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‎README.md‎

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CBMPy
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=====
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# CBMPy
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PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
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Copyright (C) 2010-2018 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
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Copyright (C) 2010-2021 Brett G. Olivier, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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This program is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <http://www.gnu.org/licenses/>
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Author: Brett G. Olivier
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Contact email: [email protected]
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Last edit: $Author: bgoli $ ($Id: CBConfig.py 144 2014-01-16 22:27:55Z bgoli $)
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Installation
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============
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Author: Brett G. Olivier (@bgoli)
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# About
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PySCeS CBMPy (http://cbmpy.sourceforge.net) is a new platform for constraint
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based modelling and analysis. It has been designed using principles developed
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in the PySCeS simulation software project: usability, flexibility and accessibility.
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- GUI, for quick access to a visual representation of the model, analysis methods and annotation tools
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- SOAP based web services: using the Mariner framework much high level functionality is exposed for integration into web tools
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For more information on the development and use of PySCeS CBMPy feel free to contact me:
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PySCeS-CBMPy has been tested on Windows 7 and 8.1, Mac OSX and Ubuntu Linux 12.04, 14.04, 16.04.
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It is compatible with both Python 2.7+ and includes experimental support for Python 3.4+ It is highly recommend to use
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Python 2.7 as not all Python package dependencies (extended functionality) are available for Python 3.
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PySCeS CBMPy is now accessible as a Python module **cbmpy** in place of the the previously used **pyscescbm** which is no longer supported. CBMPy includes support for reading/writing models in SBML3 FBC versions 1 and 2 as well as COBRA dialect, Excel spreadsheets and Python.
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To use follow the installation instructions given below and try the following in a Python shell::
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import cbmpy
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cmod = cbmpy.readSBML3FBC('cbmpy_test_core')
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cbmpy.doFBA(cmod)
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New Ipython notebook tutorials are available. Happy modelling!
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New cross-platform conda support
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--------------------------------
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CBMPy is now available as a crosss platform Anaconda package available for Win32/64, Linux32/64 and OSX from the Anaconda cloud (https://anaconda.org/bgoli/repo). This is the first
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major release using the conda platform and all feedback is welcomed. If you have Anaconda installed (tested with 4.2.0) simply try the following::
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conda install -c bgoli -c SBMLTeam cbmpy
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which should install CBMPy, libSBML and all the required (non-solver) dependencies. If you do not use Anaconda or would
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like to try install things in a semi-automated way carry on reading.
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The following installation instructions are for Ubuntu 16.04 but should be adaptable to any
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Linux package managment system, OSX, Debian, etc. Except for GLPK (4.47) and SymPy (0.7.4 or newer)
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no specific library version is required. For more detailed installation instructions and Windows
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please see the online documentation http://cbmpy.sourceforge.net/reference/install_doc.html
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Auto-dependency configuration
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-----------------------------
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I am in the process of creating automated dependency checking and building tools for CBMPy.
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Ubuntu support is complete with cross platform conda support now available for testing (https://github.com/bgoli/cbmpy-build.git)::
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To start with download the install script that will run the system test::
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curl --remote-name https://raw.githubusercontent.com/bgoli/cbmpy-build/master/ubuntu/1_install_cbmpy_dependencies.py
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This script will analyse your Python distribution for missing dependencies and generate a shell script that will auto-install them.
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For an installation using the native Python supplied with Ubuntu run::
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python 1_install_cbmpy_dependencies.py UBUNTU
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For a local user installation of Anaconda try the following. This is not strictly necessary if only CBMPy is going to be installed (see above)::
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python 1_install_cbmpy_dependencies.py CONDA
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in both cases a shell script `metatoolkit_install_dependencies.sh` is generated and printed to the screen. Run this script
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or install the relevant packages by hand.
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Installing or upgrading CBMPy
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-----------------------------
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Installing or upgrading CBMPy can easily be done with pip::
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sudo pip install cbmpy
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sudo pip install --upgrade cbmpy
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or try the new CONDA support::
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conda install -c bgoli -c SBMLTeam cbmpy
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conda update cbmpy
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For more information on the development and use of CBMPy (https://github.com/SystemsBioinformatics/cbmpy)
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or download the relevant source from SourceForge:
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CBMPy has been tested on Windows 7 and 8.1, 10, Mac OSX and Ubuntu Linux 12.04, 14.04, 16.04, 20.04.
