Cc: CuypersBart Subject: Re: [escher] visualisation (#69)

Hi Bart. The trouble here is that you are passing the model data to the Builder as map data. If you are interested in viewing maps of E. coli metabolism, you have to specify a map in additions to a model.

Which version of Escher are you using? (import escher; print escher.version)

— Reply to this email directly or view it on GitHub https://github.com/zakandrewking/escher/issues/69#issuecomment-61507994 . https://github.com/notifications/beacon/AJFtus-ZWGPYxj1d_9MqHZSI6lFW1Ln6ks5nJ6mAgaJpZM4C2Qbh.gif

[zakandrewking]

Yes. You can download the COBRApy model as a JSON file, as show here:

http://nbviewer.ipython.org/github/zakandrewking/escher/blob/master/docs/notebooks/json_models_in_cobrapy.ipynb

Then, in the Builder, you can use the Model > Load COBRA model JSON command to load the model, and begin building your map.

Please note that a new, stable release of Escher is coming out in December, but there may be bugs in this current Beta release. Also, documentation is coming for the stable release, which may help out.

[CuypersBart]

Thanks a lot, it works now.

Is there any way to produce a map automatically? I have over 1200 reactions that I would like to visualise.

[zakandrewking]

That's on our development roadmap, but it's still a ways off.

You could try http://csbl.bitbucket.org/metdraw/ in the meantime.