Data repositories
One goal of the Physiome Project is to make all models freely available in XML-encoded form (CellML, FieldML, etc) on web-accessible databases once the models have been published in refereed journals.
The Physiome Project has created anatomically and physically based models at the levels of organ system, organ, tissue, cell and sub-cellular protein module (ion channels, signalling and metabolic pathways).
Anatomical models
Progress on developing Physiome-style models of organ systems, in which physical conservation laws are solved on anatomically-based models, is well underway for all twelve organ systems, and especially the heart, lungs, musculo-skeletal system, digestive system and some sensory organs. In all of these projects the goal is to construct models that incorporate the detailed anatomy and tissue structure of the organs in a way that allows the inclusion of cell-based models and the spatial distribution of protein expression. Note that organs are built from tissue for which there exist four basic types: muscle, connective, epithelial and nerve tissue. Cells are an obvious unit of biological function and there are about 200 cell types. In the next section we list the organs, tissue types and cell types that exist within each of the twelve organ systems and give examples of organ models together with the types of physical laws that are being solved on these organ models. In the subsequent sections we list the identifying characteristics of each tissue and cell type.
Cell modelling
The primary functions of cells are transport, metabolism, signalling, motility, organising the cyto-skeletal structure and performing the cell cycle. We characterise cell function for somatic cell types under the following headings:
- Membrane receptors
- Membrane ion channels
- Signalling pathways
- Metabolism
- Transport
- Motility
- Maintenance
- Mitosis
There are about 40 types of ion channel, 30 types of receptor, 25 signalling pathways and 21 metabolic pathways. In the following sections we give the key protein, carbohydrate and lipid components in each system and, where known, the relationships between the components. Where available, we also give links to the CellML file containing the mathematical model describing a particular cellular function.