GSR: Simulator - GenomeSimla
Attribute | Value |
---|---|
Title | GenomeSimla |
Short Description | GenomeSIMLA is currently under development- however, we have a beta release that we are asking to be tested |
Long Description | GenomeSimla uses Hardy-Weinburg mating to advance simulated genetic data forward through time from generation to generation. Next, we included two distinct algorithms to aide the user in developing various types of disease models: SIMLA for diseases with interactions and main effects and simPEN for embedding purely epistatic models. |
Version | 1.0.1 |
Project Started | 2008 |
Last Release | 16 years ago |
Homepage | https://ritchielab.org/research/research-areas/statistical-genetics-and-gen-epi/methods/genomesimla |
Citations | Edwards TL, Bush WS, Turner SD, Dudek SM, Torstenson ES, Schmidt M, Martin E, Ritchie MD, Generating Linkage Disequilibrium Patterns in Data Simulations Using genomeSIMLA, Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics Lecture Notes in Computer Science , 01-01-2008 [ Abstract ] |
GSR Certification | Accessibility |
Last evaluated | 08-21-2019 (1675 days ago) |
Author verification | The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator. |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Genotype at Genetic Markers, |
Variations | Biallelic Marker, Single Nucleotide Variation, |
Simulation Method | Forward-time, |
Input | |
Data Type | Allele Frequencies, |
File format | |
Output | |
Data Type | Genotype or Sequence, Linkage Disequilibrium, |
Sequencing Reads | |
File Format | |
Sample Type | |
Phenotype | |
Trait Type | |
Determinants | |
Evolutionary Features | |
Demographic | |
Population Size Changes | Exponential Growth or Decline, Logistic Growth, Carrying Capacity, |
Gene Flow | |
Spatiality | |
Life Cycle | |
Mating System | Random Mating, |
Fecundity | |
Natural Selection | |
Determinant | |
Models | |
Recombination | Uniform, Varying Recombination Rates, |
Mutation Models | |
Events Allowed | |
Other | |
Interface | Command-line, |
Development | |
Tested Platforms | Windows, Mac OS X, Linux and Unix, |
Language | C or C++, |
License | GNU Public License, |
GSR Certification | Documentation, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 14
The following 14 publications are selected examples of applications that used GenomeSimla.
2013
Cummings AC, Torstenson E, Davis MF, D'Aoust LN, Scott WK, Pericak-Vance MA, Bush WS, Haines JL, Evaluating power and type 1 error in large pedigree analyses of binary traits., PLoS One, 01-01-2013 [Abstract]
Park YS, Schmidt M, Martin ER, Pericak-Vance MA, Chung RH, Pathway-PDT: a flexible pathway analysis tool for nuclear families., BMC Bioinformatics, 09-04-2013 [Abstract]
Zuo X, Rao S, Fan A, Lin M, Li H, Zhao X, Qin J, To control false positives in gene-gene interaction analysis: two novel conditional entropy-based approaches., PLoS One, 01-01-2013 [Abstract]
2012
Chung RH, Chen YE, A two-stage random forest-based pathway analysis method., PLoS One, 01-01-2012 [Abstract]
2011
Hussman JP, Chung RH, Griswold AJ, Jaworski JM, Salyakina D, Ma D, Konidari I, Whitehead PL, Vance JM, Martin ER, Cuccaro ML, et al., A noise-reduction GWAS analysis implicates altered regulation of neurite outgrowth and guidance in autism., Mol Autism, 01-19-2011 [Abstract]
Grady BJ, Torstenson ES, Ritchie MD, The effects of linkage disequilibrium in large scale SNP datasets for MDR., BioData Min, 05-05-2011 [Abstract]
Chung RH, Schmidt MA, Martin ER, CAPL: an efficient association software package using family and case-control data and accounting for population stratification., BMC Bioinformatics, 05-25-2011 [Abstract]
Rao S, Yuan M, Zuo X, Su W, Zhang F, Huang K, Lin M, Ding Y, A novel evolution-based method for detecting gene-gene interactions., PLoS One, 01-01-2011 [Abstract]
2010
Edwards TL, Torstensen E, Dudek S, Martin ER, Ritchie MD, A cross-validation procedure for general pedigrees and matched odds ratio fitness metric implemented for the multifactor dimensionality reduction pedigree disequilibrium test., Genet Epidemiol, 02-01-2010 [Abstract]
Edwards TL, Turner SD, Torstenson ES, Dudek SM, Martin ER, Ritchie MD, A general framework for formal tests of interaction after exhaustive search methods with applications to MDR and MDR-PDT., PLoS One, 02-23-2010 [Abstract]
Gayán J, González-Pérez A, Ruiz A, "Does replication groups scoring reduce false positive rate in SNP interaction discovery? Response"., BMC Genomics, 06-24-2010 [Abstract]
Lescai F, Franceschi C, The impact of phenocopy on the genetic analysis of complex traits., PLoS One, 07-29-2010 [Abstract]
Turner SD, Dudek SM, Ritchie MD, ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci., BioData Min, 09-27-2010 [Abstract]
2009
Bush WS, Chen G, Torstenson ES, Ritchie MD, LD-spline: mapping SNPs on genotyping platforms to genomic regions using patterns of linkage disequilibrium., BioData Min, 12-03-2009 [Abstract]