pysces

The official PySCeS project source code repository.

https://github.com/pysces/pysces

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 5 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Academic email domains
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (19.1%) to scientific vocabulary

Keywords

bioinformatics console-application kinetic-modeling mca python sbml simulation steady-state

Last synced: 6 months ago · JSON representation ·

Repository

The official PySCeS project source code repository.

Basic Info

Host: GitHub
Owner: PySCeS
License: other
Language: Python
Default Branch: main
Homepage: https://pysces.github.io
Size: 10.5 MB

Statistics

Stars: 39
Watchers: 3
Forks: 11
Open Issues: 7
Releases: 15

Topics

bioinformatics console-application kinetic-modeling mca python sbml simulation steady-state

Created over 12 years ago · Last pushed 7 months ago

Metadata Files

Readme Changelog License Citation Zenodo

PySCeS - Python Simulator for Cellular Systems

PySCeS is a flexible, user-friendly tool for the analysis of cellular systems. For more information please see https://pysces.github.io/

Introduction
Installation
Getting help
Citing PySCeS
Contributing
Licence
Authors and acknowledgments

Introduction

Computer modelling has become an integral tool in the analysis and understanding of the reaction networks that underlie cellular processes. PySCeS, first released in 2003, is extremely flexible, user-extensible, open source, software actively used and developed by a community of researchers and developers.

Features

Simulate your time courses with solvers like LSODA and CVODE.
Efficiently determine steady states using a selection of non-linear, root-finding algorithms (e.g. HYBRD, NLEQ2).
Use Metabolic Control Analysis (MCA) to investigate control and regulation of cellular systems (elasticities, flux- and concentration-control and response coefficients).
Auto-generate the stoichiometric matrix and perform structural analysis, determine nullspaces and reduced stoichiometric and MCA matrices.
Investigate systems which exhibit multiple (stable and unstable) steady-state solutions using a PITCON-based bifurcation analysis module.
Define models with a human-readable Model Description Language.
Use the full power of Python available to test, build and share your modelling experiments.
User-friendly methods for generating and 1-, 2- and n-dimensional parameter scans.
Distributed parameter scanning with the ParScanner module within the ipyparallel framework.
Visualise results of simulations with flexible Matplotlib and Gnuplot interfaces.
PySCeS supports open community standards for model exchange (SBML) and archiving (SEDML, OMEX).

Installation

PySCeS releases are available on PyPI, Anaconda.org and Github

PySCeS binaries are available for Python 3.9+ on Windows, Linux and OSX and can be installed using

PyPI

bash pip install pysces

Anaconda.org

bash conda install -c conda-forge -c pysces pysces

Building from source

PySCeS requires a Python 3 development environment as well as C++ and FORTRAN compilers to build. For more information please see the INSTALL instructions.

Getting help

We currently encourage users to ask questions and request support using a GitHub issue.

General information on PySCeS can be found on the website and extensive documentation on installing, configuring and using PySCeS is available on pyscesdocs.readthedocs.io.

Citing PySCeS

Publication

Brett G. Olivier, Johann M. Rohwer and Jan-Hendrik S. Hofmeyr, Modelling cellular systems with PySCeS, Bioinformatics, Volume 21, Issue 4, 15 February 2005, Pages 560–561, https://doi.org/10.1093/bioinformatics/bti046

Published code releases

PySCeS releases are archived on Zenodo.

Contributing

Primary development is on GitHub, feel free to fork and submit pull requests! Want to add new code to PySCeS, go

Licence

PySCeS is distributed as Open Source software under a BSD style licence, please see LICENCE.txt for details. The licences of software that is bundled with, or used by, PySCeS are available in ADDITIONAL_LICENCES.md.

Authors and acknowledgments

PySCeS main authors are Brett Olivier and Johann Rohwer and in particular, PySCeS founding father Jannie Hofmeyr.

