Biological Data Sets

BioDOM is a JAVA library for easy creation of XML files according to simple XML schemas for describing biological data. It can also be used to convert other commonly used biological (possibly non-)XML data into these new formats. Platforms: Windows, Mac, Linux

GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more. Platforms: Windows, Mac, Linux

GeoDB is a set of tools and perl modules to store, retrieve and search for information on geocaching and other geographical data sets. Platforms: Windows, Mac, BSD, Linux

A MATLAB spectral clustering package to handle large data sets (200,000 RCV1 data) on a 4GB memory general machine. We implement various ways of approximating the dense similarity matrix, including nearest neighbors and the Nystrom method. Platforms: Windows, Mac, BSD

MatrixGen is a Bioinformatics application used to generate scoring matrices from analysis of aligned Amino Acid and DNA data sets. These matrices can then be used by Clustal to generate more accurate alignments. Based upon the Henikoff BLOSUM method. Platforms: Windows, Mac, BSD, Linux

MBAS -- Macro-Biological Analysis System -- provides a set of interoperable tools for aid in the analysis of biological data. The backing database is currently PostgreSQL and the primary language is C, though some data entry tools are written in Java. Platforms: Windows, Mac, BSD, Linux

The mfBox is a Matlab toolbox for performing model-free analysis of multivariate data sets. It also plugs into SPM used for the analysis of multivariate brain recordings such as fMRI, SPECT and PET data sets. Platforms: Windows, Mac, Linux

PCGen Data Manipulation/Management - For the manipulation/management of the data sets (list files) and data structure (directory tree) used within PCGen. Platforms: Windows, Mac, Linux

MIDITrail is a MIDI player which provides 3D visualization of MIDI data sets. You can enjoy not only listening but also viewing. MIDITrail supports Standard MIDI File (format 0/1), and multiple MIDI ports. Quick Start 1. Drop you Platforms: Mac

PTC Mathcad Express is free-for-life engineering math software. You get unlimited use of the most popular capabilities in PTC Mathcad - the most powerful technical calculation software available. Easily solve, document, share and reuse vital calculations. If you download and choose the trial... Platforms: Windows, Windows 8, Windows 7, Windows Server

This class can be used to generate line, bar and 2D/3D pie graphs from multiple data sets using PHP5. Offers many style and data formatting options and an extensive readme and examples page. You can customize almost any option.It can be built from data defined in a programmatic way, with data... Platforms: Windows, *nix, PHP, BSD Solaris

This toolbox includes routines for using principal component analysis (PCA) and independent component analysis (ICA) to extract cellular signals from imaging data sets. A full description and validation of the method is provided in the paper, "Automated Analysis of Cellular Signals from... Platforms: Matlab

RNEL_DB is an object oriented database solution for large data sets that need to be stored and/or analyzed within Matlab. It provides a transparent solution for people that currently store their data in matlab-structures.Using the RNEL_DB class-definition, we created a database solution that:* is... Platforms: Matlab

qmatplot is a gnuplot-like tool for plotting data sets in either two or three dimensions. It can plot many types of 2d plots, including pixmaps and contours, and 3d surfaces. It offers a full WYSIWYG mode with multiple objects on a single page. See the sc Platforms: *nix

Data::CTable is a Perl module that helps you read, write, manipulate tabular data. SYNOPSIS ## Read some data files in various tabular formats use Data::CTable; my $People = Data::CTable->new("people.merge.mac.txt"); my $Stats = Data::CTable->new("stats.tabs.unix.txt"); ## Clean stray... Platforms: *nix

Audio::Data is a module for representing audio data to perl. SYNOPSIS use Audio::Data; my $audio = Audio::Data->new(rate => , ...); $audio->method(...) $audio OP ... Audio::Data represents audio data to perl in a fairly compact and efficient manner using C via XS to hold data as a C... Platforms: *nix

A program to find frequent item sets (also closed and maximal) with the relim algorithm (recursive elimination), which is inspired by the FP-growth algorithm, but does its work without prefix trees or any other complicated data structures. The main strength of this algorithm is not its speed... Platforms: Windows

Modular toolkit for Data Processing (MDP) is a Python data processing framework. Implemented algorithms include: Principal Component Analysis (PCA), Independent Component Analysis (ICA), Slow Feature Analysis (SFA), Growing Neural Gas (GNG), Factor Analysis, Fisher Discriminant Analysis (FDA),... Platforms: Windows, Mac, *nix, Python, BSD Solaris

Nowadays due to the yearly multiplying data comes always the claim for useful methods and algorithms that make the processing of these data easier. For the solution of this problem data mining tools come into existence, to which the clustering algorithms belong. At the Department of Process... Platforms: Matlab

ErmineJ performs analyses of gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are "doing something interesting" in the data. The software is designed to be used by biologists... Platforms: Mac