PySB swMATH ID: 13437 Software Authors: Lopez, C. F., Muhlich, J. L., Bachman, J. A., Sorger, P. K. Description: PySB is a framework for building mathematical models of biochemical systems as Python programs. PySB abstracts the complex process of creating equations describing interactions among multiple proteins or other biomolecules into a simple and intuitive domain specific programming language (see example below), which is internally translated into BioNetGen or Kappa rules and from there into systems of equations. PySB makes it straightforward to divide models into modules and to call libraries of reusable elements (macros) that encode standard biochemical actions. These features promote model transparency, reuse and accuracy. PySB also interoperates with standard scientific Python libraries such as NumPy, SciPy and SymPy enabling model simulation and analysis. Homepage: http://pysb.org/ Related Software: BioNetGen; Smoldyn; STEPS; MesoRD; URDME; rxncon; libSBML; Chromar; COPASI; APL; SNOOPY; Haskell; Python; pyModelChecking; eBCSgen; JuMP; DifferentialEquations.jl; Gillespie.jl; GillespieSSA; StochPy Cited in: 11 Publications all top 5 Cited by 22 Authors 4 Honorato-Zimmer, Ricardo 3 Brim, Luboš 3 Šafránek, David 2 Danos, Vincent 2 Engblom, Stefan 2 Hellander, Andreas 2 Lötstedt, Per 2 Millar, Andrew J. 2 Plotkin, Gordon D. 2 Troják, Matej 2 Zardilis, Argyris 1 Blanc, Emilie 1 Brozmann, Branislav 1 Červený, Jan 1 Ewald, Roland 1 Harmer, Russell S. 1 Heindel, Tobias 1 Kraikivski, Pavel 1 Nižnan, J. 1 Šalagovič, Jakub 1 Stucki, Sandro 1 Uhrmacher, Adelinde M. Cited in 4 Serials 1 Theoretical Computer Science 1 ACM Transactions on Modeling and Computer Simulation 1 Multiscale Modeling & Simulation 1 Logical Methods in Computer Science all top 5 Cited in 6 Fields 8 Biology and other natural sciences (92-XX) 4 Computer science (68-XX) 2 Partial differential equations (35-XX) 2 Probability theory and stochastic processes (60-XX) 1 Numerical analysis (65-XX) 1 Classical thermodynamics, heat transfer (80-XX) Citations by Year