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Good day.
Referring to Issue #663, I have been trying to export styrene model example #537 to SBML format:
```
from gillespy2 import export_SBML
import libsbml
gillespy2.core.model.export_SBML(S…
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If you create a model using the new api it doesn’t create correct sbml. The sbml validator will flag it as invalid sbml. The reason is that the listofmodifiers section is missing from reactions. The l…
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Converting a Python expression string to a "polyglot" string (for example, changing the Python exponent operator `**` to an explicit call to `pow()`) occurs for `Reaction.propensity_function` [here](h…
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As discussed at a few SBML Editor's meetings: we propose that no SBML element should have a required child SBML element. This both allows greater flexibility on the part of modelers creating 'in-pro…
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There seems to be a major bug with amounts and concentrations when using `getCurrentSBML` (reported below). I noticed the same strange behavior when trying to copy state manully between models by usin…
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I did run the [example protocol](https://github.com/segrelab/COMETS_Protocols/blob/master/COMETS_protocols/COMETS_example_Ecoli_CoreModel_WellMixed/Python/P1_test_tube.ipynb) with another E. coli mode…
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SBML L2V2R1
Pages/lines: p. 59 line 39
Description:
Andrew Finney suggests changing the wording "When a model contains values ..." to "When a model contains true values ...".
MH
Reported by: …
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Example model:
- BioModels [BIOMD0000000012](https://www.ebi.ac.uk/biomodels/BIOMD0000000012)
- SBML file: [BIOMD0000000012_url.xml.txt](https://github.com/StochSS/GillesPy2/files/6971073/BIOMD0000…
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SBML L2v3r1 p. 114 line 61:
The text says the values are in concentration, but the model SBML gives them as amount. Which should was intended? Either the text or the model are incorrect, dependin…
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Versions used:
```
clyngor | 0.3.31
Meneco | 2.0.1
```
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This is probably more a clyngor issue, but I'll post it here because that's where it affected me :)
I noticed a heavy perform…