A modeller is anyone that has a model of a cellular system in mind - this can be biological concepts, mathematical concepts, or a formulation that brings biological and mathematical concepts together in a model instance that can be used for simulation.


The overall goal of a modeller is to express a model in a language and toolset that is familiar to them, and to retrieve results in a form useful to their domain of interpretation. A modeller is someone who has a biological, or mathematical background, or both. The key outcome is the mathematical representation of a biological system.

Detailed goals

  • to model biological processes. The modeller will have an understanding of the biological entities involved, the physiological processes, and perhaps experimental data measuring aspects of these.

    Examples include :

    • biochemical pathways
    • control of gene expression(gene regulation networks)
    • ion transport, electrochemical events
    • cytoskeleton structure
    • cell-cell interaction - e.g. recognition, adhesion, signaling
    • developmental processes
    • evolution

    Use case: Represent a biological process or structure


  • to model the mathematics of physiological processes and formulate these into representations for simulation.

    Use case: Represent the mathematics of the biological process or structure


  • run simulations and interpret output

    Use case: Simulate a model(SimulateAModel)

  • review and annotate published models

    Use case: Review a model(ReviewAModel)

  • locate existing models

    Use case: Find a model(FindAModelModeller)

  • visualize models - this may be representations describing the process or structure being modelled, say a biochemical pathway, or the results of simulation.

    Use case: Visualize a model(VisualizeAModel)

  • share models

    Use case: ShareAModel

  • reuse models within new models

    Use case: ReuseAModel