BioNetGenLanguage is a language for modular, structure-based modeling of biochemical reaction networks.
- fixed parameters
In AMICI, fixed parameters are parameters with respect to which no sensitivities are computed. They usually correspond to experimental conditions. For fixed parameters, different values can be set for preequilibration, presimulation and simulation.
Ordinary Differential Equation
Simulating or solving the dynamical system for the steadystate.
Simulation for a fixed time before the regular simulation. Can be used to specify pretreatments.
PySB is a tool for specifying rule-based systems biology models as Python code.
The Systems Biology Markup Language is a commonly used format for specifying systems biology models.
SWIG is a tool that creates interfaces for C(++) code to a variety of languages. Much of the AMICI Python interface is generated by SWIG.