Biological Data Sets

Chart::Plot is a Perl module to plot two dimensional data in an image. SYNOPSIS use Chart::Plot; my $img = Chart::Plot->new(); my $anotherImg = Chart::Plot->new ($image_width, $image_height); $img->setData (@dataset) or die( $img->error() ); $img->setData (@xdataset, @ydataset);... Platforms: *nix

JOpenChart provides a Java library and toolkit for generating and embedding charts into applications. JOpenChart is a free Java Toolkit and library for embedding charts into different kinds of applications, no matter if they are server side, desktop or web applications. Commercial solutions are... Platforms: *nix

Chart::XMGR is a Perl object for displaying data via XMGR. SYNOPSIS use Chart::XMGR; xmgr($a, { SYMBOL => plus}; use Chart::XMGR (); $xmgr = new Chart::XMGR; $xmgr->line($pdl); $pdl->$xmgr->line; xmgr($pdl, { LINESTYLE => dotted }); Provides a perl/PDL interface to the XMGR... Platforms: *nix

Chart::GRACE is a Perl object for displaying data via Xmgrace. SYNOPSIS use Chart::GRACE; xmgrace($a, { SYMBOL => plus}; use Chart::GRACE (); $grace = new Chart::GRACE; $grace->plot($pdl); xmgrace($pdl, { LINESTYLE => dotted }); Provides a perl/PDL interface to the XMGR plotting... Platforms: *nix

Scaffold Hunter is an accessible Java-based application built for the analysis of structure-related biochemical data. The program is able to facilitate the interactive exploration of chemical space by enabling generation of and navigation in a scaffold tree hierarchy annotated with various... Platforms: Windows, Windows Vista, 7

PSPP is a program for statistical analysis of sampled data. It is a Free replacement for the proprietary program SPSS, and appears very similar to it with a few exceptions. The most important of these exceptions are, that there are no 'time bombs'; your copy of PSPP will not 'expire' or... Platforms: Windows

As an example, suppose you had taken 155 seconds of data of the location (x,y,z) of a particle as a function of time (t). It is convenient to put that all into a struct, such as this one:>> datadata = t: [155000x1 double] x: [155000x1 double] y: [155000x1 double] z: [155000x1 double]If you wanted... Platforms: Matlab

fitChiSquare is a generalized chi-square fitting routine for any model function when data measurement errors are known; it returns the model parameters and their uncertainties at the delta chi-square = 1 boundary (68% confidence interval). It also returns the chi-square and degrees of freedom... Platforms: Matlab

PathVisio is a tool for displaying and editing biological pathways. In a sense PathVisio lets you draw pathways as you would in any drawing program, like PowerPoint or Photoshop. But the difference is that PathVisio can understand the biological context of a pathway, because you can link... Platforms: Mac

InterMine is a powerful open source data warehouse system. Using InterMine, you can create databases of biological data accessed by sophisticated web query tools. Parsers are provided for integrating data from several common biological formats and there is a framework for adding your own data. Platforms: *nix

Obtain data from images of graphs scanned from articles or available as image. Import the graph into ScanIt from a scanner or file, or from the clipboard. Define locations of the graph's axes by indicating known points. Extract data from the graph by manually picking points, by scanning for... Platforms: Windows, Windows 8, Windows 7, Windows Server

openDICOM.NET software implements a new approach towards DICOM (Digital Imaging and Communications in Medicine) libraries. DICOM is a worldwide standard in Medical IT and is provided by the National Electrical Manufacturers Assocation (NEMA). This standard specifies the way medical images and... Platforms: *nix

PDL::Impatient is a PDL for the impatient. SYNOPSIS A brief summary of the main PDL features and how to use them. Perl is an extremely good and versatile scripting language, well suited to beginners and allows rapid prototyping. However until recently it did not support data structures... Platforms: *nix

GD::Graph is a graph plotting module for Perl 5. SYNOPSIS use GD::Graph::moduleName; GD::Graph is a perl5 module to create charts using the GD module. The following classes for graphs with axes are defined: GD::Graph::lines Create a line chart. GD::Graph::bars and GD::Graph::hbars... Platforms: *nix

flow-tools is a set of programs for processing and managing NetFlow exports from Cisco and Juniper routers. The tools included are: flow-capture, flow-cat, flow-dscan, flow-expire, flow-export, flow-fanout, flow-filter, flow-gen, flow-header, flow-import, flow-mask, flow-merge, flow-nfilter,... Platforms: *nix

ObjStore::Internals is a Perl module with a few notes on the implementation. SYNOPSIS You dont have to understand anything about the technical implementation. Just know that: ObjectStore is outrageously powerful; sophisticated; and even over-engineered. The perl interface is optimized to... Platforms: *nix

Berkeley DB Java Edition is a high performance, transactional storage engine written entirely in Java. Like the highly successful Berkeley DB product, Berkeley DB Java Edition executes in the address space of the application, without the overhead of client/server communication. Berkeley DB Java... Platforms: *nix

Transparent Parallel I/O Environment is a software environment (written in C++) that facilitates the implementation of external memory algorithms. The goal of theoretical work in the area of external memory algorithms (also called I/O algorithms or out-of-core algorithms) has been to develop... Platforms: *nix

Bio::GMOD is a unified API for Model Organism Databases. SYNOPSIS Check the installed version of a MOD use Bio::GMOD::Util::CheckVersions.pm my $mod = Bio::GMOD::Util::CheckVersions->new(-mod=>WormBase); my $version = $mod->live_version; Update a MOD installation use Bio::GMOD::Update;... Platforms: *nix

KoalaCalc is a free multi-purpose calculator for Mac OS X. In its compacted state, it looks similar to the standard calculator that comes with Mac OS X. However, simply click the 'advanced features' box and KoalaCalc comes to life to become one of the most advanced scientific, conversion,... Platforms: Mac