Tag: Simulation

SimMLST 1.0 – Simulation of MLST data under a Neutral Model

SimMLST 1.0

:: DESCRIPTION

SimMLST, a coalescent method to jointly simulate MLST data and the clonal genealogy that gave rise to the sample. Such simulations are useful to make interpretations about real datasets.Multi-locus sequence typing (MLST) is a widely used method of characterization of bacterial isolates. It has been applied to over 50,000 isolates in over 50 different species and its results are freely available from the pubMLST website.

::DEVELOPER

Xavier Didelot

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 SimMLST

:: MORE INFORMATION

Citation

Didelot, Lawson and Falush (2009)
SimMLST: simulation of multi-locus sequence typing data under a neutral model
Bioinformatics (2009) 25 (11): 1442-1444.

geneRegulationSimulation – Perform Simulations for Transcription Regulation Network

geneRegulationSimulation

:: DESCRIPTION

geneRegulationSimulation (Gene Regulation Simulation Tool) is based on the computational model described in ““Faithful modeling of transient expression and its application to elucidating negative feedback regulation”” with several extensions. It consists of two programs. The first (“net2text”) implements an interface for the user and the second (“model”) performs the simulations and outputs their results.

::DEVELOPER

Laboratory of Computational Biology , Technion

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 geneRegulationSimulation

:: MORE INFORMATION

Citation

Amir Rubinstein, Vyacheslav Gurevich, Zohar Kasulin-Boneh, Lilach Pnueli, Yona Kassir, and Ron Y.Pinter,
“Faithful modeling of transient expression and its application to elucidating negative feedback regulation”,
PNAS April 10, 2007 vol. 104 no. 15 6241-6246

PNK 2e – Modeling and Simulation of Biological Processes

PNK 2e

:: DESCRIPTION

The PNK (Petri Net Kernel) 2e is a software environment for the modeling and simulation of biological processes. It was developed as part of a M.Sc. project at the University of Edinburgh, UK. The software uses Stochastic Petri Nets (SPNs), a graphical representation of Markov Jump Processes.

::DEVELOPER

Ole Schulz-Trieglaff

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 PNK

:: MORE INFORMATION

JigCell 7.1.0 – Modeling and Simulation software

JigCell 7.1.0

:: DESCRIPTION

JigCell is a modeling and simulation software that also enable parameter estimation.The goal of this project is to support building and testing models for studying complex biochemical regulatory systems in general, and the cell cycle control system in particular.

::DEVELOPER

JigCell Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

 JigCell

:: MORE INFORMATION

Citation:

Vass, M., N Allen, C.A. Shaffer, N. Ramakrishnan, L.T. Watson, and J.J. Tyson,
The JigCell Model Builder and Run Manager,
Bioinformatics 20, 18(2004), 3680-3681.

MaSK 1.3.0 – Molecular Modeling and Simulation Kit

MaSK 1.3.0

:: DESCRIPTION

MaSK (Molecular Modeling and Simulation Kit) is the software that is useful in the visualization of various molecular properties calculated by either GAMESS/Firefly or Gaussian? computational chemistry programs.

::DEVELOPER

Yevgeniy Podolyan

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MaSK

:: MORE INFORMATION

Citation

Y. Podolyan, J. Leszczynski.
MaSK: A Visualization Tool for Teaching and Research in Computational Chemistry.
Int. J. Quantum Chem. 2009, 109(1), 8-16.

ProtoMol 3.3 – Molecular Dynamics (MD) Simulation

ProtoMol 3.3

:: DESCRIPTION

ProtoMol is an object-oriented, component based, framework for molecular dynamics (MD) simulations. The framework supports the CHARMM 19 and 28a2 force fields and is able to process PDB, PSF, XYZ and DCD trajectory files. It is designed for high flexibility, easy extendibility and maintenance, and high performance demands, including parallelization. The technique of multiple time-stepping is used to improve long-term efficiency. The use of fast electrostatic force evaluation algorithms like Ewald, particle Mesh Ewald (PME), and Multigrid (MG) summation further enhances performance. Longer time steps are possible using MOLLY, Langevin Molly and Hybrid Monte Carlo, Nose-Hoover, and Langevin integrators.

::DEVELOPER

ProtoMol Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • perl/tk

:: DOWNLOAD

 ProtoMol

:: MORE INFORMATION

Citation

T. Matthey, T. Cickovski, S. S. Hampton, A. Ko, Q. Ma, M. Nyerges, T. Raeder, T. Slabach, and J. A. Izaguirre.
ProtoMol: An object-oriented framework for prototyping novel algorithms for molecular dynamics.
ACM Trans. Math. Softw., 30(3):237-265 (2004)

NAST 1.0 – Nucleic Acid Simulation Tool

NAST 1.0

:: DESCRIPTION

NAST (Nucleic Acid Simulation Toolkit) is a knowledge-based coarse-grained tool for modeling RNA structures. It produces a diverse set of plausible 3D structures that satisfy user-provided constraints based on:

1. primary sequence
2. known or predicted secondary structure
3. known or predicted tertiary contacts (optional)

Additionally, NAST can use residue-resolution experimental data (e.g. hydroxyl radical footprinting) to filter the generated decoy structures.

::DEVELOPER

NAST Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NAST

:: MORE INFORMATION

Citation

Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, Altman RB.
Coarse-grained modeling of large RNA molecules with knowledge-based potentialsand structural filters.
RNA. 2009 Feb;15(2):189-99.PMID: 19144906 (2009)

SIBSIM 2.1.3 – Phenotype Simulation in Extended Pedigrees

SIBSIM 2.1.3

:: DESCRIPTION

Sibsim is designed to simulate either genotype and/or quantitative phenotype data in family structures in a modern, easy to use and highly scaleable way. sibsim is based on XML, completely written in C++ and published under the GNU General Public License

::DEVELOPER

Daniel Franke (University Hospital Schleswig-Holstein)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • C++ Complier

:: DOWNLOAD

 SIBSIM

:: MORE INFORMATION

Citation:

Franke, Daniel, Kleensang, André, Ziegler, Andreas
SIBSIM – quantitative phenotype simulation in extended pedigrees
GMS Med Inform Biom Epidemiol 2006;2(1):Doc02

GASP 3.31 – Genometric Analysis Simulation Program

GASP 3.31

:: DESCRIPTION

GASP (Genometric Analysis Simulation Program) is a software tool that can generate samples of family data based on user specified genetic models.

:DEVELOPER

GASP Team @ NHGRI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • DEC Alpha   Digital Unix 4.0B / Silicon Graphics Challenge  IRIX 6.2 / Sun Sparcstation  SunOS 5.5

:: DOWNLOAD

 GASP

:: MORE INFORMATION

Citation:

Wilson, A.F., Bailey-Wilson, J.E., Pugh, E.W., Sorant, A.J.M. 1996.
The Genometric Analysis Simulation Program (G.A.S.P.): a software tool for testing and investigating methods in statistical genetics.
Am J Hum Genet. 59:A193.

CardioLab 3.0 – Simulation of in vivo Cardiovascular Pharmacology Experiments

CardioLab 3.0

:: DESCRIPTION

CardioLab costs less than a single dog or cat, yet can be used repeatedly to simulate chart recorder outputs of experiments on anesthetised (normal or reserpinised) animals and pithed animals. The simulated heart rate and blood pressure traces appear on screen and can be printed out.

::DEVELOPER

Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

CardioLab

:: MORE INFORMATION

Ordering