Kinsolver – Simulator for Biochemical and Gene Regulatory Networks

Kinsolver

:: DESCRIPTION

Kinsolver is a simulator for biochemical and gene regulatory networks

::DEVELOPER

Boanerges Aleman-Meza

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA
  • C++ Compiler

:: DOWNLOAD

 Kinsolver

:: MORE INFORMATION

MAmodel 20060511 – Microarray Simulator

MAmodel 20060511

:: DESCRIPTION

MAmodel is a microarray simulation model which can be used to validate different kinds of data analysis algorithms. The proposed model is unique in the sense that it includes all the steps that affect the quality of real microarray data. These steps include the simulation of biological ground truth data, applying biological and measurement technology specific error models, and finally simulating the microarray slide manufacturing and hybridization. After all these steps are taken into account, the simulated data has realistic biological and statistical characteristics.

::DEVELOPER

Computational Systems Biology Research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • MATLAB

:: DOWNLOAD

MAmodel

:: MORE INFORMATION

Citation:

M. Nykter, T. Aho, M. Ahdesmäki, P. Ruusuvuori, A. Lehmussola, and O. Yli-Harja.
Simulation of microarray data with realistic characteristics.
BMC Bioinformatics, 7(349), 2006.

ReadSim 0.12 – Simulator for Sanger and 454 Sequencing

ReadSim 0.12

:: DESCRIPTION

ReadSim is  a sequencing simulator that simulates the sequencing of reads both for Sanger and pyro-sequencing, optionally involving mate-pairs.

::DEVELOPER

Darwin Rocks Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

ReadSim

:: MORE INFORMATION

ReadSim is no longer maintained. All concepts of ReadSim are integrated into our new software MetaSim.

Ilya – Reaction-Diffusion Simulator

Ilya

:: DESCRIPTION

Ilya is a small program for Windows which simulates a reaction-diffusion model based on the Brusselator reaction scheme. Ilya simulates a 2-dimensional rectangular plane with opposite edges connected so that the plane actually forms a torus. The plane is divided up into many small area elements (one area element per screen pixel). The simulation involves computing the rates of change of two chemical species labeled X and Y as a result of both chemical transformations (Brusselator scheme) and diffusion of X and Y to and from adjacent area elements.

::DEVELOPER

PRIDE Converter Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Ilya

:: MORE INFORMATION

Ilya is freely available for educational, private study and research purposes.

BacSim – Simulator of Bacterial Growth

BacSim

:: DESCRIPTION

BacSim is a simulator for individual-based modelling of bacterial colony growth. The potential of this approach is in relating the properties of microscopic entities – cells – to the properties of macroscopic, complex systems such as biofilms. Here, the growth of a single Escherichia coli cell into a colony was studied.

::DEVELOPER

the Kreft Group at the University of Birmingham

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

BacSim the colony model and the biofilm/EPS models ; Java Source Code

:: MORE INFORMATION

Citation:

Jan-Ulrich Kreft, Ginger Booth, and Julian W. T. Wimpenny (1998)
BacSim, a simulator for individual-based modelling of bacterial colony growth.
Microbiology 144:3275-3287.

Evolver – Whole-genome Sequence Evolution Simulator

Evolver

:: DESCRIPTION

Evolver is a collection of programs designed to simulate the evolution of the nucleotide sequence of a whole genome. Evolver simulates the evolution of a representative genome of a species over periods long compared with its generation time.

::DEVELOPER

Robert Edgar , George Asimenos, Serafim Batzoglou and Arend Sidow.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Evolver

:: MORE INFORMATION

N/A

BCT 4.4 – Bacterial Chemotaxis Modelling & Simulator

BCT 4.4

:: DESCRIPTION

BCT is a text-based, deterministic simulator of the chemotaxis signal transduction pathway in E. coli. The BCT (bacterial chemotaxis) model is built from units representing the molecular components in the pathway, almost all of which can be assigned experimentally determined intracellular concentrations and enzymatic rate or binding constants.

::DEVELOPER

Bray Group: Computer Models of Bacterial Chemotaxis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac

:: DOWNLOAD

BCT

:: MORE INFORMATION

N/A