The International Union of Physiological Sciences (IUPS) launched the Physiome Project at the IUPS World Congress in St Petersburg in 1997 in order to bring quantitative bioengineering approaches to the study of anatomy and physiology. In particular this approach advocates the use of anatomically and biophysically based mathematical models that deal with physiological processes operating over multiple spatial and temporal scales. The major focus of the project has been the creation of standards, tools and databases for reproducible and reusable mathematical models of physiological processes (www.physiomeproject.org). Note that:
A model simulation is repeatable when re-running it produces a consistent result.
A model is reproducible when its outputs can be reproduced by a machine from an unambiguous statement of the model equations, together with specified values of the model parameters, initial conditions and boundary conditions. Markup languages such as CellML, SBML, NeuroML and FieldML are designed to encode a model in unambiguous form. The markup language SED-ML is designed to specify the simulation protocol for running the model with specified inputs and outputs.
A model is reusable when it can be used as an independent model or as a module within another model. This requires that the appropriate use of the model is well documented and that its limitations are clear, and that the model is semantically annotated to provide the biological and biophysical meaning of all of its variables and components. One of the goals of the Physiome Project is to encourage modular approaches to modeling to facilitate the reuse of well documented and validated modules.
A model is discoverable when it has been annotated with metadata that describe the purpose and use of the model sufficiently to allow the model to be retrieved via a webservice.
A model is validated when its predictions under specified conditions match experimental observations.
The Physiome journal publishes models that are reproducible, reusable and discoverable. It is the role of the companion primary journal to ensure that the model has been validated.