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It would be good to be able to include constraints on functions of parameters.
e.g ```par1 = par2 + par3``` where only ```par2``` and ```par3``` are to be estimated but bounds on ```par1``` are avail…
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Hi all,
I have been experiencing a peculiar problem with my genome-scale reconstructions being unable to take up any substrates/metabolites or excrete any products/metabolites. I provide a mineral …
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Model [01186](https://github.com/sbmlteam/sbml-test-suite/blob/7ab011efe471877987b5d6dcba8cc19a6ff71254/cases/semantic/01186/01186-model.m) (steady state metabolic model) is expected to pass in COBRAp…
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Dear college,
Have you got an example(s) for using your PetriNet simulator solution? If yes, can you provide it?
Best regards, Aleksey.
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The test takes much too long to run. This creates a ton of problems. E.g. very long travis runtimes and also very long runtimes for the local tests. Tests should normally run < 100ms, upper bound is s…
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Trying to prevent cobra from prefixing my identifiers when writing SBML, I got this (using the textbook model, model history error is unrelated):
`cobra.io.write_sbml_model(model, 'test.xml', f_rep…
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Example document:
```xml
```
The snippet below illustrates the issue. The SED-ML elements inher…
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Currently these concepts are not well documented/linked on the homepage.
* Ontologies Used Kinetic Simulation Algorithm Ontology (https://bioportal.bioontology.org/ontologies/KISAO)
* https://…
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In Translation module we have SBMLmodelgenrator python script which contains
```
## create species
for One_Species_ID in Translation_Species_List:
## TODO parse initial amount
ini…
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I picked up an issue when species are in conc, and output is in conc as well, with a model that has compartments (even only a single compartment) with a volume other than 1.
Illustrated with a simp…