libSDE is an open-source Java library for simulating systems of stochastic differential equations (SDE). As an example, libSDE is used to simulate molecular noise in the dynamics of gene regulatory networks. libSDE is a part of GeneNetWeaver (GNW), a Java tool for in silico benchmark generation and performance profiling of network inference methods (Schaffter et al., 2011). The model described by Schaffter et al. (2009) has been used to organize the fourth Dialogue for Reverse Engineering and Assessments and Methods (DREAM) challenge.
The main features of libSDE are:
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Itô and Stratonovich schemes
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Euler-Maruyama, Euler-Heun, derivative-free Milstein and Stochastic Runge-Kutta (SRK15) solvers
A brief introduction to the simulation of SDE systems is given in Numerical Integration of SDE: A Short Tutorial (Schaffter, 2009).
Related Projects
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In silico benchmark generation and performance profiling of network inference methods |
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An extensible toolkit for modularity detection |
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Observation and interaction in experimental environments |
Publications
Journal Articles
Fluorescence Behavioral Imaging (FBI) tracks identity in heterogeneous groups of Drosophila
PLOS One. 2012. Vol. 7, num. 11, p. e48381. DOI : 10.1371/journal.pone.0048381.GeneNetWeaver: In silico benchmark generation and performance profiling of network inference methods
Bioinformatics. 2011. Vol. 27, num. 16, p. 2263-2270. DOI : 10.1093/bioinformatics/btr373.Revealing strengths and weaknesses of methods for gene network inference
PNAS. 2010. Vol. 107, num. 14, p. 6286-6291. DOI : 10.1073/pnas.0913357107.Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods
Journal of Computational Biology. 2009. Vol. 16, num. 2, p. 229-239. DOI : 10.1089/cmb.2008.09TT.Reports
Numerical Integration of SDEs: A Short Tutorial
2010
Stochastic Simulations for DREAM4
2009