112 citations · 186 across the 4 of their papers we have counts for
5 papers
Exploration of methods for computing sensitivities in ODE models at dynamic and steady states
Polina Lakrisenko, Dilan Pathirana, Daniel Weindl +1
Estimating parameters of dynamic models from experimental data is a challenging, and often computationally-demanding task. It requires a large number of model simulations and objec…
pyPESTO: A modular and scalable tool for parameter estimation for dynamic models
Yannik Schälte, Fabian Fröhlich, Paul J. Jost +14
Mechanistic models are important tools to describe and understand biological processes. However, they typically rely on unknown parameters, the estimation of which can be challengi…
A protocol for dynamic model calibration
Alejandro F. Villaverde, Dilan Pathirana, Fabian Fröhlich +2
Ordinary differential equation models are nowadays widely used for the mechanistic description of biological processes and their temporal evolution. These models typically have man…
AMICI: High-Performance Sensitivity Analysis for Large Ordinary Differential Equation Models
Fabian Fröhlich, Daniel Weindl, Yannik Schälte +5
Ordinary differential equation models facilitate the understanding of cellular signal transduction and other biological processes. However, for large and comprehensive models, the…
PEtab -- interoperable specification of parameter estimation problems in systems biology
Leonard Schmiester, Yannik Schälte, Frank T. Bergmann +26
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 p…