Embedded Files
- SELANSI is a software toolbox for the simulation of stochastic multidimensional Gene Regulatory Networks (GRNs).
- SELANSI is a software toolbox for the simulation of stochastic multidimensional Gene Regulatory Networks (GRNs).
- SELANSI exploits intrinsic structural properties of GRNs to accurately approximate the corresponding Chemical Master Equation (CME) with a partial integral differential equation (PIDE) that is solved by a semi-lagrangian method with high efficiency.
- SELANSI exploits intrinsic structural properties of GRNs to accurately approximate the corresponding Chemical Master Equation (CME) with a partial integral differential equation (PIDE) that is solved by a semi-lagrangian method with high efficiency.
- The validity of the method is not restricted to a particular type of kinetics. The tool offers total flexibility regarding network topology, kinetics and parameterization, as well as simulation options.
- The validity of the method is not restricted to a particular type of kinetics. The tool offers total flexibility regarding network topology, kinetics and parameterization, as well as simulation options.
- SELANSI runs under MATLAB (Windows, Linux and MacOS)
- SELANSI runs under MATLAB (Windows, Linux and MacOS)
- Networks under consideration might involve multiple genes with self and cross regulations, in which genes can be regulated by different transcription factors.
- Networks under consideration might involve multiple genes with self and cross regulations, in which genes can be regulated by different transcription factors.
- SELANSI computes the (approximated) numerical solution of the Chemical Master Equation (CME) obtaining the temporal evolution of the species’ probability density function (and its stationary state)
- SELANSI computes the (approximated) numerical solution of the Chemical Master Equation (CME) obtaining the temporal evolution of the species’ probability density function (and its stationary state)
DOWNLOAD SELANSI V 1.0.0 (link to github repository):
DOWNLOAD SELANSI V 1.0.0 (link to github repository):
Please cite:
SELANSI: a toolbox for simulation of stochastic gene regulatory networks.
SELANSI: a toolbox for simulation of stochastic gene regulatory networks.
Pájaro M, Otero-Muras I, Vázquez C, Alonso AA.
Bioinformatics. 2018 Mar 1;34(5):893-895. doi: 10.1093/bioinformatics/btx645.
https://www.ncbi.nlm.nih.gov/pubmed/29040384
Stochastic modeling and numerical simulation of gene regulatory networks with protein bursting.
Stochastic modeling and numerical simulation of gene regulatory networks with protein bursting.
Pájaro M, Alonso AA, Otero-Muras I, Vázquez C.
J Theor Biol. 2017 May 21;421:51-70. doi: 10.1016/j.jtbi.2017.03.017. Epub 2017 Mar 21.
https://www.ncbi.nlm.nih.gov/pubmed/28341132
Google Sites
Report abuse