What is SysGenSIM?

SysGenSIM is a bioinformatics toolbox for MATLAB to create artificial gene expression datasets by simulating Systems Genetics experiments.

Requirements

To run SysGenSIM you need Mathworks MATLAB version 7.9 (R2009b) or later, with Bioinformatics Toolbox and Statistics Toolbox.

Publications

SysGenSIM is described in this paper:

• A. Pinna, N. Soranzo, I. Hoeschele, A. de la Fuente
  “Simulating system genetics data with SysGenSIM”
  Bioinformatics 27(17), pp. 2459-2462, 2011

We kindly ask you to cite the previous paper in your publications if you use SysGenSIM in your work.

Data produced with SysGenSIM have been already used for the following scientific papers:

• M. Vignes, J. Vandel, D. Allouche, N. Ramadan-Alban, C. Cierco-Ayrolles, T. Schiex, B. Mangin, S. de Givry
  “Gene Regulatory Network Reconstruction Using Bayesian Networks, the Dantzig Selector, the Lasso and Their Meta-Analysis”
  PLoS ONE 6(12), e29165, 2011
• M. Bhattacharjee, M. J. Sillanpää
  “A Bayesian Mixed Regression Based Prediction of Quantitative Traits from Molecular Marker and Gene Expression Data”
  PLoS ONE 6(11), e26959, 2011
• A. Pinna, N. Soranzo, A. de la Fuente
  “From Knockouts to Networks: Establishing Direct Cause-Effect Relationships through Graph Analysis”
  PLoS ONE 5(10), e12912, 2010
• B. Liu, A. de la Fuente, I. Hoeschele
  “Gene Network Inference via Structural Equation Modeling in Genetical Genomics Experiments”
  Genetics 178(3), pp. 1763-1776, 2008

Moreover, SysGenSIM has been used to produce the benchmark datasets for:

• the Pula-Magdeburg single-gene knockout huge compendium (2013)
• StatSeq (2012)
• the DREAM 5 Systems Genetics In-silico network subchallenge (2010)

News

2015-03-05

SysGenSIM 1.2, updated to run with the most recent versions of MATLAB, is now available for download!

2014-01-04

Book Gene Network Inference - Verification of Methods for Systems Genetics Data, where the StatSeq benchmark dataset is analyzed by several techniques, has been published by Springer!

2013-08-08

Article Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their performance, where the Pula-Magdeburg dataset is analyzed, has been published on BMC Systems Biology!

2013-08-06

SysGenSIM 1.1.1 has been released with a regenerated PDF manual!

2013-03-06

Pula-Magdeburg single-gene knockout benchmark dataset has been published!

2013-01-17

SysGenSIM 1.1 has been released with a revamped user interface and the possibility to simulate experimental perturbations!

SysGenSIM developers

SysGenSIM has been developed by: Andrea Pinna, Nicola Soranzo, Ina Hoeschele, Alberto de la Fuente.

CRS4, Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA) Italy

Virginia Bioinformatics Institute Washington Street, MC 0477 Blacksburg, VA United States

License

SysGenSIM is free and open-source software, released under the GNU General Public License, version 2 or later.
This license is governed by the Laws of Italy. Disputes shall be settled by Cagliari City Court.

MATLAB is registered trademark of The MathWorks, Inc.