F. E. Aas, M. Wolfgang, S. Frye, S. Dunham, C. Lvold et al., Competence for natural transformation in Neisseria gonorrhoeae: components of DNA binding and uptake linked to type IV pilus expression, Molecular Microbiology, vol.42, issue.3, pp.749-760, 2002.
DOI : 10.1046/j.1365-2958.2002.03193.x

M. Allesen-holm, K. B. Barken, L. Yang, M. Klausen, J. S. Webb et al., A characterization of DNA release in Pseudomonas aeruginosa cultures and biofilms, Molecular Microbiology, vol.156, issue.4, pp.1114-1128, 2006.
DOI : 10.1126/science.295.5559.1487

E. Alpkvist, C. Picioreanu, M. C. Van-loosdrecht, and A. Heyden, Three-dimensional biofilm model with individual cells and continuum EPS matrix, Biotechnology and Bioengineering, vol.91, issue.5, pp.961-979, 2006.
DOI : 10.1002/bit.20917

K. B. Barken, S. J. Pamp, L. Yang, M. Gjermansen, J. J. Bertrand et al., biofilms, Environmental Microbiology, vol.153, issue.9, pp.2331-2343, 2008.
DOI : 10.1111/j.1462-2920.2008.01658.x

G. C. Barker and M. J. Grimson, A cellular automaton model of microbial growth, Binary, vol.5, pp.132-137, 1993.

H. M. Dalton, A. E. Goodman, and K. C. Marshall, Diversity in surface colonization behavior in marine bacteria, Journal of Industrial Microbiology & Biotechnology, vol.56, issue.3-4, pp.228-234, 1996.
DOI : 10.1007/BF01574697

H. M. Dalton, L. Poulsen, P. Halaz, M. Angles, and A. Goodman, Substratum-induced morphological changes in a marine bacterium and their relevance to biofilm structure., Journal of Bacteriology, vol.176, issue.22, pp.6900-6906, 1994.
DOI : 10.1128/jb.176.22.6900-6906.1994

M. E. Davey and G. A. O-'toole, Microbial Biofilms: from Ecology to Molecular Genetics, Microbiology and Molecular Biology Reviews, vol.64, issue.4, pp.847-867, 2000.
DOI : 10.1128/MMBR.64.4.847-867.2000
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC99016

J. Ferrer, C. Prats, and D. Lopez, Individual-based Modelling: An Essential Tool for Microbiology, Journal of Biological Physics, vol.20, issue.21, pp.19-37, 2008.
DOI : 10.1007/s10867-008-9082-3

M. Ginovart, D. Lopez, J. Valls, and M. Silbert, Individual based simulations of bacterial growth on agar plates, Physica A: Statistical Mechanics and its Applications, vol.305, issue.3-4, pp.604-618, 2002.
DOI : 10.1016/S0378-4371(01)00581-7

V. Grimm, Ten years of individual-based modelling in ecology: what have we learned and what could we learn in the future?, Ecological Modelling, vol.115, issue.2-3, pp.129-148, 1999.
DOI : 10.1016/S0304-3800(98)00188-4

G. Pe-'er, C. Piou, S. F. Railsback, A. M. Robbins, M. M. Robbins et al., A standard protocol for describing individual-based and agent-based models, Ecological Modelling, vol.198, pp.115-126, 2006.

V. Grimm and S. F. Railsback, Individual-based Modeling and Ecology, 2005.
DOI : 10.1515/9781400850624

F. L. Hellweger and V. Bucci, A bunch of tiny individuals???Individual-based modeling for microbes, Ecological Modelling, vol.220, issue.1, pp.8-22, 2009.
DOI : 10.1016/j.ecolmodel.2008.09.004

M. Hestenes, R. Stiefel, and E. , Methods of conjugate gradients for solving linear systems

S. M. Hunt, M. A. Hamilton, J. T. Sears, G. Harkin, and J. Reno, A computer investigation of chemically mediated detachment in bacterial biofilms, Microbiology, vol.149, issue.5, pp.1155-1163, 2003.
DOI : 10.1099/mic.0.26134-0

L. R. Johnson, Microcolony and biofilm formation as a survival strategy for bacteria, Journal of Theoretical Biology, vol.251, issue.1, pp.24-34, 2008.
DOI : 10.1016/j.jtbi.2007.10.039

T. Tolker-nielsen, Biofilm formation by Pseudomonas aeruginosa wild type, flagella and type IV pili mutants, Molecular Microbiology, vol.48, pp.1511-1524, 2003.

