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1. Use a reliable simulator (e.g., COPASI) to create a "gold standard" for each test COMBINE archive
2. Save these results to the test suite repo (Biosimulations_COMBINE_archive_test_suite)
3. Expan…
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Obtain models from bigg.ucsd.edu in SBML format
Create SED-ML files to run FBA simulations
Save to Biosimulations_COMBINE_archive_test_suite
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Obtain models in SBML-qual format from CellCollective
Create SED-ML files to run simulations (e.g., asynchronous updating)
Add to Biosimulations_COMBINE_archive_test_suite
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I'm trying to use this workflow to get tokens to POST/PUT simulators to the BioSimulators api.
1. Use client id/secret for "GitHub Simulators Actions" application to get an auth token
2. Use token w…
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## Solvers to initially support
KISAO terms exist for each of these algorithms and each of their parameters
- `gillespy2.solvers.numpy.ode_solver.ODESolver` (`integrator`=`lsoda`): KISAO:0000088
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Example: KISAO_0000036 at https://biosimulators.org/simulators/copasi/latest
- KISAO_0000036 passes the validation in the BioSimulators API
- But the UI can't find KISAO_0000036
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```
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NET::ERR_CERT_AUT…
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The Simulators API has been changed to use its own authentication system. The "API audience" field in the authentication flow should be updated to "api.biosimulators.org" instead of the previous "a…
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To enable #1602, we need to automate the generation of singularity images. There's multiple possibilities including
- Integrating this into the workflow for accepting simulators into the registry:…