Tag: Simulation Environment

SIMUPOP 1.1.10 – Population Genetics Simulation Environment

SIMUPOP 1.1.10

:: DESCRIPTION

simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. The core of simuPOP is a scripting language (Python) that provides a large number of objects and functions to manipulate populations, and a mechanism to evolve populations forward in time. Using this R/Splus-like environment, users can create, manipulate and evolve populations interactively, or write a script and run it as a batch file. Owing to its flexible and extensible design, simuPOP can simulate large and complex evolutionary processes with ease. At a more user-friendly level, simuPOP provides an increasing number of built-in scripts that perform simulations ranging from implementation of basic population genetics models to generating datasets under complex evolutionary scenarios.

::DEVELOPER

Bo Peng, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows  / Linux / MacOsX
  • Python

:: DOWNLOAD

 SIMUPOP

:: MORE INFORMATION

Citation

Bo Peng and Marek Kimmal (2005)
simuPOP: a forward-time population genetics simulation environment.
bioinformatics, 21(18): 3686-3687.

Moose 3.2.0 – Multiscale Object-Oriented Simulation Environment

Moose 3.2.0

:: DESCRIPTION

Moose is the core of a modern software platform for the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, large networks, and systems-level processes.

::DEVELOPER

Bhalla Lab

:: SCREENSHOTS

MOOSE

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Moose

:: MORE INFORMATION

Citation

Front Neuroinform. 2008;2:6. doi: 10.3389/neuro.11.006.2008. Epub 2008 Dec 19.
PyMOOSE: Interoperable Scripting in Python for MOOSE.
Ray S, Bhalla US.

LBIBCell 0.2 – Cell-Based Simulation Environment for Morphogenetic Problems

LBIBCell 0.2

:: DESCRIPTION

LBIBCell (Lattice Boltzmann Immersed Boundary) is a 2D simulation software to study the interplay between cell and tissue mechanics and biomolecular signaling.

::DEVELOPER

Computational Biology (CoBi)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LBIBCell

:: MORE INFORMATION

Citation

LBIBCell: A Cell-Based Simulation Environment for Morphogenetic Problems.
Tanaka S, Sichau D, Iber D.
Bioinformatics. 2015 Mar 13. pii: btv147.

STSE – Spatio-Temporal Simulation Environment

STSE

:: DESCRIPTION

The STSE is a set of open-source tools provided to conduct spatio-temporal simulations in discrete structures based on microscopy images.

::DEVELOPER

The STSE Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 STSE

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2011 Apr 28;12:126. doi: 10.1186/1471-2105-12-126.
STSE: Spatio-Temporal Simulation Environment Dedicated to Biology.
Stoma S, Fröhlich M, Gerber S, Klipp E.

BISEN 1.0.6 – Biochemical Simulation Environment

BISEN 1.0.6

:: DESCRIPTION

The BISEN software package is a suite of tools for generating equations and associated computer programs for simulating biochemical systems

::DEVELOPER

The Virtual Physiological Rat Project

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • MatLab

:: DOWNLOAD

 BISEN

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Mar 15;25(6):836-7. doi: 10.1093/bioinformatics/btp069. Epub 2009 Feb 25.
BISEN: Biochemical Simulation Environment.
Vanlier J, Wu F, Qi F, Vinnakota KC, Han Y, Dash RK, Yang F, Beard DA.

Trend / jTrend 1.01 – Cellular Automata Simulation Environment

Trend / jTrend 1.01

:: DESCRIPTION

Trend is a general purpose cellular automata simulation environment with an integrated high level language compiler, a beautiful graphical user interface, and a fast, three stage cached simulation engine. This is the simulation system that was used to discover the first emergent self-replicating cellular automata rule set, and the first problem solving self-replication loop.

jTrend is a Java-based cellular automata simulator modeled after Trend. It inherits all the features of Trend such as dynamically changing cellular space sizes and defining the cellular automata rules “on the fly” using the Trend programming language.

::DEVELOPER

Complex Computation Laboratory ,Iowa State University

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /Mac OsX
  • JAVA

:: DOWNLOAD

Registration First ; Trend / jTrend

:: MORE INFORMATION

N/A