Lattice Microbes 2.3 – Simulation method for the Reaction-diffusion Master Equation

Lattice Microbes 2.3

:: DESCRIPTION

Lattice Microbes is a software package for efficiently sampling trajectories from the chemical and reaction-diffusion master equations (CME/RDME) on high performance computing (HPC) infrastructure using both exact and approximate methods.

::DEVELOPER

The Luthey-Schulten Group – University of Illinois at Urbana-Champaign

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
VMD

:: DOWNLOAD

Lattice Microbes

:: MORE INFORMATION

Citation

Elijah Roberts, John E Stone, and Zaida Luthey-Schulten.
Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation,
J.Comp.Chem, 34(3):245-255, 2013.

HGT_simul 1.2 – Phylogenomic Simulation

HGT_simul 1.2

:: DESCRIPTION

HGT_simul implements the phylogenomic simulation procedure described in:
Galtier N. 2007. A model of horizontal gene transfer and the bacterial phylogeny problem. Systematic Biology (in press)
The underlying model incorporates horizontal gene transfers between lineages, gene tree depth, genome-wide or gene-specific departure from the molecular clock, across-site rate variation, and various nucleotide or amino-acid substitution processes.

::DEVELOPER

Nicolas Galtier – galtier@univ-montp2.fr

:: SCREENSHOTS

N/A

::REQUIREMENTS

Windows / Linux/ MacOsX
C++ Compiler

:: DOWNLOAD

HGT_simul

:: MORE INFORMATION

Syst Biol. 2007 Aug;56(4):633-42.
A model of horizontal gene transfer and the bacterial phylogeny problem.
Galtier N.

MDWeb / MDMoby – Web-based Platform for Molecular Dynamics Simulations

MDWeb / MDMoby

:: DESCRIPTION

MDWeb is a personal workspace providing standard protocols to prepare structures, run standard molecular dynamics simulations and to analyze trajectories. MDWeb and MDMoby constitute a web-based platform to help access to molecular dynamics (MD) in the standard and high-throughput regime. The platform provides tools to prepare systems from PDB structures mimicking the procedures followed by human experts. It provides inputs and can send simulations for three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis of trajectories, either provided by the user or retrieved from our MoDEL database are also incorporated.

::DEVELOPER

the Molecular Recognition & Bioinformatics Group.

:: SCREENSHOTS

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations.
Hospital A, Andrio P, Fenollosa C, Cicin-Sain D, Orozco M, Gelpí JL.
Bioinformatics. 2012 May 1;28(9):1278-9. Epub 2012 Mar 21.

GNA 8.7.1.1 – Modelling & Simulation of Genetic Regulatory Networks

GNA 8.7.1.1

:: DESCRIPTION

GNA (Genetic Network Analyzer) is a computer tool for the qualitative modeling and simulation of genetic regulatory networks. GNA assists you in constructing a model of a genetic regulatory network using knowledge about regulatory interactions in combination with gene expression data. Moreover, it allows you to simulate the qualitative behavior of the network in response to external perturbations. The mathematical models created with GNA can be tested against observed properties of the network.

::DEVELOPER

Bruno Besson, Hidde de Jong, Pedro Monteiro, and Michel Page.

:: SCREENSHOTS

:: REQUIREMENTS

Windows/MacOsx/Linux
Java

:: DOWNLOAD

GNA

:: MORE INFORMATION

Citation

Methods Mol Biol. 2012;804:439-62. doi: 10.1007/978-1-61779-361-5_22.
Genetic network analyzer: a tool for the qualitative modeling and simulation of bacterial regulatory networks.
Batt G1, Besson B, Ciron PE, de Jong H, Dumas E, Geiselmann J, Monte R, Monteiro PT, Page M, Rechenmann F, Ropers D.

H. de Jong, J. Geiselmann, C. Hernandez, M. Page (2003),
Genetic Network Analyzer : Qualitative simulation of genetic regulatory networks,
Bioinformatics, 19(3):336-344

SIMLA 3.3 – SIMulation of Pedigree Data for Linkage and Association Studies

SIMLA 3.3

:: DESCRIPTION

SIMLA (SIMulation of pedigree data for Linkage and Association studies) is a SIMulation program that generates data sets of families for use in Linkage and Association studies. It allows the user flexibility in specifying marker and disease placement, locus heterogeneity, disequilibrium between markers and between markers and disease loci. Output is in the form of a LINKAGE pedigree file and is easily utilized, either directly or with minimal reformatting, as input for various genetic analysis packages.

