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biosimulators / Biosimulators_utils

Utilities for building standardized command-line interfaces for biosimulation software packages
https://docs.biosimulators.org/Biosimulators_utils
MIT License
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Allow more-specific algorithm substitution. #105

Closed luciansmith closed 1 year ago

luciansmith commented 2 years ago

When validating biomodels models, I get the following error a lot:

NotImplementedError: Algorithm substitution for "steady state method" (http://www.biomodels.net/kisao/KISAO#KISAO_0000407) for policy SAME_VARIABLES is not supported.

(See, for example, biomodels BIOMD0000000498/BIOMD0000000498.sedml)

KiSAO term 407 is the generic steady state algorithm, so it is likely that the problem is that substituting a more-specific algorithm for the generic one has not been implemented. I could be wrong, and I could also be wrong about what repository the error message came from! But this was my best guess.

jonrkarr commented 2 years ago

Not much has been done with steady state. To start, it would be helpful to get code from Frank Bergmann for use with COPASI. There's minimal bandwidth for now.

luciansmith commented 1 year ago

Fixed in libkisao.