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.
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.
ROOT is an OO framework for large-scale scientific data analysis and data mining. It contains an efficient hierarchical OO database, a C++ interpreter, advanced statistical analysis, visualization, introspection, documentation, networking, and GUI classes. The command/scripting language is C++, and large scripts can be compiled and dynamically linked in. Using the PROOF (Parallel ROOT Facility) extension, large databases can be analyzed in parallel. The system runs on all known POSIX platforms, Windows, and MacOS X.
Entrance is a program for browsing MySQL databases. It includes a "match box" search facility that is simlar to the Mac's Spotlight. Entrance can create charts based on query results, and these charts can be zoomed and panned. Entrance also supports an innovative feature called "data painting" that allows users to select and paint data points interactively.
RapidMiner (formerly YALE) is a flexible Java environment for knowledge discovery in databases, machine learning, and data mining. Many nestable learning and preprocessing operators (including Weka) are provided. It features an XML-based graphical user interface, a plugin mechanism, and high-dimensional plotting, and provides an easy-to-use extension mechanism that makes it possible to integrate new operators and adapt the system to your personal requirements. A command line version is also included.
The NCBI C++ Toolkit provides portable libraries and applications for assisting genetic science. These include libraries for networking, SQL and BerkeleyDB access, CGI and HTML handling, ASN.1 and XML handling, sequence alignment engines, sequence retrieval engines, BLAST database engines, FLTK and OpenGL graphics toolkits, and basic system utilities.
JReferences is a program written in Java for managing bibliographic references in the BibTeXML format. Storage is done in a binary file database or, optionally, in a MySQL database. A PHP Web frontend is available. It can input BibTex, RIS, BibTeXML, and DocBook formated references.