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## BioSimulators utils
- [x] Execute each SED document, task, and output
- [x] Catch exceptions so that the execution doesn't stop on the first failure
- [x] Collect all exceptions and raise…
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Hi @copasi @pmendes. As you probably know, we're containerizing COPASI to make it available through [BioSimulations](https://biosimulations.dev). The metadata about COPASI is captured in [`biosimulato…
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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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Because data generators can involve variables from multiple tasks, the variables which contribute to a data generator can have different shapes. Similarly, outputs can involve data generators that hav…
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This uses KISAO:0000029`. This algorithm only has on parameter 488 whose value is an integer. This needs to be changed.
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Question for tellurium/libRoadRunner developers:
Algorithms
- euler
- NLEQ1: KISAO_0000568
Algorithm parameters (`tellurium name: default`)
- CVODE
- stiff: true
- multiple_steps: false…
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As discussed in #25, this package cannot support the hybrid RK45 method because python-COPASI doesn't support setting the partitioning parameter. @fbergmann please let us know when python-COPASI is up…
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Currently, the following are flagged for not using standard/recommended licenses:
WARN SBO license: 'http://opensource.org/licenses/Artistic-2.0' is not a recommended license
WARN MAMO license: 'h…
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The current types are `boolean`, `number`, and `string`.
We need to add a couple of types
- `kisaoId`: needed to capture nested algorithms. e.g., an option of the CMBPy FBA algorithm is the simpl…
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Needed to update annotations of simulation tools