Glossary

BNGL

BioNetGenLanguage is a language for modular, structure-based modeling of biochemical reaction networks.

CVODES

CVODES is a solver for stiff and non-stiff ODE systems with sensitivity analysis capabilities and is used by AMICI. It is part of the SUNDIALS solver suite.

DAE

Differential-Algebraic Equation

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.

IDAS

IDAS is a solver DAE systems with sensitivity analysis capabilities and is used by AMICI. It is part of the SUNDIALS solver suite.

ODE

Ordinary Differential Equation

PEtab

PEtab is a format for specifying parameter estimation problems. It is based on an SBML model and tab-separated value files specifying the observation model and experimental conditions.

preequilibration

Simulating or solving the dynamical system for the steadystate.

presimulation

Simulation for a fixed time before the regular simulation. Can be used to specify pretreatments.

PySB

PySB is a tool for specifying rule-based systems biology models as Python code.

SBML

The Systems Biology Markup Language is a commonly used format for specifying systems biology models.

SUNDIALS

SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic equation Solvers. Provides the CVODES and IDAS solvers used by AMICI.

SWIG

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.