{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,10]],"date-time":"2025-11-10T21:04:17Z","timestamp":1762808657876,"version":"3.37.3"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2018,5,22]],"date-time":"2018-05-22T00:00:00Z","timestamp":1526947200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000341","name":"Arthritis Research UK","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000341","id-type":"DOI","asserted-by":"publisher"}]},{"name":"MRC-Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing"},{"DOI":"10.13039\/501100001271","name":"CIMA","doi-asserted-by":"publisher","award":["MR\/K006312\/1"],"award-info":[{"award-number":["MR\/K006312\/1"]}],"id":[{"id":"10.13039\/501100001271","id-type":"DOI","asserted-by":"publisher"}]},{"name":"BBSRC LINK","award":["BB\/K019260\/1"],"award-info":[{"award-number":["BB\/K019260\/1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>COPASI is an open source software package for constructing, simulating and analyzing dynamic models of biochemical networks. COPASI is primarily intended to be used with a graphical user interface but often it is desirable to be able to access COPASI features programmatically, with a high level interface.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>PyCoTools is a Python package aimed at providing a high level interface to COPASI tasks with an emphasis on model calibration. PyCoTools enables the construction of COPASI models and the execution of a subset of COPASI tasks including time courses, parameter scans and parameter estimations. Additional \u2018composite\u2019 tasks which use COPASI tasks as building blocks are available for increasing parameter estimation throughput, performing identifiability analysis and performing model selection. PyCoTools supports exploratory data analysis on parameter estimation data to assist with troubleshooting model calibrations. We demonstrate PyCoTools by posing a model selection problem designed to show case PyCoTools within a realistic scenario. The aim of the model selection problem is to test the feasibility of three alternative hypotheses in explaining experimental data derived from neonatal dermal fibroblasts in response to TGF-\u03b2 over time. PyCoTools is used to critically analyze the parameter estimations and propose strategies for model improvement.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PyCoTools can be downloaded from the Python Package Index (PyPI) using the command \u2019pip install pycotools\u2019 or directly from GitHub (https:\/\/github.com\/CiaranWelsh\/pycotools). Documentation at http:\/\/pycotools.readthedocs.io.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty409","type":"journal-article","created":{"date-parts":[[2018,5,18]],"date-time":"2018-05-18T19:15:03Z","timestamp":1526670903000},"page":"3702-3710","source":"Crossref","is-referenced-by-count":19,"title":["PyCoTools: a Python toolbox for COPASI"],"prefix":"10.1093","volume":"34","author":[{"given":"Ciaran M","family":"Welsh","sequence":"first","affiliation":[{"name":"Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, UK"}]},{"given":"Nicola","family":"Fullard","sequence":"additional","affiliation":[{"name":"Department of Biosciences, Durham University, Durham, UK"}]},{"given":"Carole J","family":"Proctor","sequence":"additional","affiliation":[{"name":"Institute of Cellular Medicine, Newcastle University, Newcastle, UK"}]},{"given":"Alvaro","family":"Martinez-Guimera","sequence":"additional","affiliation":[{"name":"Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, UK"}]},{"given":"Robert J","family":"Isfort","sequence":"additional","affiliation":[{"name":"The Proctor & Gamble Company, Cincinnati, USA"}]},{"given":"Charles C","family":"Bascom","sequence":"additional","affiliation":[{"name":"The Proctor & Gamble Company, Cincinnati, USA"}]},{"given":"Ryan","family":"Tasseff","sequence":"additional","affiliation":[{"name":"The Proctor & Gamble Company, Cincinnati, USA"}]},{"given":"Stefan A","family":"Przyborski","sequence":"additional","affiliation":[{"name":"Department of Biosciences, Durham University, Durham, UK"}]},{"given":"Daryl P","family":"Shanley","sequence":"additional","affiliation":[{"name":"Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, UK"}]}],"member":"286","published-online":{"date-parts":[[2018,5,22]]},"reference":[{"key":"2023012712374132700_bty409-B1","doi-asserted-by":"crossref","first-page":"12057.","DOI":"10.1038\/ncomms12057","article-title":"Signal transduction controls heterogeneous nf-[kappa] b dynamics and target gene expression through cytokine-specific refractory states","volume":"7","author":"Adamson","year":"2016","journal-title":"Nat. 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