INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

High-performance sensitivity analysis for large ordinary differential equation models

Jupyter widget for the dynamic and static visualizations of systems biology models written in PySB, BNGL, and SBML

Parameter estimation and model calibration using Genetic Algorithm optimization in Python.

Tool that uses tropical algebra concepts to 'decompose' species trajectories in the protein-protein interactions that drive changes of concentration in time

PySB add-on providing utilities to add units to models and perform dimensional analysis.

Simplified model of mTOR written using PySB. mTOR is modeled such that its activation is due to insulin receptor activation, and inhibited by binding of rapamycin-FKBP complex.

PAR2 Activation and calcium signaling Reaction Model in PySB