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Create overview table like the one below for locally ran `LEMS_NML2_Ex9_FN` model.
- [x] run with biosimulators docker locally (on all the different engines)
The resulting minimal omex file SBML…
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I tried the example in the "Switching to the file logger" section. Nothing is saved to the log file.
pyomexmeta: 1.2.12
python: 3.9.5
OS: Ubuntu
_Originally posted by @jonrkarr in https://gith…
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Biosimulators requires an omex file as input, but it does not seem to accept the omex files we created. Why are the omex files not accepted? To figure out why, create a 'minimal' omex file that has th…
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# Issue
Currently it is not possible to access variables in models based on model composition.
This is a general problem of composed models where part of the model XML definition is in external fil…
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During patching of Biosimulation's Biosimulator_Utils, a bug was discovered where combine archive contents were extracted as directories rather than as files (if curious, see: [Biosimulators_utils/blo…
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---
id: pysces
version: 1.2.1
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_PySCeS/2d97929994747fd30b5684393bb850839955b5eb/biosimulators.json
specificationsPatch:
…
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The namespace related errors in this issue are likely due to a missing namespace attribute near the top of the sedml file
https://github.com/robertvi/SBMLShowcase/issues/5
We manually fixed this …
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[create_omex](https://github.com/robertvi/SBMLShowcase/blob/2c38d1abe0542196ed51e45f3e1f24b4c73e2e1e/utils/__init__.py#L44) function has some [hardcoded bits](https://github.com/robertvi/SBMLShowcase/…
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#### Problem description
Please explain:
* trying to create a COMBINE archive from a SEDML and an SBML file to pass to biosimulators docker to run eg tellurium, COPASI etc
* using Omex.add_entry …
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To facilitate the use of SED-ML beyond kinetic models encoded in SMBL, I think it would be helpful to add URNs for the SBML-fbc, multi, and qual packages. Because these packages are largely used separ…