NeuroSim 4 – Neurophysiology Simulations

NeuroSim 4

:: DESCRIPTION

NeuroSim for Windows is a computer program intended for use in teaching neurophysiology, primarily at the undergraduate and beginning graduate-student level. It may also provide entertainment, and perhaps some useful insights, for experienced neurophysiologists. It contains several modules, each of which simulates a particular aspect of neural function. The modules operate independently of each other, but share a common interface. The user first selects the experimental and neurophysiological parameters desired for the particular simulation, and then runs an experiment. The computer generates results that are similar to that of an oscilloscope in a genuine electrophysiological experiment. The user can then vary the parameters to explore the effects of differing conditions. NeuroSim has an intuitive interface so students can concentrate on the underlying science. The programs have been designed for maximum flexibility and configurability, so that each simulation can be used at a range of levels, from simple illustration of phenomena suitable for junior courses, through to advanced data handling and analysis. NeuroSim currently contains six modules. It has won an important prize for Technology in Learning.

::DEVELOPER

Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

NeuroSim

:: MORE INFORMATION

Ordering

Diffusion Simulator – Simple Diffusion Random Walk Simulation

Diffusion Simulator

:: DESCRIPTION

Diffusion Simulator is a simple diffusion random walk simulation. Run single trajectories or many. Compute the average distancetraveled in the x and y direction in addition to the Euclidean distance.

::DEVELOPER

PRIDE Converter Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

Diffusion Simulator

:: MORE INFORMATION

mlcoalsim 1.42 – Multilocus Coalescent Simulations

mlcoalsim 1.42

:: DESCRIPTION

mlcoalsim (Multilocus Coalescent Simulations) is an integrated software application aimed at researchers interested in molecular evolution.The application adds important new features to improve methodology (uncertainty and conditional methods for mutation and recombination), models (including strong positive selection, finite sites and heterogeneity in mutation and recombination rates) and analyses (calculating a number of statistics used in population genetics and P-values for observed data).

::DEVELOPER

Molecular Evolutionary Genetics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac OsX/ Linux
C++ Complier

:: DOWNLOAD

mlcoalsim

:: MORE INFORMATION

Citation

Sebastian E. Ramos-Onsins and Thomas Mithell-Olds.
mlcoalsim: Multilocus Coalescent Simulations.
Evolutionary Bioinformatics 2007:2 41-44.

COSMOS 5.0 / COSMOS Viewer 3.0 – Computer Simulation & Visualisation of Molecular Structures

COSMOS 5.0 / COSMOS Viewer 3.0

:: DESCRIPTION

COSMOS is the advanced software package for PC that integrates modeling, crystallography and NMR spectroscopy.

COSMOS Viewer is a freeware product for presentation of molecules. It works with files in COSMOS (*.coo) -format und files in the PDB – Protein Data Bank (*.pdb,*.ent), HYPERCHEM (*.hin), SYBYL (*.mo2), SHELX (*.res, *.ins), GAUSSIAN94,98 (*.out, *.log) and INSIGHT (*.car) format. You can use various styles for graphic representation like stick model, ball-stick model and CPK model, stereo and perspective representation. You can also messure the geometry like distances and angles and perform some calculation tools.

::DEVELOPER

COSMOS Software

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

COSMOS ; COSMOS Viewer

:: MORE INFORMATION

N/A

DarwinPond 2005 – Artificial Life Simulation

Darwin Pond 2005

:: DESCRIPTION

Darwin Pond is an imaginary gene pool, a primordial puddle of genetic surprises. More technically, Darwin Pond is an Artificial Life Simulation: a virtual world exhibiting the emergence of life-like behaviors. But it’s more than just a fun and informative thing to watch, you can participate in this artificial life simulation by building scenarios and setting up experiments.

::DEVELOPER

JJ Ventrella

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

DarwinPond

:: MORE INFORMATION

Questions Comments? … Info@Ventrella.com

Bio-SPICE Dashboard 7.0 – Viological Simulation Program for Intra- & Inter-Cellular Evaluation

Bio-SPICE Dashboard 7.0

:: DESCRIPTION

Bio-SPICE, an open source framework and software toolset for Systems Biology, is intended to assist biological researchers in the modeling and simulation of spatio-temporal processes in living cells. In addition, our goal is to develop and serve a user community committed to using, extending, and exploiting these tools to further our knowledge of biological processes.

Bio-SPICE is intended for modeling and simulation of spatio-temporal processes in living cells.

The core of the Bio-SPICE application is called the Dashboard. The Bio-SPICE Dashboard has an Update Center and allows for different tool functionality to be downloaded, data to be specified, and both to be integrated into tool chains and work flows for modeling, analysis, and simulation.

::DEVELOPER

Biospice Project Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows/ Linux / Mac OsX
JAVA

:: DOWNLOAD

Bio-SPICE Dashboard ; Tutorial ; plugin modules

:: MORE INFORMATION

Bio-SPICE is now released under the open-source Bio-SPICE BSD License.

Cellware 3.0.1 – Modeling & Simulation Tool for Modeling Cellular Transactions

Cellware 3.0.1

:: DESCRIPTION

Cellware is a new modeling and simulation tool for modeling cellular transactions.Cellware has been designed to model whole cell biochemical reactions. Besides the capabilities of simulating biochemical pathways that consist of gene regulation networks and metabolic pathways, Cellware also includes analysis tools like parameter estimation and graph layout algorithms.

Cellware has not only been designed to conduct modeling and simulation of gene regulatory and metabolic pathways but also offer an integrated environment for diverse mathematical representations, parameter estimation and optimization. In addition, a user-friendly graphical display and capability to run large and complex models would be provided by default. A very special feature of Cellware is that it would be the first grid based modeling and simulation tool in the field of Systems Biology

::DEVELOPER

Systems Biology Group ,Bioinformatics Institute, Singapore

:: SCREENSHOTS

:: REQUIREMENTS

Windows/ Linux / Mac OsX
JAVA

:: DOWNLOAD

Cellware ; manual

:: MORE INFORMATION

Citation:

Tan Chee Meng, Sandeep Somani, Li Ye, Anand Sairam, Zhu Hao, Arun Krishnan, Kishore Sakharkar, Pawan Dhar “Cellware: The Grid-Enabled Tool for Cell Modeling And Simulation”, Bioinformatics 2004