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>`__.
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"description": "KiSAO\n=====\n\nPython package for working with the the `Kinetic Simulation Algorithm\nOntology <http://co.mbine.org/standards/kisao>`__ (KiSAO), an ontology\nof algorithms for simulating and analyzing biological models, as well as\nthe characteristics of these algorithms, their input parameters, and\ntheir outputs.\n\nInstalling this package\n-----------------------\n\nRequirements\n~~~~~~~~~~~~\n\n- Python >= 3.7\n- pip\n\nInstallation\n~~~~~~~~~~~~\n\nPlease run the following command to install this package:\n\n::\n\n pip install kisao\n\nTo generate a matrix of the substitutability among algorithms, install\nthis package with the ``substitutability-matrix`` option:\n\n::\n\n pip install kisao[substitutability-matrix]\n\nTutorial\n--------\n\n.. code:: python\n\n from kisao import Kisao\n from kisao import utils\n from kisao.data_model import AlgorithmSubstitutionPolicy\n\n # load the ontology\n kisao = Kisao()\n\n # get a term\n term = kisao.get_term('KISAO_0000019')\n\n # get the name of the term\n term.name\n >> 'CVODE'\n\n # get sets of methods\n algs = utils.get_ode_algorithms()\n sorted([alg.name for alg in algs])[0:5]\n >> [\n 'Adams method',\n 'Adams predictor-corrector method',\n 'Adams-Bashforth method',\n 'Adams-Moulton method',\n 'Bader-Deuflhard method',\n ]\n\n algs = utils.get_sde_algorithms()\n algs = utils.get_pde_algorithms()\n algs = utils.get_tau_leaping_algorithms()\n algs = utils.get_ode_algorithms()\n algs = utils.get_gillespie_like_algorithms()\n algs = utils.get_tau_leaping_algorithms()\n algs = utils.get_rule_based_algorithms()\n algs = utils.get_sde_algorithms()\n algs = utils.get_pde_algorithms()\n algs = utils.get_flux_balance_algorithms()\n algs = utils.get_logical_algorithms()\n algs = utils.get_hybrid_algorithms()\n\n # get a set of substitutable algorithms for a specific substitution policy\n cvode = kisao.get_term('KISAO_0000019')\n euler_forward = kisao.get_term('KISAO_0000030')\n lsoda = kisao.get_term('KISAO_0000088')\n lsodar = kisao.get_term('KISAO_0000089')\n fba = kisao.get_term('KISAO_0000437')\n fva = kisao.get_term('KISAO_0000526')\n\n alt_algs = utils.get_substitutable_algorithms_for_policy(cvode,\n substitution_policy=AlgorithmSubstitutionPolicy.SIMILAR_APPROXIMATIONS)\n sorted([alt_alg.name for alt_alg in alt_algs])[0:5]\n >> [\n 'Adams method',\n 'Adams predictor-corrector method',\n 'Adams-Bashforth method',\n 'Adams-Moulton method',\n 'Bader-Deuflhard method',\n ]\n\n # get a preferred substitution for an algorithm\n requested_alg = lsoda\n implemented_algs_in_preferred_order = [cvode, lsoda, lsodar, euler_forward]\n alt_alg = utils.get_preferred_substitute_algorithm(requested_alg, implemented_algs_in_preferred_order,\n substitution_policy=AlgorithmSubstitutionPolicy.SIMILAR_APPROXIMATIONS)\n alt_alg.name\n >> 'LSODA'\n\n requested_alg = lsoda\n implemented_algs_in_preferred_order = [cvode, euler_forward]\n alt_alg = utils.get_preferred_substitute_algorithm(requested_alg, implemented_algs_in_preferred_order,\n substitution_policy=AlgorithmSubstitutionPolicy.SIMILAR_APPROXIMATIONS)\n alt_alg.name\n >> 'CVODE'\n\n requested_alg = lsoda\n implemented_algs_in_preferred_order = [fba, fva]\n alt_alg = utils.get_preferred_substitute_algorithm(requested_alg, implemented_algs_in_preferred_order,\n substitution_policy=AlgorithmSubstitutionPolicy.SIMILAR_APPROXIMATIONS)\n alt_alg\n >> None\n\nBrowsing KiSAO\n--------------\n\nKiSAO can be browsed through\n`BioPortal <https://bioportal.bioontology.org/ontologies/KISAO>`__ and\n`OLS <https://www.ebi.ac.uk/ols/ontologies/kisao>`__.\n\nBrowsing the substitutability of algorithms catalogued by KiSAO\n---------------------------------------------------------------\n\nA matrix of the substitutability of algorithms catalogued by KiSAO is\navailable\n`here <https://github.com/SED-ML/KiSAO/blob/dev/libkisao/python/docs/algorithm-substitutability.csv>`__.\nThe documentation for this package describes the queries and rules used\nto define this matrix.\n\nContributing to KiSAO\n---------------------\n\nPlease see the `KiSAO repository <https://github.com/SED-ML/KiSAO/>`__\nfor information about contributing to KiSAO and this package.\n\nLicense\n-------\n\nThis package is released under `Artistic License\n2.0 <https://github.com/SED-ML/KiSAO/blob/dev/LICENSE>`__.\n\n\n",
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