PySB

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.


References in zbMATH (referenced in 10 articles )

Showing results 1 to 10 of 10.
Sorted by year (citations)

  1. Troják, Matej; Šafránek, David; Brim, Luboš; Šalagovič, Jakub; Červený, Jan: Executable biochemical space for specification and analysis of biochemical systems (2020)
  2. Honorato-Zimmer, Ricardo; Millar, Andrew J.; Plotkin, Gordon D.; Zardilis, Argyris: Chromar, a language of parameterised agents (2019)
  3. Alfonso Landeros, Timothy Stutz, Kevin L. Keys, Alexander Alekseyenko, Janet S. Sinsheimer, Kenneth Lange, Mary Sehl: BioSimulator.jl: Stochastic simulation in Julia (2018) arXiv
  4. Engblom, Stefan; Hellander, Andreas; Lötstedt, Per: Multiscale simulation of stochastic reaction-diffusion networks (2017)
  5. Blanc, Emilie; Engblom, Stefan; Hellander, Andreas; Lötstedt, Per: Mesoscopic modeling of stochastic reaction-diffusion kinetics in the subdiffusive regime (2016)
  6. Drawert, Brian; Trogdon, Michael; Toor, Salman; Petzold, Linda; Hellander, Andreas: MOLNs: a cloud platform for interactive, reproducible, and scalable spatial stochastic computational experiments in systems biology using pyurdme (2016) ioport
  7. Brim, L.; Nižnan, J.; Šafránek, D.: Compact representation of photosynthesis dynamics by rule-based models (2015)
  8. Danos, Vincent; Harmer, Russell; Honorato-Zimmer, Ricardo: Thermodynamic graph-rewriting (2015)
  9. Danos, Vincent; Heindel, Tobias; Honorato-Zimmer, Ricardo; Stucki, Sandro: Moment semantics for reversible rule-based systems (2015)
  10. Ewald, Roland; Uhrmacher, Adelinde M.: SESSL: a domain-specific language for simulation experiments (2014)