The IUPS Physiome Project

Summary form only given. The Physiome Project of the International Union of Physiological Sciences (IUPS) is attempting to provide a comprehensive framework for modelling the physiology of the human body using multi-scale computational methods which can incorporate the biochemistry, biophysics and anatomy of cells, tissues and organs. A major goal of the project is to use computational modelling to analyse integrative biological function in terms of underlying structure and molecular mechanisms. It is an internationally collaborative open-source project that is providing a public domain framework for computational physiology, including the development of modeling standards, computational tools and web-accessible databases of models of structure and function at all spatial scales. It aims to develop an infrastructure for linking models of biological structure and function across multiple levels of spatial organization and multiple time scales. To support that goal the project is developing the XML markup languages CellML & FieldML for encoding models, open source software tools for creating, visualizing and executing these models, and databases of models based on peer-reviewed publications. The CellML model repository currently has about 450 models (derived from peer-reviewed journal publications) of cellular function that includes gene regulatory networks, signal transduction pathways, ion channel electrophysiology, metabolic pathways, calcium transport, myofilament mechanics, the cell cycle, and cell motility. These 'level 1' models are initially encoded to match the publication, including any errors, and then subsequently curated to level 2 such that the models can be run (by clicking on the website link) and produce results that match those in the source publication.