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
- equilibration
In AMICI, equilibration refers to the process of simulating or solving a dynamical system for steady state. “Equilibration” refers to approaching an equilibrium point of a dynamical system and does not imply thermodynamic equilibrium.
- 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 pre-equilibration, pre-simulation and the main simulation. See also simulation periods.
- 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.
- post-equilibration
equilibration after the main simulation. See also simulation periods.
- pre-equilibration
Equilibration before the pre-simulation or main simulation. Pre-equilibration is useful if the system is assumed to be at steady state at the start of some experiment, but the initial state is not known. The model time is reset to its initial time after pre-equilibration. See also simulation periods.
- pre-simulation
Simulation for a fixed time before the regular simulation. Can be used to specify pretreatments. Pre-simulation starts at \(t_0 - t_{presim}\). Dedicated fixed parameters can be specified for pre-simulation. See also simulation periods.
- 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.
- simulation periods
In AMICI a model simulation may consist of multiple periods:
A pre-equilibration period, which is used to simulate the system until it reaches steady state.
A pre-simulation period, which is used to simulate the system for a fixed time before the main simulation.
The main simulation period.
A post-equilibration period, to simulate the system until it reaches steady state.
The main simulation and post-equilibration periods are the only periods for which output timepoints can be specified and during which measurements are assumed to be taken.
(Non-fixed) model parameters (\(p\)) are the same throughout those periods, but different sets of fixed parameters (\(k\)) can be specified for each period, except for post-equilibration, which always uses the fixed parameters of the main simulation period.
For SBML models, initial assignments and initial values of event triggers are only applied once at the start of the first period.
- steady state
In AMICI, a model is considered to be at steady state if the time derivative of the state variables is zero, up to the specified tolerances, even if there are discontinuities in the model (e.g., due to events) that may change the model state at a later time point.
- 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.