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Internally, we store the rates of change of the variables controlled by a rate rule or by reactions. The 'rateOf' csymbol introduced in SBML L3v2 allows models to access those rates as well. It shou…
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Is the input file an sbml file? Should multiple sbml files be merged into one file? I opened the modelsaa file given by MAMBO and found it was garbled.
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Since MOCCASIN converts from Matlab -> XPP -> SBML, I wonder whether it would be possible to skip the first step, and let a user provide an XPP script, that is then send directly to biocham for transl…
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**Describe the bug**
sybil-SBML will raise compilation errors during install with libSBML version 5.19 or above.
**Steps to reproduce**
Install a recent libSBML, then run
```R
remotes::in…
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I noticed recently that the models generated via all of the modelseed services have explicitly-represented boundary metabolites rather than the standard use of a true boundary (e.g., standard is extra…
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---
id: pysces
version: 1.2.0
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_PySCeS/42b2e7787368e1db359ae33368ba0fa80b7eaa63/biosimulators.json
specificationsPatch:
…
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Hi,
I am using you software to combine different models into one big meta-metabolic network. And I am wondering if there is a way to paralelize the process specially in the bottle neck that is the …
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I included links to protein complexes that carry out reactions.
For example: http://identifiers.org/complexportal/CPX-1664
See below for the status from SBML/BiGG validation for files with and wit…
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The flattening algorithm implemented in JSBML should be improved. A better version has been implemented in the form of a [fork](https://github.com/eikept/jsbml). It is nearly ready but requires more e…
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MEMOTE has recently been throwing errors when trying to run it. This is odd as I haven't updated MEMOTE from my end in quite a while (I'm using version 0.13.0). When I try to run MEMOTE, I get the fol…