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PyCoTools: a Python toolbox for COPASI

Welsh, Ciaran M.; Fullard, Nicola; Proctor, Carole J.; Martinez-Guimera, Alvaro; Isfort, Robert J.; Bascom, Charles C.; Tasseff, Ryan; Przyborski, Stefan A.; Shanley, Daryl P.

PyCoTools: a Python toolbox for COPASI Thumbnail


Authors

Ciaran M. Welsh

Carole J. Proctor

Alvaro Martinez-Guimera

Robert J. Isfort

Charles C. Bascom

Ryan Tasseff

Daryl P. Shanley



Abstract

Motivation 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. Results 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 ‘composite’ 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-β over time. PyCoTools is used to critically analyze the parameter estimations and propose strategies for model improvement. Availability and implementation PyCoTools can be downloaded from the Python Package Index (PyPI) using the command ’pip install pycotools’ or directly from GitHub (https://github.com/CiaranWelsh/pycotools). Documentation at http://pycotools.readthedocs.io. Supplementary information Supplementary data are available at Bioinformatics online.

Citation

Welsh, C. M., Fullard, N., Proctor, C. J., Martinez-Guimera, A., Isfort, R. J., Bascom, C. C., …Shanley, D. P. (2018). PyCoTools: a Python toolbox for COPASI. Bioinformatics, 34(21), 3702-3710. https://doi.org/10.1093/bioinformatics/bty409

Journal Article Type Article
Acceptance Date May 18, 2018
Online Publication Date May 22, 2018
Publication Date Nov 1, 2018
Deposit Date Nov 8, 2018
Publicly Available Date Mar 28, 2024
Journal Bioinformatics
Print ISSN 1367-4803
Electronic ISSN 1460-2059
Publisher Oxford University Press
Peer Reviewed Peer Reviewed
Volume 34
Issue 21
Pages 3702-3710
DOI https://doi.org/10.1093/bioinformatics/bty409

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