SimBoolNet 1.0 – Simulate the Dynamics of Signaling Transduction using Boolean networks

SimBoolNet 1.0

:: DESCRIPTION

SimBoolNet is an open source Cytoscape plugin that simulates the dynamics of signaling transduction using Boolean networks. Given a user-specified level of stimulation to signal receptors, SimBoolNet simulates the response of downstream molecules and visualizes with animation and records the dynamic changes of the network.

::DEVELOPER

Teresa Przytycka Research Group

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows/ MacOsX
Java
Cytoscape

:: DOWNLOAD

SimBoolNet

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jan 1;26(1):141-2. doi: 10.1093/bioinformatics/btp617. Epub 2009 Nov 3.
SimBoolNet–a Cytoscape plugin for dynamic simulation of signaling networks.
Zheng J1, Zhang D, Przytycki PF, Zielinski R, Capala J, Przytycka TM.

BoolNet 2.1.5 – Generation,Reconstruction and analysis of Boolean networks

BoolNet 2.1.5

:: DESCRIPTION

BoolNet is an R package for the generation, reconstruction, simulation and analysis of Boolean networks

::DEVELOPER

Medical Systems Biology, University of Ulm

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Mac OsX/ Windows
R package

:: DOWNLOAD

BoolNet

:: MORE INFORMATION

Citation

Bioinformatics. 2010 May 15;26(10):1378-80. doi: 10.1093/bioinformatics/btq124. Epub 2010 Apr 7.
BoolNet–an R package for generation, reconstruction and analysis of Boolean networks.
Müssel C1, Hopfensitz M, Kestler HA.

GeneFAtt – Computing Attractors of Synchronous and Asynchronous Boolean Networks

GeneFAtt

:: DESCRIPTION

GeneFAtt is a tool that can compute all attractors in synchronous dynamic models and asynchronous dynamic models. It is helpful for biologist to deep understand the genetic regulatory networks.

::DEVELOPER

Desheng Zheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GeneFAtt

:: MORE INFORMATION

Citation

PLoS One. 2013 Apr 9;8(4):e60593. doi: 10.1371/journal.pone.0060593. Print 2013.
An efficient algorithm for computing attractors of synchronous and asynchronous Boolean networks.
Zheng D1, Yang G, Li X, Wang Z, Liu F, He L.

BN/PBN Toolbox – Toolbox of Boolean Networks and Probabilistic Boolean Networks

BN/PBN Toolbox

:: DESCRIPTION

BN/PBN (Boolean Networks and Probabilistic Boolean Networks) is written in MATLAB and can be used to work with Boolean Networks and Probabilistic Boolean Networks. It includes functions for simulating the network dynamics, computing network statistics (numbers and sizes of attractors, basins, transient lengths, Derrida curves, percolation on 2-D lattices, influence matrices), computing state transition matrices and obtaining stationary distributions, inferring networks from data, generating random networks and functions, visualization and printing, intervention, and membership testing of Boolean functions.

::DEVELOPER

Harri Lähdesmäki andIlya Shmulevich

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows
MATLAB

:: DOWNLOAD

BN/PBN

:: MORE INFORMATION