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Open Access Methodology article

Continuous time boolean modeling for biological signaling: application of Gillespie algorithm

Gautier Stoll123*, Eric Viara4, Emmanuel Barillot123 and Laurence Calzone123

Author Affiliations

1 Institut Curie, 26 rue d’Ulm, Paris, F-75248 France

2 INSERM, Paris, U900, F-75248 France

3 Mines ParisTech, Fontainebleau, F-77300 France

4 Sysra, Yerres, F-91330 France

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BMC Systems Biology 2012, 6:116  doi:10.1186/1752-0509-6-116

Published: 29 August 2012

Additional files

Additional file 1:

Supplementary material. Basic information on Markov process, abbreviations, definitions and algorithms.

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Additional file 2:

Model of the mammalian cell cycle with GINsim, BoolNet and MaBoSS. The cell cycle presented in the “Examples” section has been modeled using three tools: GINsim, BoolNet, and MaBoSS. The results for each tool are presented: (1) GINsim provides steady state solutions and transition graphs for two different initial conditions: when CycD=0 and CycD=1. For the synchronous strategy, the transition graph can be visualized whereas for the asynchronous strategy, it is not easy to read or use; BoolNet constructs two graphical representations of the trajectories based on synchronous update strategy, for the case of CycD=0 (steady state) and CycD=1 (cycle); (3) MaBoSS estimates indecomposable stationary distributions for the case of CycD=0 (one fixed point, not shown) and CycD=1 (distribution of probabilities of different network states), and time-dependent activities of the cyclins showing damped oscillations. All results are coherent but are presented differently with a different focus for each tool.

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