AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models

Published April 8, 2022 | Version v0.11.28

Software Open

New features:

Added Solver.setSteadyStateToleranceFactor and Solver.setSteadyStateSensiToleranceFactor to specify a steady state tolerance factor by @dilpath in https://github.com/AMICI-dev/AMICI/pull/1758 NOTE: This also relaxes the default steady state (sensitivity) tolerances by a factor of 100.
Added support for pathlib.Path by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1769
Allow specifying initial timepoint with ExpData by @dilpath in https://github.com/AMICI-dev/AMICI/pull/1776

Performance:

Speedup for models with conservation laws by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1765
Improved efficiency of newton step convergence check by @FFroehlich in https://github.com/AMICI-dev/AMICI/pull/1775

Fixes:

Fixed deprecation warning for pandas.DataFrame.append in rdatas_to_measurement_df by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1770
Fixed Rule-target handling in PEtab import by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1753

Removed functionality:

Removed long deprecated sbml2amici arguments modelName and constantParameters by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1774

Notes

If you use this software, please cite both the article from preferred-citation and the software itself.

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