BioJava aims to provide a comprehensive set of Java components for the rapid development of applications in Bioinformatics. It contains interfaces for representing Sequences, Features, and other important bioinformatics concepts. It can also read and write sequence data in a variety of common formats and communicate with Ensembl databases and with DAS and BioCorba servers.
eXtace is a visual sound display/analysis program. It requires Esound (esd) for its audio source. It includes various fast fourier transforms of the audio data in realtime. Its displays include a 3D wireframe flying landscape, a 3D textured flying landscape, a 16-256 channel graphic EQ, three types of scopes, a 3D "spike" flying landscape, and two forms of spectragrams. The 3D traces can be picked up, manipulated, and displayed at nearly any angle. eXtace also features a 3D direction control widget for controlling the angle and speed at which the trace runs away and a gradient/colormap editor for changing the colormap to suit your needs. No OpenGL is required.
Flounder is a program to quickly visualize 4D data (x,y,z,t). It can produce isosurfaces, solid renderings, as well as 2D slices. Several data sets can be viewed simultaneously. Temporal data at a spatial location can be examined with output in several formats including PNG and GIF animations.
graphviz is a set of graph drawing tools and libraries. It supports hierarchical and mass-spring drawings; although the tools are scalable, their emphasis is on making very good drawings of reasonably-sized graphs. Package components include batch layout filters and interactive editors for X11, Java, and a TCL/tk extension. The batch filters can be configured as a web visualization service (using GIF and click-maps). Typical applications include display of finite state machines, software diagrams, database schemas, and communication networks.
GtkDatabox is a widget for the GTK+ library designed to display large amounts of numerical data quickly and easily. It allows for one or more data sets of thousands of data points (X and Y coordinates) to be displayed and updated in split seconds. It offers the ability to zoom into and out of the data, and to navigate through your data by scrolling. In addition to rulers and a simple coordinate cross, it allows you to add one (or even more) configurable grids like on an oscilloscope. Data may be presented as dots, lines connecting the data, or vertical bars. The widget allows you to easily transform pixel coordinates into data coordinates, thus allowing you to easily create powerful applications for data analysis.
IBM OpenDX, the successor to IBM Visualization Data Explorer, (known simply as DX) is a general-purpose software package for data visualization and analysis. It employs a data-flow driven client-server execution model and provides a graphical program editor that allows the user to create a visualization using a point and click interface. Applications can also be built on top of portions of the Data Explorer system, so that custom, turnkey applications can be easily developed using DX as the computational and rendering engine.