| Name | Modified | Size | Downloads / Week |
|---|---|---|---|
| prerelease | 2016-02-08 | ||
| publications | 2016-01-28 | ||
| tools | 2016-01-25 | ||
| release | 2014-04-02 | ||
| updates | 2013-06-10 | ||
| models | 2013-03-07 | ||
| readme.rst | 2017-01-25 | 5.9 kB | |
| Totals: 7 Items | 5.9 kB | 0 |
CBMPy: PySCeS constraint-based modelling
PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net) Copyright (C) 2010-2017 Brett G. Olivier, VU University 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 Contact email: bgoli@users.sourceforge.net
More information in the docs directory.
(c) Brett G. Olivier, Amsterdam, 2010-2017
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).
CBMPy fully supports a number of open community standards, SBML Level 3 Core, FBC, Groups as well as OMEX and the creation of COMBINE archives. Models can be read/written in SBML FBC versions 1 and 2 as well as older SBML leve 2 dialects.
Quick/fast install (no solver)
New! CBMPy on the Anaconda Cloud (https://anaconda.org/bgoli/cbmpy) use conda for win32, win64, linux32, linux64, osx-64 installations.
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- install with conda install -c bgoli -c sbmlteam cbmpy
- update with conda update -c bgoli cbmpy
Linux
- pip install --upgrade python-libsbml
- pip install --upgrade cbmpy
Windows 64bit
- https://sourceforge.net/projects/sbml/files/libsbml/5.13.0/stable/Windows/64-bit/python/libSBML-5.13.0-win-py2.7-amd64.exe/download
- https://sourceforge.net/projects/cbmpy/files/tools/glpk/glpk-0.3.win-amd64-py2.7.exe/download
- https://sourceforge.net/projects/cbmpy/files/release/0.7/cbmpy-0.7.11.win-amd64.exe/download
- or pip install --upgrade cbmpy
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 1n3 14.04. It is compatible with both Python 2.7+ and Python 3.4+ but it is highly recommend to use Python 2.7 as not all Python package dependencies (extended functionality) are available for Python 3.
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
Brett G. Olivier 2017 ver 1.5