PySCeS Constraint Based Modelling (https://systemsbioinformatics.github.io/cbmpy/) Copyright (C) 2010-2024 Brett G. Olivier, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/
Author: Brett G. Olivier (@bgoli)
CBMPy (https://systemsbioinformatics.github.io/cbmpy/) is a new platform for constraint based modelling and analysis. It has been designed using principles developed in the PySCeS simulation software project: usability, flexibility and accessibility. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist (metabolites, reactions, compartments) while transparently translating these into the underlying mathematical structures used in advanced analysis (LP's, MILP's).
CBMPy fully supports all the SBML Flux Balance Constraints (FBC) interoperability standards.
CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as advanced methods developed specifically for the ecosystem modelling: minimal distance methods, flux minimization and input selection. To cater for a diverse range of modelling needs CBMPy supports user interaction via:
- interactive console, scripting for advanced use or as a library for software development
- GUI, for quick access to a visual representation of the model, analysis methods and annotation tools
- SOAP based web services: using the Mariner framework much high level functionality is exposed for integration into web tools
For more information on the development and use of CBMPy (https://systemsbioinformatics.github.io/cbmpy/)
CBMPy has been tested on Windows 7 and 8.1, 10, 11, Mac OSX and Ubuntu Linux 12.04, 14.04, 16.04, 20.04, 22.04 CBMPy is currently developed on Python 3.10 and Python 3.8 or newer is highly recommended
The best way to get the basic CBMPy running is to install from PyPI or create an Anaconda environment. CBMPy is developed on GitHub (https://systemsbioinformatics.github.io/cbmpy/)
From a terrminal or command prompt try to install the required packages
pip install -r requirements.txt
pip install cbmpy
From a terminal or command prompt try:
conda env create -f=environment.yml
This creates an environment cbmpy3 that can be accessed from the command line using conda activate cbmpy3
To check you installation follow the installation try the following in a Python shell:
import cbmpy
cmod = cbmpy.readSBML3FBC('cbmpy_test_core')
cbmpy.doFBA(cmod)
Once you have installed CBMPy it can be easily upgraded.
pip install --upgrade cbmpy
conda update cbmpy
(c) Brett G. Olivier, Amsterdam, 2014-2024