Spinneret is a structured storage engine that can be thought of as an extended tuple storage system. It takes the best aspects of relational, object, and hierarchical databases and throws away the dead weight associated with those technologies. The benefit of Spinneret is that its data model is incredibly flexible, allowing it to expose its underlying data in any number of ways. It operates similar to an object database, but without hard ties to an originating language, and can also behave like a relational database without the burden of complex joins.
ServingXML is a markup language for expressing XML pipelines and an extensible Java framework for defining the elements of the language. It defines a vocabulary for expressing flat-XML, XML-flat, flat-flat, and XML-XML transformations in pipelines. The accompanying console app supports reading content as XML files, flat files, SQL queries, or SAX events, and writing it as XML, HTML, PDF, or mail attachments. This software is especially suited for converting flat file or database records to XML, with its support for namespaces, variant record types, multi-valued fields, segments and repeating groups, hierarchical grouping of records, and row-by-row validation with XML Schema. There is also an API for embedding the software in a Java application.
Daisy is an enterprise content management solution, bridging the gap between classic Web site content management and the Wiki style of information management and discovery. It is ideally suited for intranet knowledge bases, product and/or project documentation, and management of content-rich Web sites. It consists of a repository server with powerful querying and versioning capabilities, and a Wiki-like front-end Web user interface with in-browser rich-text authoring.
UIMA SDK is a software architecture and framework for supporting the development, integration, and deployment of search and analysis technologies. It can be used to analyze large volumes of unstructured information (text, audio, video, images, etc.) to discover, organize, and deliver relevant knowledge to the client or application end user.
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.
Jiplet Container (Java SIP Servlet) is a servlet-like development and runtime environment for SIP applications. The SIP protocol is widely used for voice services over IP networks. This product enables developers to create server-side SIP applications using a component-based model similar to that envisioned by the J2EE architecture. The Jiplet container runs as a standalone server as well as a JBOSS service.
Jerimoth is a Web application that allows users to submit resumes and search for technical jobs. Jerimoth stores resumes and employment postings in a highly-structured XML format that has tremendous advantages over ad hoc formats. This format is compatible with the HR-XML standard.