PySCeSToolbox: a collection of metabolic pathway analysis tools

Carl D Christensen; Jan-Hendrik S Hofmeyr; Johann M Rohwer

doi:10.1093/bioinformatics/btx567

PySCeSToolbox: a collection of metabolic pathway analysis tools

Bioinformatics. 2018 Jan 1;34(1):124-125. doi: 10.1093/bioinformatics/btx567.

Authors

Carl D Christensen¹, Jan-Hendrik S Hofmeyr^{1

2}, Johann M Rohwer¹

Affiliations

¹ Department of Biochemistry, Laboratory for Molecular Systems Biology, Stellenbosch University, South Africa.
² Centre for Complex Systems in Transition, School of Public Leadership, Stellenbosch University, Stellenbosch 7602, South Africa.

PMID: 28968872
DOI: 10.1093/bioinformatics/btx567

Abstract

Summary: PySCeSToolbox is an extension to the Python Simulator for Cellular Systems (PySCeS) that includes tools for performing generalized supply-demand analysis, symbolic metabolic control analysis, and a framework for investigating the kinetic and thermodynamic aspects of enzyme-catalyzed reactions. Each tool addresses a different aspect of metabolic behaviour, control, and regulation; the tools complement each other and can be used in conjunction to better understand higher level system behaviour.

Availability and implementation: PySCeSToolbox is available on Linux, Mac OS X and Windows. It is licensed under the BSD 3-clause licence. Code, setup instructions and a link to documentation can be found at https://github.com/PySCeS/PyscesToolbox.

Contact: jr@sun.ac.za.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods*
Enzymes / chemistry
Enzymes / metabolism
Kinetics
Metabolic Networks and Pathways*
Models, Biological*
Software*
Thermodynamics

Substances

Enzymes