GRASS (the Geographic Resources Analysis Support System) is a software raster- and vector-based GIS (Geographic Information System), image processing system, graphics production system, and spatial modeling system. It contains many modules for raster data manipulation, vector data manipulation, rendering images on the monitor or paper, multispectral image geocoding and processing, point data management and general data management. It also has tools for interfacing with digitizers, scanners, and the PostgreSQL, DBF, and ODBC connected databases. GRASS operates on all common operating systems.
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.
Tulip is an information visualization framework dedicated to the analysis and visualization of relational data. Tulip aims to provide the developer with a complete library, supporting the design of interactive information visualization applications for relational data that can be tailored to the problems being faced. Written in C++, the framework enables the development of algorithms, visual encodings, interaction techniques, data models, and domain-specific visualizations. One of the goals of Tulip is to facilitate the reuse of components, and it allows developers to focus on programming their application. This development pipeline makes the framework efficient for research prototyping as well as the development of end-user applications. The framework also provides a complete software for visual analysis of relational data having attributes.
The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.
FLENS is short for Flexible Library for Efficient Numerical Solutions. This C++ can be used as a builing block for the implementation of other (higher-level) numerical libraries or numerical applications. It is a C++ library (requires a C++11 conform compiler). Easy install, as FLENS is headers only. It gives you Matrix/vector types for dense linear algebra; a generic (i.e. templated) implementation of BLAS; and a generic reimplementation of LAPACK. If high performance BLAS libraries like ATLAS, GotoBLAS, etc. are available, you simply can link against them and boost performance.
SDE for NetBeans is a UML modeling environment tightly integrated with NetBeans. It lets you draw all types of UML diagrams (use case diagram, class diagram, sequence diagram, activity diagram, etc.) in NetBeans, reverse source code (Java, C++, XML, XML Schema, CORBA IDL, etc.) to UML models, and generate Java source from UML diagrams. It features a Rational Rose importer, an XMI importer, HTML/PDF documentation generators, and plug-in and template support.
Julius MV1 is a showcase application for the Julius framework. It can be used as a fully functional DICOM 3.0 or RAW volume viewer as well as a viewer for large polymesh datasets. It also provides basic data processing features such as volume segmentation or polymesh decimation. Julius MV1 can be used as a basis and testbed for other applications developed with the Julius Framework. The Julius Framework (which comes bundled with MV1) is a general software architecture for medical visualization, simulation, and navigation.
Jeff's Java Scanf Library is an implementation of the C-Runtime scanf, fscanf, and sscanf functions. The syntax of format strings is very similar (%*s, %3d, etc.) to that of the standard C implementation of scanf. Instead of taking wrapper objects, all scanf functions return an Object, whose types can be inferred from the format string.
BALLView is an extensible viewer for bio-molecular structures. It provides all standard models and offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER, CHARMM, and MMFF94 force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, secondary structure calculation, molecular editing and docking. Since BALLView is based on BALL (the Biochemical ALgorithms Library), it is easily extensible on the level of C++ code. In addition, it provides a Python interface with Integrated Development Environment features to allow interactive rapid prototyping.