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CBMPy is currently developed on Python 3.7 and Python 3.6 or newer is highly recommended
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https://sourceforge.net/projects/cbmpy/files/release/0.7/
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# Install
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The best way to get the basic CBMPy running is to install with Pip or create an Anaconda environment. CBMPy is developed on GitHub (https://github.com/SystemsBioinformatics/cbmpy)
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and run::
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## Install with pip using requirements.txt
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From a terrminal or command prompt try:
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python setup.py build sdist
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sudo python setup.py install
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`pip install -r requirements.txt`
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Installing glpk/python-glpk
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---------------------------
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## Install by creating an Anaconda environment using environment.yml
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From a terrminal or command prompt try:
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CBMPy requires a linear solver for numerical analysis, the open source (glpk) solver can be automatically built and installed as follows (requires git to be installed and accessible):
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`conda env create -f=environment.yml`
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Download the install script that will install GLPK/PyGLPK for CBMPy on Ubuntu 14.04 or newer::
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This creates an environment **cbmpy** that can be accessed from the command line using `conda activate cbmpy3`
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curl --remote-name https://raw.githubusercontent.com/bgoli/cbmpy-glpk/master/install_glpk.sh
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## Check the basic installation
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To check you installation follow the installation try the following in a Python shell:
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Make executable::
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chmod 744 install_glpk.sh
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and run::
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./install_glpk.sh
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Note this script is designed to be used for building containers and will remove any installed version of GLPK and build and install the correct version needed for PyGLPK.
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No warranty of any kind assumed or otherwise, use at own risk!
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Legacy installation
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===================
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Python2
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-------
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First we create a scientific Python workbench::
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sudo apt-get install python-dev python-numpy python-scipy python-matplotlib python-pip
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sudo apt-get install python-sympy python-suds python-xlrd python-xlwt python-h5py
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sudo apt-get install python-wxgtk2.8
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sudo apt-get install ipython ipython-notebook
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libSBML
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~~~~~~~
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Installing libSBML is now easy using Pip::
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sudo apt-get install libxml2 libxml2-dev
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sudo apt-get install zlib1g zlib1g-dev
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sudo apt-get install bzip2 libbz2-dev
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sudo pip install --update python-libsbml
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Extended functionality
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~~~~~~~~~~~~~~~~~~~~~~
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sudo pip install biopython docx
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Windows
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~~~~~~~
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Use easy_install, pip or your package manager (e.g. conda) to install the following packages::
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numpy scipy matplotlib sympy xlrd xlwt
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biopython docx suds wxPython
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pip install --update python-libsbml
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Python3 (experimental)
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----------------------
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Not all dependencies are available for Python3::
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sudo apt-get install python3-dev python3-numpy python3-scipy python3-matplotlib python3-pip
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sudo apt-get install python3-xlrd python3-h5py
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# need to find out what is going on with Python3 and xlwt suds
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# easy_install3 sympy ???
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# wxPython and PyQt4 not in Ubuntu P3 builds yet
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sudo apt-get install ipython3 ipython3-notebook
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sudo apt-get install libxml2 libxml2-dev
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sudo apt-get install zlib1g zlib1g-dev
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sudo apt-get install bzip2 libbz2-dev
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sudo pip3 install python-libsbml-experimental
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```
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import cbmpy
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cmod = cbmpy.readSBML3FBC('cbmpy_test_core')
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cbmpy.doFBA(cmod)
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```
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# Updating CBMPy
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Once you have installed CBMPy it can be easily upgraded.
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sudo apt-get install python-sip python-sip-dev build-essential
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## Pip update
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`pip install --upgrade cbmpy`
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More information in the docs/ directory.
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## Anaconda update
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`conda update cbmpy`
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(c) Brett G. Olivier, Amsterdam, 2014-2018
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(c) Brett G. Olivier, Amsterdam, 2014-2021

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