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sys-bio / tellurium

Python Environment for Modeling and Simulating Biological Systems
http://tellurium.analogmachine.org/
Apache License 2.0
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Exporting COMBINE archives with results #207

Open 0u812 opened 6 years ago

0u812 commented 6 years ago

Frank's SED-ML Web Tools allow exporting COMBINE archives with results. When the SED-ML specifies a plot in the output, the archive contains a png. When the SED-ML specifies a report, the output contains a report in NuML. I'd like to add this ability to Tellurium before the paper submission.

matthiaskoenig commented 6 years ago

Also need this feature, see https://github.com/matthiaskoenig/tellurium-web/issues/28

Please make sure to put the results in a subfolder and not the root of the archive, and create subfolders for all sedml files. I have archives with multiple sedml files which should all be executed but not overwrite each others results if the outputs have the same id

I.e. something in the direction of:

/__tellurium__/sedml1/plot1.png
/__tellurium__/sedml1/plot2.png
/__tellurium__/sedml1/report1.png
/__tellurium__/sedml2/report1.png

My idea is that the different tools can just add there subfolders with the results to the combine archive, i.e. the Sedml webtools would add ideally:

/__sedml-webtools__/sedml1/plot1.png
/__sedml-webtools__/sedml1/plot2.png
/__sedml-webtools__/sedml1/report1.png
/__sedml-webtools__/sedml2/report1.png

Same for copasi, ... That would allow to execute the archive with all tools and collect the results for comparison. M