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 StatSeq (2012) and for the DREAM 5 Systems Genetics In-silico network subchallenge (2010). More recently, the Pula-Magdeburg single-gene knockout huge compendium (2013) has been released.

News

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!

2012-05-23

SysGenSIM 1.0.3 has been released with a bug fix and a minor new feature!

2012-05-15

StatSeq benchmark dataset has been published!

2012-05-08

SysGenSIM 1.0.2 has been released with two bug fixes!

2012-04-26

SysGenSIM 1.0.1 has been released with minor bug fixes!

2011-07-13

SysGenSIM 1.0.0 has been released with minor new features to celebrate paper acceptance!

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.