:: DESCRIPTION
StarGenetics is a Mendelian genetics cross simulator. StarGenetics allows students to simulate mating experiments between organisms that are genetically different across a range of traits to analyze the nature of the traits in question. Its goal is to teach students about genetic experimental design and genetic concepts.
:: DEVELOPER
The STAR program at MIT
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Ped-sim enables simulations of data for individuals from a given pedigree structure. It can use sex-specific genetic maps to incorporate differences in male and female recombination events.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Caballero M, Seidman DN, Qiao Y, Sannerud J, Dyer TD, Lehman DM, Curran JE, Duggirala R, Blangero J, Carmi S, Williams AL.
Crossover interference and sex-specific genetic maps shape identical by descent sharing in close relatives.
PLoS Genet. 2019 Dec 20;15(12):e1007979. doi: 10.1371/journal.pgen.1007979. PMID: 31860654; PMCID: PMC6944377.
:: DESCRIPTION
PacBio sequencers produced two types of characteristic reads: CCS (short and low error rate) and CLR (long and high error rate), both of which could be useful for de novo assembly of genomes. PBSIM simulates those PacBio reads by using either a model-based or sampling-based simulation.
::DEVELOPER
Yukiteru Ono ,Kiyoshi Asai ,Michiaki Hamada
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2013 Jan 1;29(1):119-21. doi: 10.1093/bioinformatics/bts649.
PBSIM: PacBio reads simulator–toward accurate genome assembly.
Ono Y, Asai K, Hamada M.
:: DESCRIPTION
QMSim (Qtl and Marker SIMulator) was designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data.
::DEVELOPER
Mehdi Sargolzaei , Flavio Schenkel
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sargolzaei, M. and F. S. Schenkel. 2009.
QMSim: a large-scale genome simulator for livestock.
Bioinformatics, 25: 680-681. doi:10.1093 /bioinformatics/btp045
:: DESCRIPTION
SCRIP provides a flexible Gamma-Poisson mixture and a Beta-Gamma-Poisson mixture framework to simulate scRNA-seq data.
::DEVELOPER
Fei Qin [aut, cre, cph]
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Qin F, Luo X, Xiao F, Cai G.
SCRIP: an accurate simulator for single-cell RNA sequencing data.
Bioinformatics. 2021 Dec 7:btab824. doi: 10.1093/bioinformatics/btab824. Epub ahead of print. PMID: 34874992.
:: DESCRIPTION
CellLine is a simulator of the dynamics of gene regulatory networks (GRN) in the cells of a lineage. From user-defined reactions and initial substance quantities, it generates cell lineages, i.e. genealogic pedigrees of cells related through mitotic division. Each cell’s dynamics is driven by a delayed stochastic simulation algorithm (delayed SSA), allowing multiple time delayed reactions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Andre S. Ribeiro, Daniel A. Charlebois, Jason Lloyd-Price,
“CellLine, a stochastic cell lineage simulator“,
Bioinformatics, (accepted), Sept. 2007.
:: DESCRIPTION
SGNSim (Stochastic Gene Networks Simulator) is a tool to model gene regulatory networks (GRN) where transcription and translation are modeled as multiple time delayed events and its dynamics is driven by a stochastic simulation algorithm (SSA) able to deal with multiple time delayed events. The delays can be drawn from several distributions and the reaction rates from complex functions or from physical parameters. SGNSim can generate ensembles of GRNs, within a set of user-defined parameters, such as topology. It can also be used to model specific GRNs and systems of chemical reactions. Perturbations, e.g. gene deletion, over-expression, copy and mutation, can be modeled as well.
SGNS2 (Simulator of delayed stochastic genetic circuits. Version 2, which includes transient compartmentalization of reactions)
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Lloyd-Price J, Gupta A, Ribeiro AS.
SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations.
Bioinformatics. 2012 Nov 15;28(22):3004-5. doi: 10.1093/bioinformatics/bts556. Epub 2012 Sep 26. PMID: 23014631.
Andre S. Ribeiro; Jason Lloyd-Price, (2007)
SGN Sim, a Stochastic Genetic Networks Simulator
Bioinformatics, 23(6):777-779. doi:10.1093/bioinformatics/btm004.
:: DESCRIPTION
AdmixSim is an individual-based forward-time simulation tool that can flexibly and efficiently simulate population genomics data under complex evolutionary scenarios. It is based on the extended Wright-Fisher model, and it implements many common evolutionary parameters to involve gene flow, natural selection, recombination, and mutation.
::DEVELOPER
Population Genomics Group (PGG)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhang R, Liu C, Yuan K, Ni X, Pan Y, Xu S.
AdmixSim 2: a forward-time simulator for modeling complex population admixture.
BMC Bioinformatics. 2021 Oct 18;22(1):506. doi: 10.1186/s12859-021-04415-x. PMID: 34663213; PMCID: PMC8522168.
:: DESCRIPTION
HAP-SAMPLE is an application for simulating SNP genotypes for case-control and affected-child trio studies by resampling from Phase I/II HapMap SNP data. The user provides a list of SNPs to be “genotyped,” along with a disease model file that describes causal SNPs and their effect sizes. The simulation tool is appropriate for candidate regions or whole-genome scans.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Wright, F.A, Huang, H., Guan, X., Gamiel, K, Jeffries, C., Barry, W.T., de Villena, F.P., Sullivan, P.F., Wilhelmsen, K.C., and Zou. F. (2007)
Simulating association studies: a data-based resampling method for candidate regions or whole genome scans,
Bioinformatics 23: 2581-2588.
:: DESCRIPTION
MESA is a web application for the assessment of DNA fragments based on limitations of DNA synthesis, amplification, cloning, sequencing methods and biological restrictions of host organisms.
::DEVELOPER
Distributed Systems and Intelligent Computing
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Schwarz M, Welzel M, Kabdullayeva T, Becker A, Freisleben B, Heider D.
MESA: automated assessment of synthetic DNA fragments and simulation of DNA synthesis, storage, sequencing and PCR errors.
Bioinformatics. 2020 Jun 1;36(11):3322-3326. doi: 10.1093/bioinformatics/btaa140. PMID: 32129840; PMCID: PMC7267826.
