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

Ordinary differential equation models facilitate the understanding of cellular signal transduction and other biological processes. However, for large and comprehensive models, the computational cost of simulating or calibrating can be limiting. AMICI is a modular toolbox implemented in C++/Python/MATLAB that provides efficient simulation and sensitivity analysis routines tailored for scalable, gradient-based parameter estimation and uncertainty quantification. AMICI is published under the permissive BSD-3-Clause license with source code publicly available on https://github.com/AMICI-dev/AMICI. Citeable releases are archived on Zenodo

pyPESTO: A modular and scalable tool for parameter estimation for dynamic models

Mechanistic models are important tools to describe and understand biological processes. However, they typically rely on unknown parameters, the estimation of which can be challenging for large and complex systems. We present pyPESTO, a modular framework for systematic parameter estimation, with scalable algorithms for optimization and uncertainty quantification. While tailored to ordinary differential equation problems, pyPESTO is broadly applicable to black-box parameter estimation problems. Besides own implementations, it provides a unified interface to various popular simulation and inference methods. pyPESTO is implemented in Python, open-source under a 3-Clause BSD license. Code and documentation are available on GitHub (https://github.com/icb-dcm/pypesto)

PEtab -- interoperable specification of parameter estimation problems in systems biology

Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been -- so far -- no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing the observation model and experimental data as well as parameters to be estimated. We already implemented PEtab support into eight well-established model simulation and parameter estimation toolboxes with hundreds of users in total. We provide a Python library for validation and modification of a PEtab problem and currently 20 example parameter estimation problems based on recent studies. Specifications of PEtab, the PEtab Python library, as well as links to examples, and all supporting software tools are available at https://github.com/PEtab-dev/PEtab, a snapshot is available at https://doi.org/10.5281/zenodo.3732958. All original content is available under permissive licenses

Informative and adaptive distances and summary statistics in sequential approximate Bayesian computation.

Calibrating model parameters on heterogeneous data can be challenging and inefficient. This holds especially for likelihood-free methods such as approximate Bayesian computation (ABC), which rely on the comparison of relevant features in simulated and observed data and are popular for otherwise intractable problems. To address this problem, methods have been developed to scale-normalize data, and to derive informative low-dimensional summary statistics using inverse regression models of parameters on data. However, while approaches only correcting for scale can be inefficient on partly uninformative data, the use of summary statistics can lead to information loss and relies on the accuracy of employed methods. In this work, we first show that the combination of adaptive scale normalization with regression-based summary statistics is advantageous on heterogeneous parameter scales. Second, we present an approach employing regression models not to transform data, but to inform sensitivity weights quantifying data informativeness. Third, we discuss problems for regression models under non-identifiability, and present a solution using target augmentation. We demonstrate improved accuracy and efficiency of the presented approach on various problems, in particular robustness and wide applicability of the sensitivity weights. Our findings demonstrate the potential of the adaptive approach. The developed algorithms have been made available in the open-source Python toolbox pyABC

ICB-DCM/PEtab v0.0.0a11

PEtab - a tsv-based data format for parameter estimation problems in systems biolog

ICB-DCM/pyABC: Release 0.12.14

<p>Visualization:</p> <ul> <li>Selected plotly versions of matplotlib visualizations</li> </ul> <p>General:</p> <ul> <li>Added functionality to evaluate the model using boundary values of parameter</li> </ul&gt

FitMultiCell: Simulating and parameterizing computational models of multi-scale and multi-cellular processes

<p>Supplementary Data to the publication "FitMultiCell: Simulating and parameterizing computational models of multi-scale and multi-cellular processes", Alamoudi et al. 2023.</p&gt

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

<p><strong>Fixes</strong></p> <ul> <li>Fixed CMake cmake_minimum_required deprecation warning by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2183</li> <li>Fixed misleading preequilibration failure messages by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2181</li> <li>Removed setuptools<64 restriction by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2180</li> <li>Fixed ExpData equality operator for Python by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2194</li> <li>Enabled deepcopy for ExpData(View) by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2196</li> <li>Allowed subsetting simulation conditions in simulate_petab by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2199</li> <li>Set CMake CMP0144 to prevent warning by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2209</li> </ul> <p><strong>Features</strong></p> <ul> <li>Possibility to evaluate and plot symbolic expressions based on simulation results by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2152</li> <li>Easier access to timepoints via ExpDataView by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2193</li> <li>Nicer <code>__repr__</code> for ReturnDataView by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2192</li> </ul> <p><strong>Documentation</strong></p> <ul> <li>Added installation instructions for Arch Linux by @stephanmg in https://github.com/AMICI-dev/AMICI/pull/2173</li> <li>Updated reference list by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2172</li> <li>Installation guide: optional requirements by @dweindl in https://github.com/AMICI-dev/AMICI/pull/2207</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/AMICI-dev/AMICI/compare/v0.19.0...v0.20.0</p>If you use this software, please cite both the article from preferred-citation and the software itself