KiMoSys

KiMoSys is a powerful and user-friendly platform designed to support the kinetic modeling of biological systems. The platform is composed of a public data repository of published experimental data, including concentration data of metabolites and enzymes and flux data. This data repository offers a web-based interface and uploads facility to turn available data into publicly accessible, centralized, and structured-format data files.

One of the main motivations behind KiMoSys development is to automate the process of building kinetic models, which is usually composed of three steps: model building, simulation, and analysis. In the first step, it is usually required to set initial metabolite concentrations, assign kinetic rate laws, and estimate parameter values using kinetic data through optimization when these are unknown. The development of high-throughput methods has generated much omics data; however, experimentalists often present only a summary of the obtained results for publication, and the experimental data files are not usually submitted to any public repository or simply not available at all.

KiMoSys was created to ensure data management, storage, and sharing for a wider systems biology community. The platform compiles and integrates available kinetic models associated with the data and also integrates some tools to facilitate the kinetic model construction process of large-scale metabolic networks, especially when the systems biologists perform computational research.

KiMoSys is a web-based system that integrates a public data and associated model(s) repository with computational tools, providing the systems biology community with a novel application facilitating data storage and sharing, thus supporting the construction of ODE-based kinetic models and collaborative research projects.