Benchmark Problems for Dynamic Modeling of Intracellular Processes

摘要: Motivation: Dynamic models are used in systems biology to study and understand cellular processes like gene regulation or signal transduction. Frequently, ordinary differential equation (ODE) model the time dose dependency of abundances molecular compounds as well interactions translocations. A multitude computational approaches have been developed within recent years. However, many these lack proper testing application settings because a comprehensive set benchmark problems is yet missing. Results: We present collection 20 ODE given experimental data order evaluate new existing methodologies, e.g. for parameter estimation uncertainty analysis. In addition equations dynamical system, provides measurements observation functions assumptions about measurement noise distributions parameters. The presented comprise different size, complexity numerical demands. Important characteristics methodological requirements summarized, estimated parameters provided, some example studies were performed illustrating capabilities collection. Availability: provided several standardized formats, including an easy-to-use human readable form machine-readable SBML files. Excel sheets. All files available at https://github.com/Benchmarking-Initiative/Benchmark-Models, with MATLAB code process simulate models.