Linear noise approximation with slow extrinsic fluctuations.

Author

Bjoern Bastian (bjoern.bastian@uibk.ac.at)

Version

1.0

Requirements

Python >= 2.7 / 3.x, sympy >= 0.7.3, yaml

Files:

• README.rst
• LICENSE
• ext_noise_expansion.rst: the documentation (in reStructuredText)
• ext_noise_expansion_python2.rst: the same with Python 2 doctests
• ext_noise_expansion.html: the documentation, converted to html
• setup.py: distutils-setup.py and test (run doctests)
• test_system.yaml: example reaction system definition.

In the ext_noise_expansion directory:

• definition_parser.py: string parser for reaction system definition
• definition_solvers.py: solvers for stationary state evaluation
• __init__.py: initialization of the ext_noise_expansion package
• reaction_system.py: reaction system definition and derivatives
• sum_evaluation.py: functions for sum evaluation
• sum_generation.py: functions for sum generation
• sum_parsing.py: functions for sum parsing
• tools_objects.py: test symbol and error classes
• tools_sympy.py: helper functions that require sympy
• tools_sympy_doctest_python2.rst: python 2 doctests
• tools_universal.py: general helper functions

Installation:

• use distutils, e.g. python ./setup.py install or python ./setup.py install --user
• or simply copy the directory ext_noise_expansion to a directory which is found by Python's "import", e.g. into your project-directory

Test:

python ./setup.py test

Issues:

• The ReactionSystem flag factorize=True is combination with usage of the num_eval() method may lead to wrong results.