Brief intro to AMICI for first-time users.
SBML import, observation model, sensitivity analysis, data export and visualization
A more detailed introduction to the AMICI interface, demonstrating sensitivity analysis, various options, finite difference checks, ...
How to import and simulate PEtab problems.
How to represent different experimental conditions in AMICI and how to use preequilibration.
Describes and demonstrates the various algorithms for computing steady states and steady-state sensitivities.
Demonstrates common simulation failures and gives some hints for interpreting, debugging, and fixing them.
Provides guidance on how to combine AMICI with differential programming frameworks such as JAX.
Efficient spline interpolation
Shows how to add annotated spline formulas to existing SBML models in order to speed up AMICI's model import.
A real-world application of splines
An illustration of how to apply AMICI's spline functionalities to parameter estimation for a reaction network.