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Please provide information about the requested term:
**What type of term would you like to create?**
- [ X] algorithm
- [ ] algorithm characteristic
- [ ] algorithm parameter
- [ ] algorithm ou…
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= Description =
- Integrate required words of the KiSAO ontology in the corresponding Simulation-derived classes.
= Context =
- KiSAO is an ontology of kinetic simulation algorithms; it is used for …
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Every biomodels that uses steady state uses the KISAO term 282 ('KINSOL'), and the checker returns this error:
NotImplementedError: Algorithm substitution for "KINSOL" (http://www.biomodels.net/ki…
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Currently these concepts are not well documented/linked on the homepage.
* Ontologies Used Kinetic Simulation Algorithm Ontology (https://bioportal.bioontology.org/ontologies/KISAO)
* https://…
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As a follow-up to #569, it's the case that several ontologies in the OLS don't use OBO PURLs, which means the automated code for constructing OLS (and BioPortal) URIs is broken.
E.g., for KISAO, th…
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The following links are not found:
http://co.mbine.org/standards/omex
http://co.mbine.org/standards/kisao
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The current setting only maps KiSAO terms for algorithms to LibSMLsim integrators. If LibSBMLsim exposes additional parameters for the integrators, this can also be mapped to KiSAO terms for algorithm…
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Tellurium recognizes `KISA0:0000107` for the boolean argument whether to use adaptive time steps. However, this is a term for an algorithm characteristic rather than an algorithm parameter.
I added…
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Such as
- Steady-State Analysis
- Stoichiometric State Analysis
- MCA
- Lyapunov Exponents
- Time Scale Separation
- Sensitivity Analysis
Todo
- [ ] Map each COPASI method/parameter to a Ki…
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The [Biosimulators_mpbn](https://github.com/colomoto/Biosimulators_mpbn) wrapper for [mpbn](https://mpbn.readthedocs.io) implements algorithms which require new KiSAO terms for algorithms and algorit…