Webcockpit is a Web application generator for reporting and monitoring applications. It generates complete JSP-based Web applications which contain charts and tables whose contents are retrieved using database queries. The charts and tables can be configured to link to each other, enabling master detail-like drill-down. You can provide your own HTML or JSP template files which are mixed with the generated JSP to provide a final Web application.
ProteomeCommons.org IO Framework is a proper Java framework for handling spectra and peak lists. The framework can read and write to a number of different spectra and peak list formats, and it provides a simple, intuitive Java object model for working with spectra or peak lists. All classes support two methods of handling peak list and spectrum data: in-memory or stream. The goal of this framework is to support all the popular MS and MSMS data formats, and to eliminate any time or effort involved in figuring out how to read and write peak list or spectrum files.
ProteomeCommons.org Java Analysis Framework is a framework for referencing common mass spectrometry data such as atoms and residues. This framework provides a programmer with an easy-to-use library for writing programs that rely on common mass spectrometry data. The framework also contains utilities such as an isotope calculator and a reference for residue abbreviations.
SIOX4Java (Simple Interactive Object Extraction) is a Java SDK that provides a generic segmentation engine for extracting the foreground from still images with little user interaction. The underlying method (which has also been integrated into GIMP) is noise and motion blur robust and can easily be adapted for the segmentation of objects in videos. The SDK also contains an experimental feature called the "Detail Refinement Brush", which enables the removal of spill colors and manual refinement of highly detailed textures.
Isobel is a framework to build complex information retrieval and analysis systems. Isobel can be functionally divided in two subsytems, Isobel Gatherer (the crawling and filtering subsystem) and Isobel Analyzer (the analysis subsystem). The two subsytems can also be used separately. Isobel Gatherer offers ready-to-use services like content fetching, scheduling, document format conversion, Hyperlink graph storage and analysis, content storage and indexing. A programmer may easily add new services. Isobel Analyzer uses the IBM UIMA architecture to reuse the analysis components developed for this architecture.
Pulga is a program for numerical simulation of dynamical systems. It is designed to provide a way for students and researchers who study dynamical systems to model them on a computer and analyze them numerically without the difficulty of traditional computer programming languages.
Kabeja is a Java library for parsing CAD data (i.e. Autodesk's DXF format) and converting to SVG (dxf2svg). You can use Kabeja from the command line or embed it into your application. It includes a plain DXF2SVGViewer and integration into the Cocoon XML Web development framework and the Inkscape SVG editor.
Ojax provides an OAI-PMH harvester to harvest metadata from multiple repositories and builds a single searchable Lucene index of this data. OJAX provides a dynamic user experience enabled by Ajax and full OpenSearch integration with the IE 7 and FireFox 2 search fields. It supports OpenSearch Discovery, OpenSearch Atom results, and OpenSearch Search Suggestions. Loosely coupled Web Services and OpenSearch Atom standard allow integration with a range of VLEs, CMSs, institutional repositories, and portals.