GSR: Editing - ForSim 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 ForSim. Finally, please take note of the GSR simulator privacy policy.
ForSim
ForSim: A Forward Evolutionary Computer Simulation
ForSim is a forward evolutionary simulation system designed to be highly flexible for application to a wide variety of both applied health and life science questions as well as issues in theoretical evolutionary biology. It attempts to simulate in the most natural way the evolutionary process that generates the genetic architecture that underlies present-day traits, and related phenomena such as mate choice, migration bias, population substructure, and interactions with the environment. These phenomena are related to the way natural selection affects underlying genetic variation, molding the trait’s genetic architecture. Variation over the short evolutionary scale, within species or among closely related species, is generally built upon a phylogenetically stable underlying causal genetic architecture upon which mutation, selection, and demographic effects are laid to generate subsequent variation within and among populations.
None
Continually revised
01-01-2008
01-01-2008
http://anth.la.psu.edu/research/weiss-lab/research/research

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
    • 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

      [Pubmed ID: 18565989], Lambert BW, Terwilliger JD, Weiss KM, ForSim: a tool for exploring the genetic architecture of complex traits with controlled truth., Bioinformatics, 08-15-2008, https://www.ncbi.nlm.nih.gov/pubmed/?term=18565989,Primary Citation
      [Pubmed ID: 21811076], Hiekkalinna T, Schäffer AA, Lambert B, Norrgrann P, Göring HH, Terwilliger JD, PSEUDOMARKER: a powerful program for joint linkage and/or linkage disequilibrium analysis on mixtures of singletons and related individuals., Hum Hered, 01-01-2011, https://www.ncbi.nlm.nih.gov/pubmed/?term=21811076,, Application
      [Pubmed ID: 22101685], Weiss KM, Buchanan AV, Lambert BW, The Red Queen and her king: cooperation at all levels of life., Am J Phys Anthropol, 01-01-2011, https://www.ncbi.nlm.nih.gov/pubmed/?term=22101685,, Application
      [Pubmed ID: 22682329], Zhu Y, Xiong M, Family-based association studies for next-generation sequencing., Am J Hum Genet, 06-08-2012, https://www.ncbi.nlm.nih.gov/pubmed/?term=22682329,, Application
      [Pubmed ID: 23176082], Shugart YY, Zhu Y, Guo W, Xiong M, Weighted pedigree-based statistics for testing the association of rare variants., BMC Genomics, 11-24-2012, https://www.ncbi.nlm.nih.gov/pubmed/?term=23176082,, Application
      [Pubmed ID: 24141362], Agarwala V, Flannick J, Sunyaev S, Altshuler D, Evaluating empirical bounds on complex disease genetic architecture., Nat Genet, 12-01-2013, https://www.ncbi.nlm.nih.gov/pubmed/?term=24141362,, Application
      [Pubmed ID: 24384573], Weiss KM, Lambert BW, What type of person are you? Old-fashioned thinking even in modern science., Cold Spring Harb Perspect Biol, 01-01-2014, https://www.ncbi.nlm.nih.gov/pubmed/?term=24384573,, Application
      [Pubmed ID: 24607388], Chan Y, Lim ET, Sandholm N, Wang SR, McKnight AJ, Ripke S, Daly MJ, Neale BM, Salem RM, Hirschhorn JN, An excess of risk-increasing low-frequency variants can be a signal of polygenic inheritance in complex diseases., Am J Hum Genet, 03-06-2014, https://www.ncbi.nlm.nih.gov/pubmed/?term=24607388,, Application
      [Pubmed ID: 24768551], Wang SR, Agarwala V, Flannick J, Chiang CW, Altshuler D, Hirschhorn JN, Simulation of Finnish population history, guided by empirical genetic data, to assess power of rare-variant tests in Finland., Am J Hum Genet, 05-01-2014, https://www.ncbi.nlm.nih.gov/pubmed/?term=24768551,, Application
      This email will never be published. This email is used only for verification and communication purposes.
      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).