Pascal Ballet, Sébastien Tripodi and Vincent Rodin.
MorphoBlock Programming: a way to model and simulate morphogenesis
of multicellular organisms.
Journal of Biological Physics and Chemistry, AMSI & Collegium Basilea,
9(1):37-44, March 2009.
Abstract:
Morphogenesis is a key phenomenon occurring in multicellular organisms.
It involves many mechanisms at the cellular level like differentiation,
migration, division or communication between cells. The study of such
complex living systems is difficult despite the improvement of confocal
microscopes including those working with four dimensions (space and time).
Observation has been much enhanced but comprehension of the organization
is yet to come. In virtuo simulation allows focus on the study of the
organization mechanisms (in virtuo is an extension of the in silico
paradigm where the user is a central actor of the simulation). Hence,
the use of a computer program reproducing some parts of the morphogenesis
phenomenon is complementary to real experimentation. Moreover, modelling
using a programming language facilitates exchange of knowledge between
biologists by reducing the ambiguity compared with text or diagrams.
To help the comprehension of morphogenesis, we have developed software
based on a multiagent system that reproduces the following mechanisms:
cell migration, cell division, cell apoptosis, cell signalling, cell
differentiation and cell polarization. In our software, an agent is
called a MorphoBlock, which means a block of morphogenesis. By using
these simple MorphoBlocks, the simulations show different kinds of
dynamics and generate structures that can be compared, from an abstract
point of view, to the formation of multicellular organisms. In this paper,
we focus on two main parts of our software: first the shape, behaviour
and parameters of a MorphoBlock; and second the observation of morphogenesis
from simulations with many MorphoBlocks.
Keywords:
Embryogenesis, Multiagent systems, MorphoBlock, Morphogenesis.
[doi:10.4024/14BA09A.jbpc.09.01]
[Ballet09a.pdf]