AIRnet 0.9 – Infer Gene Regulatory Networks

AIRnet 0.9

:: DESCRIPTION

The AIRnet project provides an open-source tool for inferring Gene Regulatory Networks from correlations between gene activation state changes. AIRnet uses microarray data and can read SOFT formatted family files, DataSet SOFT files, as well as other tab-separated formats.

::DEVELOPER

Computational Science Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

AIRnet

:: MORE INFORMATION

Citation:

Inferring gene regulatory networks from asynchronous microarray data with AIRnet.
Oviatt D, Clement M, Snell Q, Sundberg K, Lai CW, Allen J, Roper R.
BMC Genomics. 2010 Nov 2;11 Suppl 2:S6.

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

GRENDEL 0.2 – Gene Regulatory Network Decoding Evaluations tooL

GRENDEL 0.2

:: DESCRIPTION

GRENDEL (Gene Regulatory Network Decoding Evaluations tooL), generates random gene regulatory networks according to user defined constraints on the network topology and kinetics. It then simulates the state of each regulatory network under various user defined conditions (the experimental design) and produces simulated gene expression data.

::DEVELOPER

The Brent Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GRENDEL

:: MORE INFORMATION

Citation

Haynes B.H., Brent M.R.. 2009.
“Benchmarking regulatory network reconstruction with GRENDEL.”
Bioinformatics 25(6):801.