Stretching DNA 2.08 – Simulations of Stretching DNA

Stretching DNA 2.08

:: DESCRIPTION

Stretching DNA explores stretching just a single strand of DNA using optical tweezers or fluid flow. Experiment with the forces involved and measure the relationship between the stretched DNA length and the force required to keep it stretched. Is DNA more like a rope or like a spring?

::DEVELOPER

the PhET™ project at the University of Colorado

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac OsX / Linux
Java

:: DOWNLOAD

Stretching DNA

:: 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.

TESS 2.1.0 – Simulation of Reconstructed Phylogenetic Trees under Time-dependent Birth-death Processes

TESS 2.1.0

:: DESCRIPTION

TESS is an R-package for simulation of reconstructed phylogenetic trees under global, time-dependent birth-death processes. Speciation and extinction rates can be any function of time and mass-extinction events at specific times can be provided. Trees can be simulated either conditioned on the number of species, the time of the process, or both. Additionally, the likelihood equations are implemented for convenience and can be used for Maximum Likelihood (ML) estimation and Bayesian inference.

::DEVELOPER

HöhnaLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX / Windows
R package

:: DOWNLOAD

TESS

:: MORE INFORMATION

Citation

TESS: An R package for efficiently simulating phylogenetic trees and performing Bayesian inference of lineage diversification rates.
Höhna S, May MR, Moore BR.
Bioinformatics. 2015 Nov 4. pii: btv651.

Bioinformatics. 2013 Jun 1;29(11):1367-74. doi: 10.1093/bioinformatics/btt153
Fast simulation of reconstructed phylogenies under global, time-dependent birth-death processes.
Höhna S.

HapSim 0.31 – Haplotype Data Simulation

HapSim 0.31

:: DESCRIPTION

HapSim is a package for haplotype data simulation. Haplotypes are generated such that their allele frequencies and linkage disequilibrium coefficients match those estimated from an input data set.

::DEVELOPER

Giovanni Montana

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R package

:: DOWNLOAD

HapSim

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Dec 1;21(23):4309-11. Epub 2005 Sep 27.
HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients.
Montana G.

survGenesInterim 1.0 – Simulation of Survival Studies with Microarray Data

survGenesInterim 1.0

:: DESCRIPTION

survGenesInterim is an R package for simulation of survival studies based on simulated gene expression level and patient data. Includes functions to generate such data. Resulting error and power rate can be visualized.

::DEVELOPER

survGenesInterim team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
R

:: DOWNLOAD

survGenesInterim

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Apr 29;12:127. doi: 10.1186/1471-2105-12-127.
Sequential interim analyses of survival data in DNA microarray experiments.
Leha A1, Beissbarth T, Jung K.

GEMSiRV 20130911 – GEnome-scale Metabolic Model Simulation, Reconstruction and Visualization

GEMSiRV 20130911

:: DESCRIPTION

GEMSiRV is a software platform to provide functionalities of easy metabolic network drafting and editing, amenable network visualization for experimental data integration and flux balance analysis tools for simulation studies.

::DEVELOPER

GEMSiRV team

:: SCREENSHOTS

:: REQUIREMENTS

Linux/ Windows/ MacOsX
Java

:: DOWNLOAD

GEMSiRV

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jul 1;28(13):1752-8. doi: 10.1093/bioinformatics/bts267. Epub 2012 May 4.
GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization.
Liao YC1, Tsai MH, Chen FC, Hsiung CA.

SimFlu 1.0 – Simulation tool for predicting the Variation Pattern of Influenza A virus

SimFlu 1.0

:: DESCRIPTION

SimFlu ( Simulation tool for influenza virus) performs the sequence simulations using the codon variation patterns of influenza A viruses over time.

::DEVELOPER

KISTI & LCBB(Laboratory of Computational Biology & Bioinformatics, SNU)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX

:: DOWNLOAD

SimFlu

:: MORE INFORMATION

Citation

SimFlu: A simulation tool for predicting the variation pattern of influenza A virus.
Ahn I, Kim HY, Jung S, Lee JH, Son HS.
Comput Biol Med. 2014 Jun 16;52C:35-40. doi: 10.1016/j.compbiomed.2014.06.003.

Virtual Cat 3.0.0 – Simulation of an Anaesthetised Cat Experiment

Virtual Cat 3.0.0

:: DESCRIPTION

The Virtual Cat is a simulation of an anaesthetised cat experiment – a whole animal preparation which is used as a tool for screening the actions of pharmaceutical compounds on the cardiovascular and skeletal muscle systems. The simulation displays the effects of drugs on the cat’s blood pressure, heart rate, skeletal muscle and nictitating membrane contractions.

::DEVELOPER

the Strathclyde Institute of Pharmacy and Biomedical Sciences

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

Virtual Cat

:: MORE INFORMATION

simGWAS 0.2.0-2 – Simulation of case-control GWAS Summary Statistics

simGWAS 0.2.0-2

:: DESCRIPTION

simGWAS is a fast method for simulation of large scale case-control GWAS (genome-wide association study) summary statistics

::DEVELOPER

Wallace group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

linux/ Windows/ MacOsX
R

:: DOWNLOAD

simGWAS

:: MORE INFORMATION

Citation

Fortune MD, Wallace C.
simGWAS: a fast method for simulation of large scale case-control GWAS summary statistics.
Bioinformatics. 2019 Jun 1;35(11):1901-1906. doi: 10.1093/bioinformatics/bty898. PMID: 30371734; PMCID: PMC6546134.

Rosetta 3.13 – Simulation and Design of Protein

Rosetta 3.13

:: DESCRIPTION

ROSETTA is a software suite for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.

::DEVELOPER

Rosetta Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Rosetta

:: MORE INFORMATION

Citation

Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, Ban YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popovi? Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P (2011)
ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules
Methods Enzymol 487:545-74

pDynamo 1.9.0 – Simulation of Molecular Systems

pDynamo 1.9.0

:: DESCRIPTION

pDynamo is an open source program library that has been designed for the simulation of molecular systems using quantum chemical (QC), molecular mechanical (MM) and hybrid QC/MM potential energy functions.

::DEVELOPER

pDynamo Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux /Mac OsX / Windows
python

:: DOWNLOAD

pDynamo

:: MORE INFORMATION

Citation:

M. J. Field,
The pDynamo Library for Molecular Simulations using Hybrid Quantum Mechanical and Molecular Mechanical Potentials,
J. Chem. Theo. Comp. 4, 1151–1161 (2008)