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Dear SBGN team,
i wanted to use SBGN for the first time and tried to convert my SBML model. However, I encountered several pitfalls that made it impossible for me:
1. The link for the only convert…
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I tried to use the code to build model:
Combine_PURE=ChemicalReactionNetwork(species = flatten([CRN_TX.species, CRN_TL.species, gfp_species,degraded_species]), reactions = flatten([CRN_TX.reactions, …
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When the order of models input to COBRA and then to COMETS changes, the results are changed.
cobra.io.read_sbml_model(model_1)
cobra.io.read_sbml_model(model_2)
has different results from:
cobra…
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**What did you expect to happen?**
Sensitivities to be computed
**What has happened instead?**
`rdata.x` and `rdata.sx` are zero matrices
**To Reproduce**
Compile a model with algebraic expre…
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### Description of the issue:
* Prefixes `M_` and `R_` are added by `exprotModel` function while exporting, and removed by `importModel` while importing. This was initially designed to [follow](https…
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I imported an SBML model from COPASI. I can edit the species concentrations in the usual way, but I can't edit any variables (i.e. Vmax values).
```
import tellurium as te
r = te.loadSBMLModel('Y…
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Hi. I'm trying to convert an SBML 2 model and I've encountered a bug in the model.manipulation.modify module. Apparently there's an error in one of the functions which prevents the parser from rep…
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I'm trying to test the pipeline with provided model **ENGRO2.xml**, but the getGPRsFromModel.py said that it was not a valid SBML model (The wrong information is attached below). I have validated the …
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tellurium appears to have limits on the attributes that can be changed via `sedml:changeAttribute`. I'm guessing this applies to `computeChange.target`, `setValue.target`, and `variable.target` as wel…
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The specifications suggest that model files should define namespaces with prefixes:
```
xmlns:sbml=‘http://www.sbml.org/sbml/level3/version1/core’
```
such that XPATHs such as below are well-def…