Abstract
Systems biology aims at integrating processes at various time and spatial scales into a single and coherent formal description to allow analysis and computer simulation. In this context, we focus on rule-based modeling and its integration in the domain-specific language MGS. Through the notions of topological collections and transformations, MGS allows the modeling of biological processes at various levels of description. We validate our approach through the description of various models of a synthetic bacteria designed in the context of the International Genetically Engineered Machine Competition, from a very simple biochemical description of the process to an individual-based model on a Delaunay graph topology. This approach is a first step into providing the requirements for the emerging field of spatial systems biology which integrates spatial properties into systems biology.
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Notes
- 1.
The SMB: Synthetic Multicellular Bacterium (iGEM’07) Paris Team Web site: http://parts.mit.edu/igem07/index.php/Paris.
- 2.
Relying on a mean-field approach where the idea is to replace all interactions to any entity with an average interaction, reducing any multiple entities problem into an effective one-entity problem.
- 3.
Bailly and Longo (2006) recognize the importance of this class of dynamical systems and call it “dynamicité auto-constituante” (which could be translated to “self-producing dynamicity”), a distinctive feature of living organisms.
- 4.
The Website of the project is http://mgs.spatial-computing.org.
- 5.
The BioBricks are available in the Registry of Standard Biological Parts at the following Web site http://partsregistry.org/Main_Page.
- 6.
- 7.
The third dimension is not considered as the SMBis supposed to grow in the plane of a Petri dish, for example.
- 8.
The whole MGSprogram of the simulation is available at http://mgs.spatial-computing.org/integrative_biology.tgz.
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Acknowledgements
The authors would like to thank the reviewers for their valuable comments on a first version of this chapter.
We gratefully acknowledge all the people who contributed to make the first French participation in iGEM in 2007 a success: the students, D. Bikard, F. Caffin, N. Chiaruttini, T. Clozel, D. Guegan, T. Landrain, D. Puyraimond, A. Rizk, E. Shotar, G. Vieira, the instructors, F. Delaplace, S. Bottani, A. Jaramillo, A. Lindner, V. Schächter; the advisors, F. Le Fevre, M. Suarez, S. Smidtas, A. Spicher, and P. Tortosa.
Further acknowledgments are also due to J. Cohen, B. Calvez, F. Thonnerieux, C. Kodrnja, and F. Letierce who have contributed in various ways to the MGSproject.
This research is supported in part by the the University of Évry, the University of Paris-Est, the CNRS, GENOPOLE-Évry, the Institute for Complex Systems in Paris-Ile de France, the ANR white project AutoChem and the French working group GDR GPL/LTP.
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Spicher, A., Michel, O., Giavitto, JL. (2011). Interaction-Based Simulations for Integrative Spatial Systems Biology. In: Dubitzky, W., Southgate, J., Fuß, H. (eds) Understanding the Dynamics of Biological Systems. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-7964-3_10
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