GRAL is a library for creating high quality plots and charts in Java. Many plot types are available like scatter plot, bubble plots, line plots, area plots, pie charts, and bar charts. Additionally, GRAL can exchange and process data (smoothing), and various plug-ins allow the import and export of data and graphics to formats like CSV, JPEG, PNG, EPS, PDF, or SVG.
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.
The National Space Science Data Center's (NSSDC) Common Data Format (CDF) is a self-describing data abstraction for the storage and manipulation of multidimensional data in a platform- and discipline-independent fashion. It consists of a scientific data management package (known as the "CDF Library") that allows programmers and application developers to manage and manipulate scalar, vector, and multi-dimensional data arrays.
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.
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.
Red-Piranha is a search system that can actually learn what you are looking for. It can be used as a Web page, command line, or XML-WebService, so it will work with most languages, including Java, Perl, C#/.NET, and PHP. It includes learning abilities for the Desktop/Internet search functionality. All feedback from the user is stored in (editable) XML and RDF, and is used by the system to improve the quality of searches.
The Storage Resource Broker is client-server middleware that provides a uniform interface for connecting to heterogeneous data resources over a network and accessing replicated data sets. It, in conjunction with the Metadata Catalog (MCAT), provides a way to access data sets and resources based on their attributes and/or logical names rather than their names or physical locations.