A. Arkin, J. Ross, and H. H. Mcadams, Stochastic kinetic analysis of developmental pathway bifurcation in phage ? -infected Escherichia coli cells, Genetics, vol.149, pp.1633-1648, 1998.

M. Barboric and B. M. Peterlin, A New Paradigm in Eukaryotic Biology: HIV Tat and the Control of Transcriptional Elongation, PLoS Biology, vol.17, issue.2, pp.200-02003, 2005.
DOI : 10.1371/journal.pbio.0030076.g002

C. L. Beisel and C. D. Smolke, Design Principles for Riboswitch Function, PLoS Computational Biology, vol.12, issue.4, p.1000363, 2009.
DOI : 10.1371/journal.pcbi.1000363.s008

L. Cardelli and G. Zavattaro, On the Computational Power of Biochemistry, Proceedings of the 3rd international conference on Algebraic Biology, pp.65-80, 2008.
DOI : 10.1007/978-3-540-85101-1_6

N. Chabrier-rivier, F. Fages, and S. Soliman, The Biochemical Abstract Machine BIOCHAM, Proceedings of CMSB 2004, pp.172-191, 2005.
DOI : 10.1007/BF03037227
URL : https://hal.archives-ouvertes.fr/inria-00000814

F. Ciocchetta and J. Hillston, Bio-PEPA: A framework for the modelling and analysis of biological systems, Theoretical Computer Science, vol.410, issue.33-34, 2008.
DOI : 10.1016/j.tcs.2009.02.037

V. Danos, J. Feret, W. Fontana, R. Harmer, and J. Krivine, Rule-Based Modelling of Cellular Signalling, 18th International Conference on Concurrency Theory, pp.17-41, 2007.
DOI : 10.1007/978-3-540-74407-8_3
URL : https://hal.archives-ouvertes.fr/hal-00164297

V. Danos, J. Feret, W. Fontana, and J. Krivine, Scalable Simulation of Cellular Signaling Networks, 5th Asian Symposium on Programming Languages and Systems, pp.139-157, 2007.
DOI : 10.1007/978-3-540-76637-7_10
URL : https://hal.archives-ouvertes.fr/inria-00528409

L. Dematté, C. Priami, and A. , The Beta Workbench: a computational tool to study the dynamics of biological systems, Briefings in Bioinformatics, vol.9, issue.5, pp.437-449, 2008.
DOI : 10.1093/bib/bbn023

J. Elf and M. Ehrenberg, What makes ribosome-mediated trascriptional attenuation sensitive to amino acid limitation?, PLoS Computational Biology, vol.1, issue.1, pp.14-23, 2005.

D. T. Gillespie, A general method for numerically simulating the stochastic time evolution of coupled chemical reactions, Journal of Computational Physics, vol.22, issue.4, pp.403-434, 1976.
DOI : 10.1016/0021-9991(76)90041-3

P. Gollnick, trp Operon and Attenuation, Encyclopedia of Biological Chemistry, pp.267-271, 2004.
DOI : 10.1016/B0-12-443710-9/00247-7

A. Gutierrez-preciado, R. Jensen, C. Yanofsky, and E. Merino, New insights into regulation of the tryptophan biosynthetic operon in Gram-positive bacteria, Trends in Genetics, vol.21, issue.8, pp.432-436, 2005.
DOI : 10.1016/j.tig.2005.06.001

W. S. Hlavacek, J. R. Faeder, M. L. Blinov, R. G. Posner, M. Hucka et al., Rules for Modeling Signal-Transduction Systems, Science Signaling, vol.2006, issue.344, pp.1-18, 2006.
DOI : 10.1126/stke.3442006re6

J. Roesser, Y. N. , and C. Yanofsky, Regulation of basal level expression of the tryptophan operon of Escherichia coli, J Biol Chem, vol.264, issue.21, pp.12284-12292, 1989.

T. Kasai, Regulation of the expression of the histidine operon in Salmonella typhimurium, Nature, vol.240, issue.5457, pp.523-527, 1974.
DOI : 10.1038/249523a0

K. V. Konan and C. Yanofsky, Role of ribosome release in regulation of tna operon expression in Escherichia coli, J. Bacteriol, vol.181, pp.1530-1536, 1999.

J. Krivine, R. Milner, and A. Troina, Stochastic Bigraphs, 24th Conference on the Mathematical Foundations of Programming Semantics of Electronical notes in theoretical computer science, pp.73-96, 2008.
DOI : 10.1016/j.entcs.2008.10.006
URL : https://hal.archives-ouvertes.fr/hal-00530712

C. Kuttler, C. Lhoussaine, and J. Niehren, A Stochastic Pi Calculus for Concurrent Objects, Second International Conference on Algebraic Biology, pp.232-246, 2007.
DOI : 10.1007/978-3-540-73433-8_17
URL : https://hal.archives-ouvertes.fr/inria-00121104

A. Phillips and L. Cardelli, Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus, Computational Methods in Systems Biology, International Conference, pp.184-199, 2007.
DOI : 10.1007/978-3-540-75140-3_13

S. Pradalier, A. Credi, M. Garavelli, C. Laneve, and G. Zavattaro, Modelization and simulation of nano devices in the nano-kappa calculus, Computational Methods in Systems Biology, International Conference CMSB, 2007.

S. Ramsey, D. Orrell, and H. Bolouri, DIZZY: STOCHASTIC SIMULATION OF LARGE-SCALE GENETIC REGULATORY NETWORKS, Journal of Bioinformatics and Computational Biology, vol.03, issue.02, pp.415-436, 2005.
DOI : 10.1142/S0219720005001132

A. Regev, Computational systems biology: A calculus for biomolecular knowledge, 2002.

M. Santillan and E. S. Zeron, Dynamic influence of feedback enzyme inhibition and transcription attenuation on the tryptophan operon response to nutritional shifts, Journal of Theoretical Biology, vol.231, issue.2, pp.287-298, 2004.
DOI : 10.1016/j.jtbi.2004.06.023

E. Simão, E. Remy, D. Thieffry, and C. Chaouiya, Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.Coli, ECCB/JBI, pp.190-196, 2005.
DOI : 10.1093/bioinformatics/bti1130

N. Trun, J. Trempy, G. , L. Nilsson, and C. Blomberg, Fundamental bacterial genetics, Chapter Gene expression and regulation Translation and messenger RNA secondary structure, Journal of Theoretical Biology, vol.68, pp.191-212321, 1977.

C. Yanofsky, Attenuation in the control of expression of bacterial operons, Nature, vol.21, issue.5800, pp.751-758, 1981.
DOI : 10.1038/289751a0

C. Yanofsky, Transcription Attenuation: Once Viewed as a Novel Regulatory Strategy, Journal of Bacteriology, vol.182, issue.1, pp.1-8, 2000.
DOI : 10.1128/JB.182.1.1-8.2000

C. Yanofsky, RNA-based regulation of genes of tryptophan synthesis and degradation, in bacteria, RNA, vol.13, issue.8, pp.1141-1154, 2007.
DOI : 10.1261/rna.620507

A. Biographies and C. Lhoussaine, is assistant professor at Lille1 University and head of the bioComputing team in the LIFL lab, www2.lifl.fr/BioComputing), and reacheable by email at cedric.lhoussaine@lifl.fr