:: DESCRIPTION
PAAT is a peptide abundance statistical processing tool
::DEVELOPER
Computational Biology & Bioinformatics ,Pacific Northwest National Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: 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
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The ACT (aggregation and correlation toolbox) is an aggregation and correlation toolbox for analyses of genome tracks.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Jee*, J Rozowsky*, KY Yip*, L Lochovsky, R Bjornson, G Zhong, Z Zhang, Y Fu, J Wang, Z Weng, M Gerstein.
ACT: Aggregation and Correlation Toolbox for Analyses of Genome Tracks. (2011)
Bioinformatics. 2011 Apr 15;27(8):1152-4.
:: DESCRIPTION
BicAT is a graphical user interface software for the analysis of gene expression data. It provides five biclustering and two standard clustering algorithms.
::DEVELOPER
the Systems Optimization Group, Institut TIK, ETH Zürich
:: SCREENSHOTS
:: REQUIREMENTS
:: MORE INFORMATION
Citation
Barkow, S., Bleuler, S., Prelic, A., Zimmermann, P., and E. Zitzler.
BicAT: a biclustering analysis toolbox,
Bioinformatics, 2006 22(10):1282-1283
:: DESCRIPTION
SBMLToolbox is built on top of libSBML and provides a set of basic functions allowing SBML models to be used in MATLAB. SBMLToolbox provides functions for reading, writing, and validating SBML models; viewing model structures in a simple GUI; converting models into a symbolic form suitable for use with MATLAB’s Symbolic Math Toolbox; and simulate models using MATLAB’s ordinary differential equation solvers.
SBMLToolbox works by translating SBML models to/from a MATLAB structure calledMATLAB_SBML. It provides facilities for manipulating this and its substructures within MATLAB, as well as functions for saving and loading MATLAB_SBML structures to/from MATLAB data files.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Keating, S. M., Bornstein, B. J., Finney, A., and Hucka M. (2006) SBMLToolbox: an SBML toolbox for MATLAB users. Bioinformatics, 22(10):1275–1277.
