STOCBIONET
Stochastic simulation algorithms for Gene Regulatory Networks for delayed and non-delayed reactions.
Avaiable methods:
- Direct method (Gillespie, 1977)
- Sorting direct method (McCollum et al, 2006)
- First reaction method (Gillespie, 1976)
- Next reaction method (Gibson and Bruck, 2000)
- Modified next reaction method (Anderson, 2007)
- Simplified next reaction method (Silva, 2014)
- Rejection method (Bratsun et al, 2005)
- Optimized direct method (Cao et al, 2004)
- Rejection method using a circular list
Methods in development:
- Rejection method using Hash Tables (90%) and heap (99.9%)
- Next reaction method compact (0.0%)
Requirements:
- C++11
- CMake 3.1 or newer (only if you want to build it using CMake)
Building
- Linux
mkdir build cd build cmake .. make
- Windows (using MinGW)
mkdir build cd build cmake .. -G "MinGW Makefiles" mingw32-make
Example of use:
If you are using it in the terminal you can run it without arguments or with the following arguments: Input-file Operation-code Initial-time Maximum-time
The current operation's codes are:
DM - Direct Method
ODM - Optimized Direct Method
SDM - Sorting Direct Method
FRM - First Reaction Method
NRM - Next Reaction Method
NRMC - Next Reaction Method Compact
MNRM - Modified Next Reaction Method
SNRM - Simplified Next Reaction Method
RM-OL - Rejection Method using an ordered list
RM-H - Rejection Method using a circular list
Example of input file:
#reaction rate constants
k1=1;
k2=2;
k3=0.0042;
k4=10;
k5=1;
#delays
t1=1;
t2=10;
t3=40;
v1=10;
#specie quantities
A=1;
B=1;
C=1;
D=1;
E=1;
F=1;
G=1;
#reactions
transcription,k1:A + B -> C;
transcription,k2:B + C -> D;
transcription,k3:D + E -> E + F;
transcription,k4:F -> D + G;
transcription,k5:E + G -> A;
IMPORTANT: Comments are not supported in the input file
REFERENCES
ANDERSON, David F. A modified next reaction method for simulating chemical systems with time dependent propensities and delays. The Journal of chemical physics, v. 127, n. 21, p. 214107, 2007.
BRATSUN, Dmitri et al. Delay-induced stochastic oscillations in gene regulation. Proceedings of the National Academy of Sciences, v. 102, n. 41, p. 14593-14598, 2005.
CAO, Yang; LI, Hong; PETZOLD, Linda. Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. The journal of chemical physics, v. 121, n. 9, p. 4059-4067, 2004.
GIBSON, Michael A.; BRUCK, Jehoshua. Efficient exact stochastic simulation of chemical systems with many species and many channels. The journal of physical chemistry A, v. 104, n. 9, p. 1876-1889, 2000.
GILLESPIE, Daniel T. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of computational physics, v. 22, n. 4, p. 403-434, 1976.
GILLESPIE, Daniel T. Exact stochastic simulation of coupled chemical reactions. The journal of physical chemistry, v. 81, n. 25, p. 2340-2361, 1977.
MCCOLLUM, James M. et al. The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior. Computational biology and chemistry, v. 30, n. 1, p. 39-49, 2006.
SILVA, Camillo de Lellis Falcão da et al. Novos algoritmos de simulação estocástica com atraso para redes gênicas. 2014.
👍 Credits for the input file structure: Camillo de Lellis Falcão da Silva