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.
Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.
MayaVi is a free, cross platform, easy-to-use scientific data visualizer. It provides a powerful GUI to ease the visualization process. It is written in Python and uses the Visualization Toolkit (VTK) for the graphics. MayaVi can be scripted from other Python programs and also from the interactive Python interpreter. MayaVi includes the VTK Pipeline browser. The VTK Pipeline browser is a Python module (vtkPipeline) that enables one to view and configure the objects in the VTK pipeline graphically with a Tkinter-based GUI. The browser should work for any Python script that uses VTK. MayaVi also provides classes to pickle a VTK object and a simple class documentation browser.
Weka is a collection of machine learning algorithms for solving real-world data mining problems. It is written in Java and runs on almost any platform. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka is also well-suited for developing new machine learning schemes. The development version contains a GUI with visualization tools and direct database access.
vtkFlRenderWindowInteractor is a class which enables you to create applications with full VTK and FLTK integration and interaction. This means that VTK renders to your FLTK UI, and your FLTK UI interacts with the VTK pipelines. Standard VTK interactor styles and picking work by default. This code has been tested successfully on Linux, SGI Irix, Sun Solaris, and Windows (NT, 2000, and XP).
WilmaScope is a Java3D application that creates real-time 3D animations of dynamic graph (network) structures. It comes with a number of layout algorithm plugins, and supports the easy creation of plugins for new layout algorithms. 3D geometries for graph element glyphs and algorithms for graph generation and modification are loaded dynamically as plugins, providing an extremely flexible platform for all manner of graph visualisation applications. The system has been applied with considerable success to a number of graph visualisation problems.