GSR: Editing - GenomeSimla Simulator

You may request changes to this simulator by navigating to the Basic, Details, and Citations/Applications tabs. When you are finished, open the Submit tab. To return back to the simulator view, click GenomeSimla. Finally, please take note of the GSR simulator privacy policy.
GenomeSimla
GenomeSIMLA is currently under development- however, we have a beta release that we are asking to be tested
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.
1.0.1
03-26-2008
03-26-2008
https://ritchielab.org/research/research-areas/statistical-genetics-and-gen-epi/methods/genomesimla
None

Attribute Tree Control

Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator.

Every sub-attribute is selected
Not all sub-attributes are selected
  • Target
    • Type of Simulated Data
      • Genotype at Genetic Markers
      • Diploid DNA Sequence
      • Haploid DNA Sequence
      • RNA
      • Sex Chromosomes
      • Mitochondrial DNA
      • Protein Sequence
      • Sequencing Reads
      • Phenotype
    • Variations
      • Biallelic Marker
      • Multiallelic Marker
      • Single Nucleotide Variation
      • Amino acid variation
      • Microsatellite
      • Insertion and Deletion
      • CNV
      • Inversion and Rearrangement
      • Alternative Splicing
      • Missing Genotypes
      • Genotype or Sequencing Error
      • Other
  • Simulation Method
    • Standard Coalescent
    • Exact Coalescent
    • Machine Learning
    • Forward-time
    • Resample Existing Data
    • Phylogenetic
    • Gene dropping
    • Other
  • Input
    • Data Type
      • Allele Frequencies
      • Empirical
      • Ancestral Sequence
      • Saved simulation
      • Reference genome
      • Other
    • File format
      • Arlequin
      • CREATE
      • Fstat
      • GDA
      • Genepop
      • MIGRATE
      • MS
      • SAM or BAM
      • NEXUS
      • Phylip
      • STRUCTURE
      • XML
      • Tree Sequence
      • Program Specific
      • Other
  • Output
    • Data Type
      • Genotype or Sequence
      • Phenotypic Trait
      • Individual Relationship
      • Demographic
      • Mutation
      • Methylation
      • Gene Expression
      • Protein Expression
      • Linkage Disequilibrium
      • Diversity Measures
      • Fitness
      • Sequencing Reads
        • Illumina
        • Roche 454
        • SOLiD
        • IonTorrent
        • PacBio
        • Nanopore
        • Other
      • Other
    • File Format
      • Arlequin
      • Fasta or Fastq
      • Fstat
      • Genepop
      • Linkage
      • MIGRATE
      • MS
      • PED
      • Phylip
      • NEXUS
      • STRUCTURE
      • VCF
      • SAM or BAM
      • Tree Sequence
      • Program Specific
      • Other
    • Sample Type
      • Random or Independent
      • Sibpairs, Trios and Nuclear Families
      • Extended or Complete Pedigrees
      • Case-control
      • Longitudinal
      • Other
  • Phenotype
    • Trait Type
      • Binary or Qualitative
      • Quantitative
      • Multiple
    • Determinants
      • Single Genetic Marker
      • Multiple Genetic Markers
      • Sex-linked
      • Gene-Gene Interaction
      • Environmental Factors
      • Gene-Environment Interaction
  • Evolutionary Features
    • Demographic
      • Population Size Changes
        • Constant Size
        • Exponential Growth or Decline
        • Logistic Growth
        • Bottleneck
        • Carrying Capacity
        • User Defined
      • Gene Flow
        • Stepping Stone Models
        • Island Models
        • Continent-Island Models
        • Sex or Age-Specific Migration Rates
        • Influenced by Environmental Factors
        • Admixed Population
        • User-defined Matrix
        • Other
      • Spatiality
        • Discrete Models
        • Continuous Models
        • Landscape Factors
    • Life Cycle
      • Discrete Generation Model
      • Age structured
      • Overlapping Generation
      • User-Defined transition matrices
    • Mating System
      • Random Mating
      • Monogamous
      • Polygamous
      • Haplodiploid
      • Selfing
      • Age- or Stage-Specific
      • Assortative or Disassortative
      • Other
    • Fecundity
      • Constant Number
      • Randomly Distributed
      • Individually Determined
      • Influenced by Environment
      • Other
    • Natural Selection
      • Determinant
        • Single-locus
        • Multi-locus
        • Codon-based
        • Fitness of Offspring
        • Phenotypic Trait
        • Environmental Factors
      • Models
        • Directional Selection
        • Balancing Selection
        • Multi-locus models
        • Epistasis
        • Random Fitness Effects
        • Disruptive
        • Phenotype Threshold
        • Frequency-Dependent
        • Other
    • Recombination
      • Uniform
      • Varying Recombination Rates
      • Gene Conversion Allowed
    • Mutation Models
      • Two-allele Mutation Model
      • Markov DNA Evolution Models
      • k-Allele Model
      • Infinite-allele Model
      • Infinite-sites Model
      • Stepwise Mutation Model
      • Codon and Amino Acid Models
      • Indels and Others
      • Heterogeneity among Sites
      • Others
    • Events Allowed
      • Population Merge and Split
      • Varying Demographic Features
      • Population Events
      • Varying Genetic Features
      • Change of Mating Systems
      • Other
    • Other
      • Phenogenetic
      • Polygenic background
  • Interface
    • Command-line
    • Graphical User Interface
    • Integrated Development Environment
    • Script-based
    • Web-based
  • Development
    • Tested Platforms
      • Windows
      • Mac OS X
      • Linux and Unix
      • Solaris
      • Others
    • Language
      • C or C++
      • Java
      • R
      • Python
      • Perl
      • Visual Basic
      • Other
    • License
      • GNU Public License
      • BSD
      • Creative Commons
      • MIT
      • Other
  • GSR Certification
    • Accessibility
    • Documentation
    • Application
    • Support

