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Specification of Cell Types

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Model Specification and BuildingΒΆ

The specification and building of multi-cellular system models in Infobiotics is modular allowing parsimonious and incremental design. In this chapter, the Infobiotics modelling language is introduced using a running example consisting of the synthetic bacterial colony designed by Ron Weiss’ group in [Basu2005]. This model implements the propagation of a wave of gene expression in a bacterial colony.

The Infobiotics modelling language provides a multi-compartmental, stochastic and rule-based specification framework. A model of a multi-cellular system in Infobiotics is developed as a Lattice Population P-system (LPP-system) which consists of the specification of three main components that can be defined in a modular manner:

  1. First, the different cell types in the multi-cellular system need to be specified including their molecular species, compartmentalised structure and molecular interactions.
  2. Second, the geometric distribution of the cells in the multi-cellular system has to be captured using a finite point lattice, a regularly distributed collection of spatial points.
  3. Finally, the specific localisation of the different cells over the lattice points must be described in order to obtain the final spatial distribution in the multi-cellular system.
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Example of an LPP-system consisting of the distribution of the model of a single cell containing a negative autoregulated gene (right) over a regular rectangular lattice (left).

The specification of the different parts of a multicelluar system using the Infobiotics modelling language is specified in the following sections:


The Infobiotics modelling language was developed by Francisco J. Romero-Campero with contributions from Jamie Twycross, Jonathan Blakes and Hongqing Cao. It is being used on Systems and Synthetic Biology research projects in the University of Nottingham, U.K.