SmartCell v4.3 Beta3 – A Cell Network Simulation Program

SmartCell v4.3 Beta3

:: DESCRIPTION

SmartCell is a program developed to provide an idea of the evolution of a network in a whole, single cell. Based on stochastic algorithms, SmartCell needs multiple runs to have mean results.

::DEVELOPER

Serrano’s laboratory

:: SCREENSHOTS

SmartCell

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

 SmartCell

:: MORE INFORMATION

Citation

SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks.
Ander M, Beltrao P, Di Ventura B, Ferkinghoff-Borg J, Foglierini M, Kaplan A, Lemerle C, Tomás-Oliveira I, Serrano L.
Syst Biol (Stevenage). 2004 Jun;1(1):129-38.

TST 1.4.3 – Tissue Simulation Toolkit

TST 1.4.3

:: DESCRIPTION

TST is a two-dimensional library for the Cellular Potts Model (Graner and Glazier 1992; Phys. Rev. Lett. 69, 2013), which is increasingly used by computational biologists to study tissue patterning and developmental mechanisms.

::DEVELOPER

The Biomodeling and Biosystems Analysis Group

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  •  Linux
  • C++ Compiler

:: DOWNLOAD

 TST

:: MORE INFORMATION

Citation

R M H Merks, & J A Glazier. (2005).
A cell-centered approach to developmental biology.
Physica A, 352(1), 113–130. doi:10.1016/j.physa.2004.12.028.

VirtualLeaf 1.0.2 – Plant Tissue Simulation

VirtualLeaf 1.0.2

:: DESCRIPTION

VirtualLeaf is a cell-based computer-modeling framework for plant tissue morphogenesis.

::DEVELOPER

The Biomodeling and Biosystems Analysis Group

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  •  Linux /Windows/MacOsX

:: DOWNLOAD

 VirtualLeaf 

:: MORE INFORMATION

Citation

VirtualLeaf: an open-source framework for cell-based modeling of plant tissue growth and development.
Merks RM, Guravage M, Inzé D, Beemster GT.
Plant Physiol. 2011 Feb;155(2):656-66. doi: 10.1104/pp.110.167619.

PetriScape 1.0 – Plugin for discrete Petri net simulations in Cytoscape

PetriScape 1.0

:: DESCRIPTION

PetriScape is a tool for discrete Petri net simulation of biological networks in Cytoscape.

::DEVELOPER

Baumbach lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

PetriScape

:: MORE INFORMATION

Citation

J Integr Bioinform. 2016 Jun 4;13(1):284. doi: 10.2390/biecoll-jib-2016-284.
PetriScape – A plugin for discrete Petri net simulations in Cytoscape.
Almeida D, Azevedo V, Silva A, Baumbach J.

PhyloSim 3.0.5 – Monte Carlo Simulation of Sequence Evolution

PhyloSim 3.0.5

:: DESCRIPTION

PhyloSim is an extensible object-oriented framework for the Monte Carlo simulation of sequence evolution written in 100 percent R.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PhyloSim

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 Apr 19;12:104.
PhyloSim – Monte Carlo simulation of sequence evolution in the R statistical computing environment.
Sipos B, Massingham T, Jordan GE, Goldman N.

IBDSim 2.0 – Simulation of Genotypic data under general Isolation by Distance models

IBDSim 2.0

:: DESCRIPTION

IBDSim is a computer package for the simulation of genotypic data under general isolation by distance models.

::DEVELOPER

Raphael Leblois

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 IBDSim

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2009 Jan;9(1):107-9. doi: 10.1111/j.1755-0998.2008.02417.x. Epub 2008 Nov 10.
IBDSim: a computer program to simulate genotypic data under isolation by distance.
Leblois R, Estoup A, Rousset F.

SLiM 3.3.1 – Forward Population Genetic Simulation

SLiM 3.3.1

:: DESCRIPTION

SLiM (Selection on Linked Mutations) is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Simulations are configured via the integrated Eidos scripting language that allows interactive control over practically every aspect of the simulated evolutionary scenarios.

::DEVELOPER

Messer Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • MacOsX
:: DOWNLOAD

SLiM

:: MORE INFORMATION

Citation

SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model.
Haller BC, Messer PW.
Mol Biol Evol. 2019 Mar 1;36(3):632-637. doi: 10.1093/molbev/msy228.

SDSE 2.0 – Simulation of DNA Sequence Evolution

SDSE 2.0

:: DESCRIPTION

SDSE is an  algorithm  to  simulate  DNA  sequence  evolution  under  a  general  stochastic  model,  including  as  particular  cases  all  the  previously  used  schemes  of  nucleotide  substitution

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

SDSE

:: REQUIREMENTS

  • DOS

:: DOWNLOAD

 SDSE

:: MORE INFORMATION

Citation:

Comput Appl Biosci. 1989 Feb;5(1):47-50.
SDSE: a software package to simulate the evolution of a pair of DNA sequences.
Oliver JL, Marín A, Medina JR.

GetCrosses 0.5b – Simulation of Offspring Genotypes from a SNPs file

GetCrosses 0.5b

:: DESCRIPTION

GetCrosses is a computer program written in Perl scripting language that simulates offspring genotypes from a SNPs file for their use in relatedness analysis. Simulations are performed along given pedigrees. Following these pedigrees, individuals are computationally crossed by randomly selecting one allele of each locus from each parent to generate the alleles of a new individual. The new individuals generated in this manner are added to the output file and can be crossed with other individuals of the pedigree.

::DEVELOPER

Castresana Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOs
  • Perl

:: DOWNLOAD

GetCrosses

:: MORE INFORMATION

Citation:

Escoda, L., González-Esteban, J., Gómez, A., and Castresana, J. (2017).
Using relatedness networks to infer contemporary dispersal: application to the endangered mammal Galemys pyrenaicus.
Molecular Ecology 26, 3343-3357.

MySSP 1.0.3.5 – Simulation of DNA Sequence Evolution across a Phylogenetic Tree

MySSP 1.0.3.5

:: DESCRIPTION

MySSP is a program for the simulation of DNA sequence evolution across a phylogenetic tree

::DEVELOPER

Michael S. Rosenberg’s Laboratory

:: SCREENSHOTS

MySSP

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MySSP

:: MORE INFORMATION

Citation

Rosenberg, M.S. (2005)
MySSP: Non-stationary evolutionary sequence simulation, including indels.
Evolutionary Bioinformatics Online 1:81–83