Tag: Simulation

POPSIM 2.13 – Population Simulation program

POPSIM 2.13

:: DESCRIPTION

POPSIM creates a virtual representation of every individual,makes no prior assumptions but the Medelian rules and allows for populations of several million individuals size to be generated and to be followed over hundreds of generations.

::DEVELOPER

Institute for Clinical Molecular Biology

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows

:: DOWNLOAD

 POPSIM

:: MORE INFORMATION

Citation

Hampe J, Wienker T, Schreiber S, Nürnberg T (1998).
POPSIM: A general population simulation program.
Bioinformatics 14: 458-464

SimRNA 3.20 – Simulations of RNA Conformational Dynamics

SimRNA 3.20

:: DESCRIPTION

SimRNA is a tool for simulations of RNA conformational dynamics (folding, unfolding, multiple chain complex formation etc.), and its applications include RNA 3D structure prediction.

::DEVELOPER

Bujnicki lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 SimRNA

:: MORE INFORMATION

Citation

Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM.
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.
Nucleic Acids Res. 2016 Apr 20;44(7):e63. doi: 10.1093/nar/gkv1479. Epub 2015 Dec 19. PMID: 26687716; PMCID: PMC4838351.

symsim 0.1 – Sympatric Speciation Simulation for Recombining Microbial Populations

symsim 0.1

:: DESCRIPTION

Symsim (sympatric speciation simulation) is a discrete generations model implemented in MatLab, with varying population size, designed to investigate the colonization of a new ecological niche. Each generation consists of resource competition, population growth and recombination in a sympatric pool. Symsim models a microbial population growing in an environment composed of two distinct niches, one ancestral (niche 0) and one derived (niche 1).

::DEVELOPER

The Alm lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • MatLab

:: DOWNLOAD

 symsim

:: MORE INFORMATION

Citation

PLoS One. 2013;8(1):e53539. doi: 10.1371/journal.pone.0053539.
Sympatric speciation: when is it possible in bacteria?
Friedman J, Alm EJ, Shapiro BJ.

InterSIM 2.2.0 – Simulation of Inter-Related Genomic Datasets

InterSIM 2.2.0

:: DESCRIPTION

InterSIM is an R package for Simulation of Inter-Related Genomic Datasets. It generates three inter-related genomic datasets : methylation, gene expression and protein expression.

::DEVELOPER

Fridley Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

InterSIM

:: MORE INFORMATION

Citation:

Chalise P, Raghavan R, Fridley BL.
InterSIM: Simulation tool for multiple integrative ‘omic datasets’.
Comput Methods Programs Biomed. 2016 May;128:69-74. doi: 10.1016/j.cmpb.2016.02.011. Epub 2016 Feb 27. PMID: 27040832; PMCID: PMC4833453.

forqs 2015 – Forward-in-time Simulation of Recombination, Quantitative traits, and Selection

forqs 2015

:: DESCRIPTION

forqs is a forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. forqs also also models quantitative traits and selection on those traits.

::DEVELOPER

Novembre Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 forqs

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 Feb 15;30(4):576-7. doi: 10.1093/bioinformatics/btt712. Epub 2013 Dec 10.
forqs: forward-in-time simulation of recombination, quantitative traits and selection.
Kessner D1, Novembre J.

GenePool 6 / Swimbots 1.0 – Artificial Life Simulation

GenePool 6

:: DESCRIPTION

GenePool is a computer simulation where hundreds of virtual organisms evolve swimming skills. These organisms are called “swimbots”. You can set mate preference criteria and thus influence what the swimbots consider as attractive qualities in potential mates. The most attractive swimbots get chosen most often to have little babies, and so their genetic building blocks propogate to future generations. Eventually, swimbots get better at pursuing each other, competing for food, and becoming babes to other swimbots. Local gene pools emerge which compete for sex and food (for energy to have more sex). Eventually a dominant sub-population takes over.

::DEVELOPER

JJ Ventrella

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / IPad

:: DOWNLOAD

GenePool

:: MORE INFORMATION

Neuron 1.1.20 – Simulation of Neuron

Neuron 1.1.20

:: DESCRIPTION

Neuron stimulates a neuron and monitor what happens. Pause, rewind, and move forward in time in order to observe the ions as they move across the neuron membrane.

::DEVELOPER

the PhET™ project at the University of Colorado

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Java

:: DOWNLOAD

 Neuron

:: MORE INFORMATION

Citation

Science. 2008 Oct 31;322(5902):682-3. doi: 10.1126/science.1161948.
PHYSICS. PhET: simulations that enhance learning.
Wieman CE, Adams WK, Perkins KK.

Membrane Channels 1.00 – Simulation of Membrane Channels

Membrane Channels 1.00

:: DESCRIPTION

Membrane Channels inserts channels in a membrane and see what happens. See how different types of channels allow particles to move through the membrane.

::DEVELOPER

the PhET™ project at the University of Colorado

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Java 

:: DOWNLOAD

  Membrane Channels

:: MORE INFORMATION

Citation

Science. 2008 Oct 31;322(5902):682-3. doi: 10.1126/science.1161948.
PHYSICS. PhET: simulations that enhance learning.
Wieman CE, Adams WK, Perkins KK.

Gene Machine 1.04 – Simulation of Mutations within the Lac Operon

Gene Machine 1.04

:: DESCRIPTION

Gene Machine builds a gene network! The lac operon is a set of genes which are responsible for the metabolism of lactose in some bacterial cells. Explore the effects of mutations within the lac operon by adding or removing genes from the DNA.

::DEVELOPER

the PhET™ project at the University of Colorado

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Java

:: DOWNLOAD

 Gene Machine

:: MORE INFORMATION

Citation

Science. 2008 Oct 31;322(5902):682-3. doi: 10.1126/science.1161948.
PHYSICS. PhET: simulations that enhance learning.
Wieman CE, Adams WK, Perkins KK.

Gene Expression 1.0.18 – Simulation of Gene Expression

Gene Expression 1.0.18

:: DESCRIPTION

Gene Expression expresses yourself through your genes! See if you can generate and collect three types of protein, then move on to explore the factors that affect protein synthesis in a cell.

::DEVELOPER

the PhET™ project at the University of Colorado

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Java

:: DOWNLOAD

 Gene Expression

:: MORE INFORMATION

Citation

Science. 2008 Oct 31;322(5902):682-3. doi: 10.1126/science.1161948.
PHYSICS. PhET: simulations that enhance learning.
Wieman CE, Adams WK, Perkins KK.

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