Overview

"Over the last 20 years, progress in developmental biology has been so dramatic that developmental biologists may be excused for having the view, possibly an illusion, that the basic principles are understood, and that the next 20 years will be devoted to filling in the details. The most significant advances have come from the application of molecular techniques and a greatly improved understanding of cell biology. So we can begin to ask questions - like whether the egg is computable."

(Wolpert, 1994)



Cell-O is a software framework written in Java™ for simulation and analyses of biological processes. On top of it we have built several tools for research in three fields of 'computational embryology': cell lineage analysis, simulation of genetic regulatory networks and 4D cell simulation.

 Cell Lineages

Animals build their bodies by altering the developmental potential of cells. The way in which they do so is reflected in the topology of cell lineages and the fates of terminal cells. Cell lineages should, therefore, contain information about the molecular events that determined them. We have developed new computational tools for visualizing, simulating and analyzing cell lineages: Ales and Les.

 Genetic Networks

Gene networks regulate many cellular processes such as division, differentiation, movement and death. We have developed Gene-O-Matic, a tool for modelling and simulation of genetic networks in a multicellular environment. The 3D multicellular model allows us to incorporate cell signalling, division and movement into the genetic network simulation.
Gene networks seem to be highly robust (or canalized) for example to genetic or environmental perturbations. We have developed GeNES to simulate and study the evolution of artificial gene networks under various conditions.

 4D Cell Simulation

Cell-O-Sim is a core component of our framework for modelling, simulation and visualisation of cells in 2D and 3D over time.