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Attached are a list of amici failures on the current suite of biomodels from https://github.com/sys-bio/temp-biomodels/tree/main/omex_files
Also included is the list of tellurium failures, because …
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I was going through the model in cobrapy and doing some sensibility checked.
And I noted their were 1161 unique uniprot identifers, but 1162 unique gene ids.
So i went looking closer to see what was…
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Here's links to all the biomodels that currently fail when running PySCeS:
[pysces_failures.csv](https://github.com/biosimulators/Biosimulators_PySCeS/files/13193249/pysces_failures.csv)
(Many o…
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[tellurium_failures.xlsx](https://github.com/biosimulators/Biosimulators_COPASI/files/12446822/tellurium_failures.xlsx)
[copasi_failures.csv](https://github.com/biosimulators/Biosimulators_COPASI/fil…
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There are ~1000 curated models on https://www.ebi.ac.uk/biomodels/, mostly in SBML format.
A good number of these are relevant for neuroscience, e.g. https://www.ebi.ac.uk/biomodels/BIOMD0000000118…
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The temp-biomodels project has a lot of new SED-ML, and much of it is correctly interpreted by VCell, but there are some cases where there are breakdowns. Attached is a full list of every biomodel th…
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Possibly consider cacheing list of models from biomodels so we lessen the bulk of the api call
- Python Script for obtaining the data, run through github actions to create the JSON file to hold the…
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@Midnighter requests at https://github.com/SBRG/bigg_models/issues/368:
Many models in BiGG are currently annotated with a taxonomic identifier and a reference to the model itself, for example, as …
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Hi @GemmaTuron @miquelduranfrigola
Here is an issue [template](https://github.com/Zainab-ik/Creating-issue-templates/blob/main/.github/ISSUE_TEMPLATE/config.yml) for to incorporate BioModel annotat…
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Refactor biomodels import and switch to JavaFX GUI.
Implement unittests.