M. Klausen, A. Aaes-jorgensen, S. Molin, and T. Tolker-nielsen, Involvement of bacterial migration in the development of complex multicellular structures in Pseudomonas aeruginosa biofilms, Molecular Microbiology, vol.22, issue.1, pp.61-68, 2003.
DOI : 10.1046/j.1365-2958.2003.03677.x

J. U. Kreft, G. Booth, and J. W. Wimpenny, BacSim, a simulator for individual-based modelling of bacterial colony growth, Microbiology, vol.144, issue.12, pp.3275-3278, 1998.
DOI : 10.1099/00221287-144-12-3275

J. U. Kreft, C. Picioreanu, J. W. Wimpenny, and M. C. Van-loosdrecht, Individual-based modelling of biofilms, Microbiology, vol.147, issue.11, pp.2897-2912, 2001.
DOI : 10.1099/00221287-147-11-2897

C. Lee, M. Hoopes, J. Diehl, W. Gilliland, G. Huxel et al., Non-local Concepts and Models in Biology, Journal of Theoretical Biology, vol.210, issue.2, pp.201-219, 2001.
DOI : 10.1006/jtbi.2000.2287

S. Luke, C. Cioffi-revilla, L. Panait, and K. Sullivan, Mason : A Java multi-agent simulation toolkit, Proceedings of the SwarmFest Workshop, 2004.

W. Shi, Exopolysaccharide biosynthesis genes required for social motility in Myxococcus xanthus, Molecular Microbiology, vol.55, pp.206-220, 2005.

M. R. Parsek and T. Tolker-nielsen, Pattern formation in Pseudomonas aeruginosa biofilms, Current Opinion in Microbiology, vol.11, issue.6, pp.560-566, 2008.
DOI : 10.1016/j.mib.2008.09.015

C. Picioreanu, M. C. Van-loosdrecht, and J. J. Heijnen, A new combined differential-discrete cellular automaton approach for biofilm modeling: Application for growth in gel beads, Biotechnology and Bioengineering, vol.38, issue.6, pp.718-731, 1998.
DOI : 10.1002/(SICI)1097-0290(19980320)57:6<718::AID-BIT9>3.0.CO;2-O

C. Picioreanu, M. C. Van-loosdrecht, and J. J. Heijnen, Mathematical modeling of biofilm structure with a hybrid differential-discrete cellular automaton approach, Biotechnology and Bioengineering, vol.22, issue.1, pp.101-116, 1998.
DOI : 10.1002/(SICI)1097-0290(19980405)58:1<101::AID-BIT11>3.0.CO;2-M

C. Picioreanu, J. U. Kreft, M. Klaussen, J. A. Haagensen, T. Tolker-nielson et al., Microbial motility involvement in biofilm structure formation ??? a 3D modelling study, Water Science & Technology, vol.55, issue.8-9, pp.337-343, 2007.
DOI : 10.2166/wst.2007.275

J. G. Polhill, D. Parker, D. Brown, and V. Grimm, Using the ODD protocol for describing three agent-based social simulation models of land-use change, Journal of Artificial Societies and Social Simulation, vol.11, issue.3, 2008.

M. C. Van-loosdrecht, J. J. Heijnen, H. Eberl, J. Kreft, and C. Picioreanu, Mathematical modelling of biofilm structures, Antonie van Leeuwenhoek, vol.81, issue.1/4, pp.245-256, 2002.
DOI : 10.1023/A:1020527020464

C. Whitchurch, T. Tolker-nielsen, P. C. Ragas, and J. S. Mattick, Extracellular DNA Required for Bacterial Biofilm Formation, Science, vol.295, issue.5559, pp.1487-1487, 2002.
DOI : 10.1126/science.295.5559.1487

J. W. Wimpenny and R. Colasanti, A unifying hypothesis for the structure of microbial biofilms based on cellular automaton models, FEMS Microbiology Ecology, vol.22, issue.1, pp.1-16, 1997.
DOI : 10.1111/j.1574-6941.1997.tb00351.x

J. B. Xavier, C. Picioreanu, and M. C. Van-loosdrecht, A framework for multidimensional modelling of activity and structure of multispecies biofilms, Environmental Microbiology, vol.127, issue.8, pp.1085-1103, 2005.
DOI : 10.1016/S0168-6496(96)00078-5