Table 1. Integration with external modeling tools.

Tool	Reference	Interface	Description (relevance to PySB)
NumPy	Oliphant, 2007	Python	Efficient array and matrix operations
SciPy	Oliphant, 2007	Python	Scientific algorithms, e.g., ODE integration, statistics, and optimization
SymPy	SymPy Development Team, 2012	Python	Symbolic manipulation of mathematical expressions
Matplotlib	Hunter, 2007	Python	Plotting and other data visualizations
Graphviz	Gansner and North, 2000	Python	Layout and rendering of node-edge graphs
BNG	Faeder et al, 2009	Wrapper	Translation of rules to a reaction network; stochastic simulation
Kappa	Danos et al, 2007b	Wrapper	Stochastic simulation; visualization and analysis of rules models
SBML	Hucka, 2003	Export	Compatibility with SBML tools
Mathematica	Wolfram Research	Export	General-purpose scientific computing
MATLAB	Mathworks	Export	General-purpose scientific computing