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cbmpy 0.7.4

CBMPy: PySCeS Constraint Based Modelling

Package Documentation

Latest Version: 0.7.13

PySCeS CBMPy (http://cbmpy.sourceforge.net) 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).

PySCeS 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 PySCeS 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 PySCeS CBMPy feel free to contact me:

PySCeS-CBMPy has been tested on Windows 7 and 8.1, Mac OSX and Ubuntu Linux 12.04, 14.04, 16.04. It is compatible with both Python 2.7+ and includes experimental support for Python 3.4+ It is highly recommend to use Python 2.7 as not all Python package dependencies (extended functionality) are available for Python 3.

PySCeS CBMPy is now accessible as a Python module cbmpy in place of the the previously used pyscescbm. This release contains both modules with a reminder to update old scripts to new. CBMPy includes support for reading/writing models in SBML3 FBC versions 1 and 2 as well as COBRA dialect, Excel spreadsheets and Python.

To use follow the installation instructions given below and try the following in a Python shell:

import cbmpy
cmod = cbmpy.readSBML3FBC('cbmpy_test_core')
cbmpy.doFBA(cmod)

New Ipython notebook tutorials will be available soon. Happy modelling!

The following installation instructions are for Ubuntu 14.04 but should be adaptable to any Linux package managment system, OSX, Debian, etc. Except for GLPK (4.47) and SymPy (0.7.4 or newer) no specific library version is required. For more detailed installation instructions and Windows please see the online documentation http://cbmpy.sourceforge.net/reference/install_doc.html

Python2

First we create a scientific Python workbench:

sudo apt-get install python-dev python-numpy python-scipy python-matplotlib  python-pip
sudo apt-get install python-sympy python-suds python-xlrd python-xlwt python-h5py
sudo apt-get install python-wxgtk2.8 python-qt4
sudo apt-get install ipython ipython-notebook

libSBML

Installing libSBML is now easy using Pip:

sudo apt-get install libxml2 libxml2-dev
sudo apt-get install zlib1g zlib1g-dev
sudo apt-get install bzip2 libbz2-dev

sudo pip install python-libsbml-experimental

glpk/python-glpk

GLPK needs to be version 4.47 to work with glpk-0.3:

sudo apt-get install libgmp-dev

cd GLPK source (e.g. glpk-4.47):

./configure --with-gmp
make
make check
sudo make install
sudo ldconfig

cd to python-glpk source (glpk-0.3):

make
sudo make install

CBMPy

Finally, install CBMPy:

python setup.py build sdist
sudo python setup.py install

Python3 (experimental)

Not all dependencies are available for Python3:

sudo apt-get install python3-dev python3-numpy python3-scipy python3-matplotlib  python3-pip
sudo apt-get install python3-xlrd python3-h5py

# need to find out what is going on with Python3 and xlwt suds
# easy_install3 sympy ???
# wxPython and PyQt4 not in Ubuntu P3 builds yet

sudo apt-get install ipython3 ipython3-notebook

sudo apt-get install libxml2 libxml2-dev
sudo apt-get install zlib1g zlib1g-dev
sudo apt-get install bzip2 libbz2-dev

sudo pip3 install python-libsbml-experimental

sudo apt-get install python-qt4 python-qt4-dev python-sip python-sip-dev build-essential

More information in the docs/ directory.

 
File Type Py Version Uploaded on Size
cbmpy-0.7.4.tar.gz (md5) Source 2016-04-18 6MB
cbmpy-0.7.4.win-amd64.exe (md5) MS Windows installer 2.7 2016-04-18 4MB
cbmpy-0.7.4.win-amd64.msi (md5) MS Windows MSI installer 2.7 2016-04-18 4MB
cbmpy-0.7.4.zip (md5) Source 2016-04-18 6MB