CABERNET 1.1 – A Cytoscape APP for Augmented Boolean Models of Gene Regulatory Networks

CABERNET 1.1

:: DESCRIPTION

CABERNET is a Cytoscape 3.2.0 app for the generation, the simulation, the analysis and the visualization of Boolean models of gene regulatory networks, particularly focused on the investigation of their robustness.

::DEVELOPER

Data and Computational Biology @ University of Milan – Bicocca.

:: SCREENSHOTS

::REQUIREMENTS

Linux/windows/MacOsX
Java
Cytoscape

:: DOWNLOAD

CABERNET

:: MORE INFORMATION

Citation

CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks.
Paroni A, Graudenzi A, Caravagna G, Damiani C, Mauri G, Antoniotti M.
BMC Bioinformatics. 2016 Feb 4;17(1):64. doi: 10.1186/s12859-016-0914-z.

minRect 1.0.2.1 – Metabolic Network Pathway Design tool on a Boolean model

minRect 1.0.2.1

:: DESCRIPTION

minRect is a new metabolic network pathway design tool on a Boolean model for finding the minimum number of reactions from a reference network, so that the target compound becomes producible in the host network.

::DEVELOPER

Takeyuki Tamura

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
g++
GNU Make
CPLEX

:: DOWNLOAD

minRect

:: MORE INFORMATION

Citation:

Wei Lu,Takeyuki Tamura,Jiangning Song and Tatsuya Akutsu,
“An Integer Programming-based method of designing synthetic metabolic networks by Minimum Reaction Insertion”
PLoS One. 2014 Mar 20;9(3):e92637. doi: 10.1371/journal.pone.0092637. eCollection 2014.