Email updates

Keep up to date with the latest news and content from BMC Systems Biology and BioMed Central.

Open Access Open Badges 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

For all author emails, please log on.

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.

Format: PDF Size: 316KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

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.

Format: PDF Size: 331KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data