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BioMa is a specimen based Biodiversity database Manager. It is designed to store, organize, and manipulate biodiversity-related scientific data, either for the purposes of museums, scientific collections, or research projects.
FormatCheck screens flat files looking for violations in the format of the data. It uses a set of XML files that define the rules for each file format. The Swing front-end allows the user to run the verification, view and print the errors.
Project MOVED to Codehaus New location is http://esper.codehaus.org The Esper project aims to provide a general-purpose event processing facility in Java for complex event processing of real-time, high throughput data streams.
Driver based data access layer writen in Java. With it you can execute SQL queries between data stored in different format, servers, ... if there is a driver to access them.
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A Prolog expert system supporting querying and extending the knowledge base from a command-line interface using a format oriented on natural language, with the aim of being maintainable by the domain expert (i.e. without requiring programming skills).
treecat is a simple, interactive tool that helps you classify files or database entries into an arbitrary category tree. Items are automatically classified within a taxonomy quickly and accurately, requiring single key confirmation or correction.
The Flamenco search and browse interface framework uses hierarchical faceted metadata to allow users to both refine and expand queries, while maintaining a consistent representation of a collection and seamlessly integrating keyword queries.
Microarray Explorer (MAExplorer) is a Java microarray data-mining bioinformatics program.
It includes data management, graphics, statistics, clustering, reports, gene data-filtering, user
written MAEPlugins, documentation, tutorials, demo data.
libTopo and TopoMap are tools to use, convert, analyze and display topography maps such as ETOPO2, ETOPO5 and GLOBE. TopoMap is the command line interface to convert topography databases to raw data, images, etc...
Kura is a complete, professional system for the handling of linguistic data, especially fieldwork data from small-corpus languages. It allows users to enter texts in any language and analyze those texts
T.I.DB is a Temporal Extension to the Relational Model. It is the natural evolution of the Conditions Database (ConditionsDB), used in the ATLAS/CERN experiment. T.I.DB will support future implementations in both MySQL and Oracle, PostgreSQL and others.
Yabman is a tool for managing bibliographic references. Its key features are a quality user interface, a carefully designed data model, and sophisticated three-state hierarchical reference labeling. It is currently usable but in a pre-alpha stage.
The project will produce a small standalone Java application which will allow a user to convert ESRI Shapefiles (.shp) to the Google Earth KML format. This will allow ESRI Shapefile points, lines, and polygons to be viewed in Google Earth.
UniDPI stands for Unified Database of Protein Interactions which gives access to documented interactions in several independent and heterogeneous databases disseminated on the web.
MyGCAT: My Genome Collection With Assigned Taxonomy provides for the management of extremely large sequence databases and allows for the creation of taxon specific BLAST databases. Primariliy a set of PERL scripts and a HTML interface to a MySQL database
Thetis is a Java (OS-independent) application written to allow the linguistic and statistical analysis of the Homeric and Hesiodic Epic. Current achievement is the creation of a complete (and free) Thesaurus of the Homeric and Hesiodic poems.
Musmap is a web interface to UMN mapserver. It provides users and profiles management, advanced queries and selections, automatic decodification of columns with joins, easy-to-use configuration (colors, ...)... and so on.
JudoScript is a general-purpose, Java scripting, multi-domain scripting tool/language. It combines the powers of declarative scripting for many modern tasks and general object/procedural programming. It is simple, intuitive, practical and powerful.
PSIMAP is the Protein Structural Interactome MAP, a map of all the domain level protein-protein interactions in the Protein Data Bank (PDB). PSIsoft is an archive of the software used to generate and analyse PSIMAP.
Crackleback is a Java servlet framework for back-office business systems. Its goal is to address 90% of a system's function points, to cut development costs by 90%, and to permit the business analyst--not the programmer--to build 90% of the system.
CGNS++ is an object oriented interface to provide access to CGNS (CFD General Notation System) databases. It is similar to the existing C and FORTRAN interfaces provided by www.cgns.org, but uses an object oriented abstraction of the underlying SIDS.