cbmpy 0.7.7

PySCeS-CBMPy
============

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** 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.

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 are available. Happy modelling!

The following installation instructions are for Ubuntu 16.04 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

New! auto-dependency configuration
----------------------------------

I am in the process of creating automated dependency checking and building tools for CBMPy. These can be found at::

https://github.com/bgoli/cbmpy-build

Ubuntu support is almost complete with Windows/Conda support in development, grab form GitHub::

https://github.com/bgoli/cbmpy-build.git

Manual dependency configuration is provided below. For Windows users most of these utilities are included in
Python distributions like Anaconda (recomended)

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
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 --update python-libsbml

Extended functionality
~~~~~~~~~~~~~~~~~~~~~~

sudo pip install biopython docx

Windows
~~~~~~~

Use easy_install, pip or your package manager (e.g. conda) to install the following packages::

numpy scipy matplotlib sympy xlrd xlwt
biopython docx suds wxPython

pip install --update python-libsbml


glpk/python-glpk
~~~~~~~~~~~~~~~~

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):

Download the install script that will install GLPK/PyGLPK for CBMPy on Ubuntu 14.04 or newer::

curl --remote-name https://raw.githubusercontent.com/bgoli/cbmpy-glpk/master/install_glpk.sh

Make executable::

chmod 744 install_glpk.sh

and run::

./install_glpk.sh

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.

No warranty of any kind assumed or otherwise, use at own risk!

CBMPy
~~~~~

Finally, install CBMPy::

sudo easy_install cbmpy

or

sudo pip install cbmpy

or try the new experimental CONDA support::

conda install -c bgoli cbmpy

or download the source and run::

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-sip python-sip-dev build-essential

More information in the docs/ directory.