CBMPy

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)

About

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

Install

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/)

Install with pip using requirements.txt

From a terrminal or command prompt try to install the required packages

pip install -r requirements.txt

Then install CBMPy

pip install cbmpy

Install by creating an Anaconda environment using environment.yml

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

Check the basic installation

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)

Updating CBMPy

Once you have installed CBMPy it can be easily upgraded.

Pip update

pip install --upgrade cbmpy

Anaconda update

conda update cbmpy

(c) Brett G. Olivier, Amsterdam, 2014-2024