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Current export menu is implemented for exporting SBGNML maps to other formats such as SBML, SIF etc. and they should be working well. However, when we added other formats, SIF and SBML, we didn't put …
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At some point it would be convenient to replace the current SBML-sympification by https://github.com/dweindl/sbmlmath/.
This gives us better control over the whole process and can replace the awkwar…
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To do:
- [x] make sure runs and gives the correct output
- [x] add fix for SED-ML files with missing `xlmns:sbml` attributes
- [x] add column that records whether `xlmns:sbml` attribute is missing…
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When I run the 'Lecture 2 Compiling CRNs Colab Notebook.ipynb' downloaded from YouTube, the 'CRN.simulate_with_bioscrape_via_sbml()' returns 'NoneType' object, which is not subscriptable.
The file…
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Hello,
First, thank you for developping Antimony, it is very useful for writing simple SBML model !
I have the following code that define an Antimony model, does a plot of the dynamic and export it…
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Hello,
Is it possible to gapfill using another GEM? I know that its possible to reconstruct based on another gem but could we use one to gapfill?
Thanks.
:-D
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from issue #7
**Resources:**
- https://subcellular-bsp-epfl.apps.hbp.eu/home/
- https://subcellular-bsp-epfl.apps.hbp.eu/static/docs.html
**Info:**
- on [this page](https://subcellular-bsp-ep…
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Antimony SBML
Refer to MakeSBML or RateSB for ways to implement
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It would be great to have the feature of a PEtabSDEProblem, where the model is not a ODe but a SDE.
Maybe for a start, supporting the conversion of a SBML model to an `SDEProblem` would be a good st…
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There are ~1000 curated models on https://www.ebi.ac.uk/biomodels/, mostly in SBML format.
A good number of these are relevant for neuroscience, e.g. https://www.ebi.ac.uk/biomodels/BIOMD0000000118…