::DEVELOPER

Duke Molecular Physiology Institute

:: SCREENSHOTS

:: REQUIREMENTS

Linux / MacOsX / Windows
Java

:: DOWNLOAD

SIMLA

:: MORE INFORMATION

Citation

Schmidt MA, Hauser ER, Martin ER, Schmidt S.
Extension of the SIMLA package for gener ating pedigrees with complex inheritance patterns: Environmental covariates, gene-gene and gene-environment interaction.
Stat Appl Genet Mol Biol 4(1): article 15, 2005.

Protein Purification 1.8.0 – Protein Purification Simulation

Protein Purification 1.8.0

:: DESCRIPTION

Protein Purification is the latest version of the award-winning program that has been widely used in schools, colleges and universities since 1983. Its built-in tutorial aims to guide you through a simulation of some of the more commonly-used protein separation techniques and to let you experiment with the simulation. It starts off by letting you examine how a simple mixture of proteins behaves during gel filtration and ion-exchange chromatography and then goes on to allow the design and testing of full purification protocols using more complex mixtures of proteins.

::DEVELOPER

Andrew Booth

:: SCREENSHOTS

:: REQUIREMENTS

iPad/iPhone/Windows/Android

:: DOWNLOAD

Protein Purification

:: MORE INFORMATION

VGLII 3.3.1 – Interactive Simulation of Mendelian Genetics

VGLII 3.3.1

:: DESCRIPTION

VGLII (The Virtual Genetics Lab) is a simulation of transmission genetics that approximates, as closely as possible, the hypothesis-testing environment of genetics research. In this lab, students cross hypothetical creatures and examine the progeny in order to determine the mechanism of inheritance of a particular trait. As in actual research, it is not possible to ‘see the answer’ – the student must decide for herself when she has collected enough data to be sure of her model. The goal is to have students understand the logic of genetic analysis – how one can use crosses to determine how a trait is inherited and reinforce their understanding of transmission genetics.

::DEVELOPER

VGL Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOSX
Java

:: DOWNLOAD

VGLII

:: MORE INFORMATION

ALF 1.0 – Simulation Framework for Genome Evolution

ALF 1.0

:: DESCRIPTION

ALF simulates a wide range of evolutionary forces that act on genomes, such as character substitutions, indels, gene duplication, gene loss, lateral gene transfer and genome rearrangement.

::DEVELOPER

ALF team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Mac / Linux

:: DOWNLOAD

ALF

:: MORE INFORMATION

Citation

Daniel A Dalquen, Maria Anisimova, Gaston H Gonnet, Christophe Dessimoz:
ALF – A Simulation Framework for Genome Evolution.
Mol Biol Evol, 29(4):1115-1123, April 2012.

PopBio 3.0.3 – Population Biology Simulation package

PopBio 3.0.3

:: DESCRIPTION

“PopBio” is a population biology simulation package. It contains components for population growth, population genetics, predator/prey interactions, and interspecific competition.The program has an extremely versatile interface that students have found very easy to use. Stochastic options allow for the design of experiments and both graphic and numerical outputs allow for export to other statistical programs.

::DEVELOPER

Biology Department, Reed College

:: SCREENSHOTS

N/A

::REQUIREMENTS

MacOsX

:: DOWNLOAD

PopBio

:: MORE INFORMATION

SLINK 3.02 – Simulation program for Linkage Analysis

SLINK 3.02

:: DESCRIPTION

The program SLINK is a general computer simulation program that employs a variation of the algorithm described by Ott (1989). Suppose there are N people in a pedigree. Let x = (x1,x2,…,xN) represent the vector of phenotypes of the N people in the pedigree. Likewise, let g = (g1, g2,…,gN) represent the vector of multi-locus genotypes including phase information.

::DEVELOPER

Division of Statistical Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOS
C++ Compiler
LINKAGE

:: DOWNLOAD

SLINK

:: MORE INFORMATION

Citation:

Hum Hered. 2011;71(2):126-34. doi: 10.1159/000324177. Epub 2011 Jul 6.
Coordinated conditional simulation with SLINK and SUP of many markers linked or associated to a trait in large pedigrees.
Schäffer AA1, Lemire M, Ott J, Lathrop GM, Weeks DE.

Weeks DE, Ott J, Lathrop GM (1990)
SLINK: a general simulation program for linkage analysis.
Am J Hum Genet 47:A204