GSR: Simulator - GenomeSimla

Basic Package Attributes
AttributeValue
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 12 years, 6 months ago
Homepagehttps://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

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Documentation
Application
Support

Last evaluated08-21-2019 (423 days ago)
Author verificationThe 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.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataGenotype at Genetic Markers,
VariationsBiallelic Marker, Single Nucleotide Variation,
Simulation MethodForward-time,
Input
Data TypeAllele Frequencies,
File format
Output
Data TypeGenotype or Sequence, Linkage Disequilibrium,
Sequencing Reads
File Format
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size ChangesExponential Growth or Decline, Logistic Growth, Carrying Capacity,
Gene Flow
Spatiality
Life Cycle
Mating SystemRandom Mating,
Fecundity
Natural Selection
Determinant
Models
RecombinationUniform, Varying Recombination Rates,
Mutation Models
Events Allowed
Other
InterfaceCommand-line,
Development
Tested PlatformsWindows, Mac OS X, Linux and Unix,
LanguageC or C++,
LicenseGNU Public License,
GSR CertificationDocumentation,

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]


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