Summary of Proposed Changes

Step 2: Review list of proposed attribute addition(s) and subtraction(s).

To Add

    To Remove

      Can't Find the Attribute You Are Looking For?

      If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the Additional Comment box of the Submit tab.

      You may add citations by pmid, add citations by direct entry, remove citations (using the recycling bin icon), and edit citations (using the rarely seen edit icon) that were originally entered by direct entry.

      Summary of Proposed Changes

      To Add

      To Remove

      Current Citations/Applications

      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, http://dx.doi.org/10.1007/978-3-540-78757-0_3,Primary Citation
      [Pubmed ID: 19697353], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=19697353,, Application
      [Pubmed ID: 19954552], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=19954552,, Application
      [Pubmed ID: 20186329], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=20186329,, Application
      [Pubmed ID: 20576100], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=20576100,, Application
      [Pubmed ID: 20686705], Lescai F, Franceschi C, The impact of phenocopy on the genetic analysis of complex traits., PLoS One, 07-29-2010, https://www.ncbi.nlm.nih.gov/pubmed/?term=20686705,, Application
      [Pubmed ID: 20875103], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=20875103,, Application
      [Pubmed ID: 21247446], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=21247446,, Application
      [Pubmed ID: 21545716], Grady BJ, Torstenson ES, Ritchie MD, The effects of linkage disequilibrium in large scale SNP datasets for MDR., BioData Min, 05-05-2011, https://www.ncbi.nlm.nih.gov/pubmed/?term=21545716,, Application
      [Pubmed ID: 21612626], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=21612626,, Application
      [Pubmed ID: 22046286], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=22046286,, Application
      [Pubmed ID: 22586488], Chung RH, Chen YE, A two-stage random forest-based pathway analysis method., PLoS One, 01-01-2012, https://www.ncbi.nlm.nih.gov/pubmed/?term=22586488,, Application
      [Pubmed ID: 23658753], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=23658753,, Application
      [Pubmed ID: 24006871], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=24006871,, Application
      [Pubmed ID: 24339984], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=24339984,, Application
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      Please inform the GSR team here if you would like to see an attribute added to the attribute tree (or any other changes to the simulator description system as it exists).