We would also like to acknowledge everyone who has contributed to PySCeS and would like to thank the following (in alphabetical order):

Evert Bosdriesz
James Dominy
Jannie Hofmeyr
Morgan Hough
Jonathan Karr
Ruchir Khandelwal
Charl Moller
Danie Palm
Herbert Sauro
Lafras Uys

This information can also be found in CONTRIBUTORS.md In addition we would like to acknowledge financial support from the following funding organisations:

The South African National Bioinformatics Network (2003-2008)
The South African National Research Foundation (2000-2004)

Owner

Name: PySCeS: The Python Simulator for Cellular Systems, provides a variety of tools for the analysis of cellular systems
Login: PySCeS
Kind: organization
Location: Amsterdam, The Netherlands and Stellenbosch, South Africa

Website: http://pysces.sourceforge.net/
Repositories: 6
Profile: https://github.com/PySCeS

The Python Simulator for Cellular Systems

Citation (CITATION.cff)

# YAML 1.2
---
cff-version: "1.2.0"
message: "If you use this software, please cite it using the information provided in this metadata."
authors:
  -
    given-names: Brett
    family-names: Olivier
    affiliation: "Vrije Universiteit Amsterdam"
    orcid: "https://orcid.org/0000-0002-5293-5321"
  -
    given-names: Johann
    family-names: Rohwer
    affiliation: "Stellenbosch University"
    orcid: "https://orcid.org/0000-0001-6288-8904"
title: "The Python Simulator for Cellular Systems: PySCeS"
version: "1.2.3"
repository-code: "https://github.com/PySCeS/pysces/tree/1.2.3"
date-released: 2025-05-07
doi: "10.5281/zenodo.2600905"
license: "BSD-3-Clause"
url: https://pysces.github.io
abstract: "Computer modelling has become an integral tool in the analysis and understanding
of the reaction networks that underlie cellular processes. PySCeS, first released in 2003,
is extremely flexible, user-extendable, open source, software actively used and developed
by a community of researchers and developers."
...

GitHub Events

Total

Create event: 2
Issues event: 1
Release event: 1
Watch event: 4
Delete event: 2
Issue comment event: 6
Push event: 75
Pull request review event: 1
Pull request event: 6
Fork event: 1

Last Year

Create event: 2
Issues event: 1
Release event: 1
Watch event: 4
Delete event: 2
Issue comment event: 6
Push event: 75
Pull request review event: 1
Pull request event: 6
Fork event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 64
Total pull requests: 40
Average time to close issues: 10 months
Average time to close pull requests: 18 days
Total issue authors: 11
Total pull request authors: 6
Average comments per issue: 3.81
Average comments per pull request: 2.83
Merged pull requests: 34
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 6
Average time to close issues: N/A
Average time to close pull requests: about 3 hours
Issue authors: 1
Pull request authors: 3
Average comments per issue: 0.0
Average comments per pull request: 2.33
Merged pull requests: 4
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

bgoli (20)
jonrkarr (13)
jmrohwer (13)
yurivict (8)
exe0cdc (3)
olledejong (2)
StephanM87 (1)
elofgren (1)
matthiaskoenig (1)
ortega2247 (1)
mhucka (1)

Pull Request Authors

jmrohwer (23)
bgoli (11)
lowkeyrossi (2)
Greenie0701 (2)
c-barry (1)
katrinleinweber (1)

Top Labels

Issue Labels

enhancement (8) bug (6) question (5) wontfix (3) info (3) website (1)

Pull Request Labels

enhancement (4)

Packages

Total packages: 1
Total downloads:
- pypi 889 last-month

Total dependent packages: 2
Total dependent repositories: 8
Total versions: 27
Total maintainers: 2

pypi.org: pysces

The Python Simulator for Cellular Systems - simulation and analysis tools for modelling biological systems

Documentation: https://pysces.readthedocs.io/
License: BSD 3-Clause
Latest release: 1.2.3
published 10 months ago

Versions: 27
Dependent Packages: 2
Dependent Repositories: 8
Downloads: 889 Last month

Rankings

Dependent packages count: 3.2%

Dependent repos count: 5.2%

Average: 6.1%

Downloads: 10.1%

Maintainers (2)

bgoli jrohwer