Package: kisao
Python package for working with the theKinetic Simulation Algorithm
Ontology(KiSAO), an ontology
of algorithms for simulating and analyzing biological models, as well as
the characteristics of these algorithms, their input parameters, and
their outputs.Installing this packageRequirementsPython >= 3.7pipInstallationPlease run the following command to install this package:pip install kisaoTo generate a matrix of the substitutability among algorithms, install
this package with thesubstitutability-matrixoption:pip install kisao[substitutability-matrix]TutorialfromkisaoimportKisaofromkisaoimportutilsfromkisao.data_modelimportAlgorithmSubstitutionPolicy# load the ontologykisao=Kisao()# get a termterm=kisao.get_term('KISAO_0000019')# get the name of the termterm.name>>'CVODE'# get sets of methodsalgs=utils.get_ode_algorithms()sorted([alg.nameforalginalgs])[0:5]>>['Adams method','Adams predictor-corrector method','Adams-Bashforth method','Adams-Moulton method','Bader-Deuflhard method',]algs=utils.get_sde_algorithms()algs=utils.get_pde_algorithms()algs=utils.get_tau_leaping_algorithms()algs=utils.get_ode_algorithms()algs=utils.get_gillespie_like_algorithms()algs=utils.get_tau_leaping_algorithms()algs=utils.get_rule_based_algorithms()algs=utils.get_sde_algorithms()algs=utils.get_pde_algorithms()algs=utils.get_flux_balance_algorithms()algs=utils.get_logical_algorithms()algs=utils.get_hybrid_algorithms()# get a set of substitutable algorithms for a specific substitution policycvode=kisao.get_term('KISAO_0000019')euler_forward=kisao.get_term('KISAO_0000030')lsoda=kisao.get_term('KISAO_0000088')lsodar=kisao.get_term('KISAO_0000089')fba=kisao.get_term('KISAO_0000437')fva=kisao.get_term('KISAO_0000526')alt_algs=utils.get_substitutable_algorithms_for_policy(cvode,substitution_policy=AlgorithmSubstitutionPolicy.SIMILAR_APPROXIMATIONS)sorted([alt_alg.nameforalt_alginalt_algs])[0:5]>>['Adams method','Adams predictor-corrector method','Adams-Bashforth method','Adams-Moulton method','Bader-Deuflhard method',]# get a preferred substitution for an algorithmrequested_alg=lsodaimplemented_algs_in_preferred_order=[cvode,lsoda,lsodar,euler_forward]alt_alg=utils.get_preferred_substitute_algorithm(requested_alg,implemented_algs_in_preferred_order,substitution_policy=AlgorithmSubstitutionPolicy.SIMILAR_APPROXIMATIONS)alt_alg.name>>'LSODA'requested_alg=lsodaimplemented_algs_in_preferred_order=[cvode,euler_forward]alt_alg=utils.get_preferred_substitute_algorithm(requested_alg,implemented_algs_in_preferred_order,substitution_policy=AlgorithmSubstitutionPolicy.SIMILAR_APPROXIMATIONS)alt_alg.name>>'CVODE'requested_alg=lsodaimplemented_algs_in_preferred_order=[fba,fva]alt_alg=utils.get_preferred_substitute_algorithm(requested_alg,implemented_algs_in_preferred_order,substitution_policy=AlgorithmSubstitutionPolicy.SIMILAR_APPROXIMATIONS)alt_alg>>NoneBrowsing KiSAOKiSAO can be browsed throughBioPortalandOLS.Browsing the substitutability of algorithms catalogued by KiSAOA matrix of the substitutability of algorithms catalogued by KiSAO is
availablehere.
The documentation for this package describes the queries and rules used
to define this matrix.Contributing to KiSAOPlease see theKiSAO repositoryfor information about contributing to KiSAO and this package.LicenseThis package is released underArtistic License
2.0.