BioMASS - A Python Framework for Modeling and Analysis of Signaling Systems

BioMASS is a computational framework for modeling and analysis of biological signaling systems in Python. It provides useful tools for numerical simulation, parameter estimation, network analysis, and visualization.

Source code

https://github.com/biomass-dev/biomass

Contents:

• About
  • About BioMASS
  • License
  • Author
  • Contact
  • Citation
• Installation
  • PyPI
  • Development version
  • Docker
• Usage
  • Model preparation
  • Parameter estimation
  • Visualization of simulation results
  • Sensitivity analysis
• Example models
  • Circadian clock
  • Immediate-early gene response
  • Insulin signaling
  • MAPK cascade
  • NF-κB pathway
  • TGF-β/SMAD pathway
• API
  • BioMASS model object (biomass.exec_model)
  • BioMASS core functions (biomass.core)
  • Optimization results (biomass.results)
  • Parameter estimation (biomass.estimation)
  • Visualization options (biomass.plotting)
• References