Jérémy Rivière, Pascal Ballet, Gireg Desmeulles,
Alexandra Fronville, Vincent Rodin, Abdoulaye Sarr, Anne Jeannin-Girardon.
Model and Simulation of Complex Biological Systems.
BioSynSys 2015: 1er colloque du GDR Biologie de Synthèse et des
Systèmes, Session Posters, page 40, Paris (France), 7-10 septembre 2015.
Abstract:
The theory of complex systems has become more and more relevant over the last
thirty years to understand concepts such as emergence and self-organization
and their role in biological, physical, chemical and social systems.
The use of an Individual-Based approach to model and simulate complex systems
has proved to be an efficient way, both in research and teaching, of
manipulating these complex systems.
In our team, we use this approach to propose tools and methods for biologists
to create realistic models and simulations of complex biological systems in
order to (1) grasp the complexity of these systems, (2) test hypothesis and
investigate dynamical systems that otherwise could not be systematically
investigated.
Among our previous works with biologists, we can mention works related to
hematology [1], immunology and oncology.
We have also proposed morphogenesis simulation tools which allow to simulate
large scale tissue growth [2].
These tools are based on a flexible biomechanical cell model able to simulate
cellular deformation and migration. Finally, we also designed an intuitive and
open-source software called NetBioDyn [3] aimed at biologists for teaching and
research, that does not require any skills in computer programming.
In particular, a specific graphical user interface allows to create in a
simple way bottom-up models where unexpected behaviours can emerge from simple
interacting entities, and test hypothesis by creating various simulations.
NetBioDyn has been successfully used in middle schools, high schools and
universities since 2010.
References
- G. Desmeulles, S. Bonneaud, P. Redou, V. Rodin and J. Tisseau.
In virtuo Experiments Based on the Multi-Interaction System Framework:
the RéISCOP Meta-Model, Computer Modeling in Engineering &
Sciences, 47(3):299-330, 2009.
- A. Jeannin-Girardon, P. Ballet and V. Rodin.
Large scale tissue morphogenesis simulation on heterogenous systems based
on a flexible biomechanical cell model,
IEEE/ACM Transactions on Computational Biology and Bioinformatics,
12(5):1021-1033, September/October 2015.
- http://virtulab.univ-brest.fr
Keywords:
Individual Based Modelling, Computer Simulation, Complex Systems, Software.
[link]
[Riviere15a.pdf]