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= Description =
- Allow source attribute in sedml:model to reference other models by id.
= Context =
- SED-ML allows model to reference other models in source attributes, as shown below:
{{{
#!xm…
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Hello
I am trying to create a cobra model using sample SBML files downloaded from [KEGG converter](http://www.grissom.gr/keggconverter/). The ``io`` method ``read_sbml_model`` is able to generate m…
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= Description =
- Provide the API for adding or removing compartments in SBML models through the Change mechanism in SED-ML.
= Context =
- Compartments are an important element of the SBML language, …
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For enforcing the `wall_time_sim` for SBML models, we use a hack where the simulation is actually run in the separate script sbml-runner.py . If installing through PyPI, sbml-runner.py is not installe…
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= Description =
- Provide the API for adding or removing parameters in SBML models through the Change mechanism in SED-ML.
= Context =
- Parameters are used in reaction nodes in the SBML language; it…
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Hello,
Thank you for maintaining this project. I downloaded models from BioModels which are in SBML Level 2, hence incompatible with `rust_sbml` which follows the Level 3 specification. Is there a pl…
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Hi, just found your library! Very exciting.
Were you planning to add support for ODE simulation with diffrax?
I use diffrax to simulate my models and optimistix to fit them, and more generally wo…
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Some older models hide reaction attributes such as GPRs in notes, these are currently not parsed. Notable example:
https://systemsbiology.ucsd.edu/sites/systemsbiology.ucsd.edu/files/Attachments/Im…
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= Description =
- Provide the API for adding or removing reactions in SBML models through the Change mechanism in SED-ML.
= Context =
- Biochemical reactions are central to the SBML language; it shou…
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Hello,
Thank you all again for tellurium; it's a fantastic package. In various docs, there are sometimes visualizations of simple models in Antimony/SBML (like [this](http://pythonscriptingmanual.r…