kisao

KiSAO

Python package for working with the the Kinetic Simulation Algorithm Ontology <http://co.mbine.org/standards/kisao>__ (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 package

Requirements

-  Python >= 3.7
-  pip

Installation

Please run the following command to install this package:

::

pip install kisao

To generate a matrix of the substitutability among algorithms, install this package with the substitutability-matrix option:

::

pip install kisao[substitutability-matrix]

Tutorial

.. code:: python

from kisao import Kisao from kisao import utils from kisao.data_model import AlgorithmSubstitutionPolicy

load the ontology

kisao = Kisao()

get a term

term = kisao.get_term('KISAO_0000019')

get the name of the term

term.name

'CVODE'

get sets of methods

algs = utils.get_ode_algorithms() sorted([alg.name for alg in algs])[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 policy

cvode = 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.name for alt_alg in alt_algs])[0:5]

[ 'Adams method', 'Adams predictor-corrector method', 'Adams-Bashforth method', 'Adams-Moulton method', 'Bader-Deuflhard method', ]

get a preferred substitution for an algorithm

requested_alg = lsoda implemented_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 = lsoda implemented_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 = lsoda implemented_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

None

Browsing KiSAO

KiSAO can be browsed through BioPortal <https://bioportal.bioontology.org/ontologies/KISAO>__ and OLS <https://www.ebi.ac.uk/ols/ontologies/kisao>__.

Browsing the substitutability of algorithms catalogued by KiSAO

A matrix of the substitutability of algorithms catalogued by KiSAO is available here <https://github.com/SED-ML/KiSAO/blob/dev/libkisao/python/docs/algorithm-substitutability.csv>__. The documentation for this package describes the queries and rules used to define this matrix.

Contributing to KiSAO

Please see the KiSAO repository <https://github.com/SED-ML/KiSAO/>__ for information about contributing to KiSAO and this package.

License

This package is released under Artistic License 2.0 <https://github.com/SED-ML/KiSAO/blob/dev/LICENSE>__.