The vision of this project is to produce toolsets for both people and machines to interface with our knowledge of experimental and modelling work in physiology. Our knowledge is made up of experimental data, mathematical models and simulation methods, concepts about biology and mathematical modelling, and a context for this within physiological work world-wide.

To create useful modelling tools, we need to take account of concepts and current tools familiar to a person's domain of expertise. This means addressing the meaning of terms in their domain, data structures they are familiar with, or that are standard within their domain(e.g. particular gene/protein databases), technological tools/interfaces they use; e.g. web interfaces to databases, visual navigation and authoring environments, programmable interfaces, and machine interpretable interfaces - e.g. query interfaces, exchange languages.

CellML is intended as an exchange language for representing cell models. We want the physiological modelling community to adopt it as a standard, and we want to build tools that utilize this as a common interface to such research.

The development of "tools" for CellML has produced two related visions.

  1. To build tools that meet the needs of the cell modelling community, using CellML as a common exchange language for input and output at the machine level.
  2. To evolve the CellML language so that it meets the requirements for building these tools. This necessarily relies on developing an accepted and easy to use rules for representing and interpreting models.


These will tend to be repeated in the use cases and goals(UseCasesAndGoals) section, and in time should be generated from that. At the moment, this documentation is informal.

Note: This project is based around "cell modelling"; modelling outside of this domain, or across domains is a goal of the Physiome projectPhysiomeProject. Some of the toolsets here will provide systems within that project, these have yet to be defined, and when they do, will be included here too.

Cell models is a term that describes any model of cellular structure or function that in turn can be represented as a model for simulation and/or visualization.

The top level goals for this project are:

  • Represent models of biological processes. This means both
    • capturing the details of models (see "Model Representation":UseCasesAndGoals/ModelRepresentation )
    • maintaining repositories of models (see CellMLModelRepositories).
  • Author models within and across biological, mathematical, and formulated instances of models. (see "Modeller":UseCasesAndGoals/Modeller ).
  • Investigate the relationships between models. For example, the biological entities and processes involved, the mathematical descriptions of the systems, the structure of models formulated for simulation, results from simulation, annotations, conclusions etc. Anything we can say about a model at any level should be amenable to comparisons across models. Formally this depends on the way we represent and interpret models.
  • Locate models according to properties they share.
  • Run models in simulations, edit parameters, and visualize the output.