GSR: Simulator - GENS2

Basic Package Attributes
AttributeValue
Title GENS2
Short Description Simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions.
Long Description The Gene-Environment iNteraction Simulator 2 (GENS2) simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. GENS2 is based on data with realistic patterns of linkage disequilibrium, and imposes no limitations either on the number of individuals to be simulated or on number of non-predisposing genetic/environmental factors to be considered. The GENS2 tool is able to simulate gene-environment and gene-gene interactions. To make the Simulator more intuitive, the input parameters are expressed as standard epidemiological quantities. GENS2 is written in Python language and takes advantage of operators and modules provided by the simuPOP simulation environment. GENS2 is not intended to simulate the evolution of a population, but to simulate complex gene-environment interactions in case-control sample. It shuold be used along with simuPOP, a software that allows realistic evolutionary simulation (or an equivalent simulator), to simulate dataset on which apply disease model .
Version 2.2 beta
Project Started 2009
Last Release 8 years, 7 months ago
Homepagehttps://sourceforge.net/projects/gensim/
Citations Pinelli M, Scala G, Amato R, Cocozza S, Miele G, Simulating gene-gene and gene-environment interactions in complex diseases: Gene-Environment iNteraction Simulator 2., BMC Bioinformatics, 06-14-2012 [ Abstract, cited in PMC ]
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Last evaluated08-21-2019 (423 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataGenotype at Genetic Markers, Haploid DNA Sequence,
VariationsBiallelic Marker,
Simulation MethodForward-time, Resample Existing Data, Other (Scaling algorithm and trajectory-simulation method to control the frequency of disease-predisposing alleles),
Input
Data TypeAllele Frequencies (Of disease predisposing loci), Saved simulation, Other (Disease model),
File formatOther (Hapmap for simupop or simupop binary format - .pop files - for gens2),
Output
Data TypeGenotype or Sequence, Phenotypic Trait, Demographic, Linkage Disequilibrium,
Sequencing ReadsOther (Penetrance at genotype level and total prevalence of the disease in the output datasets),
File Format
Sample TypeRandom or Independent, Case-control,
Phenotype
Trait TypeBinary or Qualitative,
DeterminantsSingle Genetic Marker, Multiple Genetic Markers, Gene-Gene Interaction, Environmental Factors, Gene-Environment Interaction,
Evolutionary Features
Demographic
Population Size ChangesExponential Growth or Decline,
Gene FlowAdmixed Population,
Spatiality
Life CycleDiscrete Generation Model, Overlapping Generation,
Mating SystemRandom Mating, Polygamous,
FecundityConstant Number,
Natural Selection
DeterminantSingle-locus (To obtain desired initial frequencies in the starting sample), Multi-locus,
ModelsDirectional Selection (To obtain desired initial frequencies in the starting sample),
RecombinationVarying Recombination Rates (Hapmap recombination map),
Mutation ModelsTwo-allele Mutation Model, k-Allele Model,
Events Allowed
Other
InterfaceCommand-line, Graphical User Interface,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix, Solaris,
LanguagePython (Simupop),
LicenseGNU Public License (V3),
GSR CertificationAccessibility,

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