pybrn - Biochemical network analysis with Python

pybrn is a Python package for the analysis of biochemical reaction networks. It is mainly meant as a basic library for researchers developing their own model analysis routines in Python. pybrn currently features:

• basic model creation, data handling and evaluation
• import of SBML files into pybrn’s data structures
• analysis of network conservation relations
• computation of steady states and steady state branches
• integration of the network’s differential equation

The following interactive Python session shows some of the basic features:

>>> import brn
>>> net = brn.fromSBML("doc/examples/simplenet.xml")
>>> print net
Reactions:
v1:  -> 1*A; rate: 1
v2: 1*A -> 1*B; rate: k2 * A
v3: 1*B -> ; rate: k3 * B

Species initial conditions:
A = 0.0
B = 0.0

Parameter values:
k2 = 1.0
k3 = 1.0
default_compartment = 1.0
>>> net.steadystate()
array([ 1.,  1.])
>>> t,x = net.simulate(list(xrange(11)))
Found integrator vode
>>> print t[-1], x[-1]
10.0 [ 0.9999546  0.9995006]

Further information

• Download and installation
• The pybrn Tutorial
• The pybrn module reference