kisao


Namekisao JSON
Version 2.34 PyPI version JSON
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home_pagehttps://github.com/SED-ML/kisao
SummaryUtilities for working with the Kinetic Simulation Algorithm Ontology (KiSAO)
upload_time2024-03-14 19:51:55
maintainer
docs_urlNone
authorSED-ML Editors
requires_python
licenseApache 2.0
keywords systems biology modeling simulation algorithm ontology kisao sed-ml sbml
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls.
            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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