iVUN 1.2 – interactive Visualization of Uncertain Biochemical Reaction Networks

iVUN 1.2

:: DESCRIPTION

iVUN is a visualization toolbox which supports uncertainty-aware analysis of static and dynamic attributes of biochemical reaction networks

::DEVELOPER

iVUN Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOsX
Java

:: DOWNLOAD

iVUN

:: MORE INFORMATION

Citation

C. Vehlow, J. Hasenauer, A. Kramer, J. Heinrich, N. Radde, F. Allgoewer, and D. Weiskopf.
Uncertainty-aware visual analysis of biochemical reaction networks.
In Proceedings of IEEE Symposium on Biological Data Visualization(Biovis), pages 91–98, 2012.

BioJazz – Evolve and Design Biochemical Reaction Networks

BioJazz

:: DESCRIPTION

BioJazz is a tool for evolving and designing biochemical reaction networks using genetic algorithm (GA).

::DEVELOPER

OSS-Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Matlab

:: DOWNLOAD

BioJazz

:: MORE INFORMATION

Citation

BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling.
Feng S, Ollivier JF, Swain PS, Soyer OS.
Nucleic Acids Res. 2015 Jun 22. pii: gkv595.

SloppyCell – system for Modeling Biochemical Reaction Networks

SloppyCell

:: DESCRIPTION

SloppyCell is a software environment for simulation and analysis of biomolecular networks.

::DEVELOPER

Ryan Gutenkunst while in the groups of Jim Sethna and Chris Myers at Cornell University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac / Linux
Python

:: DOWNLOAD

SloppyCell

:: MORE INFORMATION

Citation

Christopher R. Myers, Ryan N. Gutenkunst, James P. Sethna
“Python unleashed on systems biology”
Computing in Science and Engineering 9:34 (2007);

METATOOL 5.1 – Biochemical Reaction Networks Elementary Modes Analysis

METATOOL 5.1

:: DESCRIPTION

METATOOL is a Program for computing the nullspace matrix, elementary modes and other structural properties of biochemical reaction networks.This version of Metatool consists partly of script files which are compatible with octave and Matlab and partly of shared libraries that are specific for the operating system and math program. In principle the script files provide all necessary functionality, but usage of the shared libraries makes elementary mode calculation far more efficient. The purpose of this distribution is to make the operations performed by Metatool more easily understandable and to allow the users to quickly adapt and extend the scripts according to their needs.

::DEVELOPER

Department of Bioinformatics, Biocenter, University of Würzburg, Germany

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux
MATLAB

:: DOWNLOAD

METATOOL

:: MORE INFORMATION

Citation:

A. von Kamp and S. Schuster:
Metatool 5.0: fast and flexible elementary modes analysis.
Bioinformatics 22 (15), 2006, 1930-1931