GSR: Simulator - GENS2
Attribute | Value |
---|---|
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 | 12 years, 1 month ago |
Homepage | https://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 ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 08-21-2019 (1675 days ago) |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Genotype at Genetic Markers, Haploid DNA Sequence, |
Variations | Biallelic Marker, |
Simulation Method | Forward-time, Resample Existing Data, Other (Scaling algorithm and trajectory-simulation method to control the frequency of disease-predisposing alleles), |
Input | |
Data Type | Allele Frequencies (Of disease predisposing loci), Saved simulation, Other (Disease model), |
File format | Other (Hapmap for simupop or simupop binary format - .pop files - for gens2), |
Output | |
Data Type | Genotype or Sequence, Phenotypic Trait, Demographic, Linkage Disequilibrium, |
Sequencing Reads | Other (Penetrance at genotype level and total prevalence of the disease in the output datasets), |
File Format | |
Sample Type | Random or Independent, Case-control, |
Phenotype | |
Trait Type | Binary or Qualitative, |
Determinants | Single Genetic Marker, Multiple Genetic Markers, Gene-Gene Interaction, Environmental Factors, Gene-Environment Interaction, |
Evolutionary Features | |
Demographic | |
Population Size Changes | Exponential Growth or Decline, |
Gene Flow | Admixed Population, |
Spatiality | |
Life Cycle | Discrete Generation Model, Overlapping Generation, |
Mating System | Random Mating, Polygamous, |
Fecundity | Constant Number, |
Natural Selection | |
Determinant | Single-locus (To obtain desired initial frequencies in the starting sample), Multi-locus, |
Models | Directional Selection (To obtain desired initial frequencies in the starting sample), |
Recombination | Varying Recombination Rates (Hapmap recombination map), |
Mutation Models | Two-allele Mutation Model, k-Allele Model, |
Events Allowed | |
Other | |
Interface | Command-line, Graphical User Interface, |
Development | |
Tested Platforms | Windows, Mac OS X, Linux and Unix, Solaris, |
Language | Python (Simupop), |
License | GNU Public License (V3), |
GSR Certification | Accessibility, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using GENS2 has been provided.
Please propose new citations if you are aware of publications that use this software.