CmePy v0.3

a Chemical Master Equation solver for Python

Features

• models can be defined using species or reaction counts
• both dense 'rectangular' and sparse state spaces are supported
• error due to state space truncation may be tracked with an FSP-style 'sink' state
• reaction propensities may be scaled by time dependent coefficients
• common statistical results are easily obtained

Dependencies

CmePy was developed for Python 2.5, and depends upon the following packages:

• SciPy 0.7
• Numpy 1.2.1
• Matplotlib (required only to plot example results)

CmePy also works with Python 2.6, provided SciPy 0.7 and Numpy 1.3 are used. The latest version of CmePy also works with Python 2.7.

Obtaining CmePy

If you have the Git version control system installed, you can check out a copy of CmePy directly from GitHub, via:

git clone git://github.com/hegland/cmepy.git

Testing and Installation

Once CmePy has been obtained, the package can be tested by running the test_all.py script via Python as follows:

python test_all.py

CmePy may then be installed via the setup.py script:

python setup.py install

More detailed installation tips are available via the online documentation.

Documentation

See http://hegland.github.com/cmepy/

Authors

• Reuben Fletcher-Costin ( reuben dot fletchercostin at gmail dot com )
• Markus Hegland ( markus dot hegland at anu dot edu dot au )