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Currently the ontology lookup service (OLS) and opo foundry still use old versions of KISAO.
This should be fixed as soon as the following is merged:
https://github.com/OBOFoundry/purl.obolibrary.or…
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Presently, algorithms must be captured as a single KiSAO term. This creates the need to create additional terms for each hybrid combination. A more flexible approach would be to allow inline descripti…
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### Contact Details
_No response_
### Location
runBiosimulations
### What happened?
I uploaded
[Figure5.omex.zip](https://github.com/biosimulations/biosimulations/files/10198550/Figure5.omex.zi…
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CoLoMoTo Docker is a start to providing access to multiple logical modeling tools through Python. The usability of the tools outside Jupyter (i.e. other Python codes) would be enhanced by factoring th…
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I am trying to run ODE_FBA.ipynb notebook and getting following error:
cell:
ode_config = {
'biosimulator_api': 'biosimulators_tellurium',
'model_source': MILLARD2016_PATH,
'mode…
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In my opinion, it should be possible to express that the value of an algorithm parameter should be null. For example, null could be used to indicate that a random algorithm shouldn't be seeded with a …
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When you submit a kinetic model to Biomodels.net, you are supposed to indicate one or more figures from the paper that should be reproducible from the model. The manual curator assigned to your submis…
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### Simulation tool
---
id: smoldyn
version: 2.73
specificationsUrl: https://raw.githubusercontent.com/ssandrews/Smoldyn/master/biosimulators.json
specificationsPatch:
version: 2.73
image:
u…
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List of functions in addition of min, max, prod, sum:
- `count`** : returns number of all elements
- `mean`** : returns mean of all elements
- `sdev`** : standard deviation of all elements
- `…
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Presently, `ChangeAttribute.newValue` has data type of `string`. It would be helpful to keep track of the true data type (e.g., Boolean, integer, float, string, etc.). This would facilitate semantic i…