The Internet Document And Report Server (IDRS) is a full Web development platform. All pages are built using an XML like dialect called the Reporting Markup Language (RML), can be generated using data from any JDBC complient database, and mostly require no programming logic. For reports that do require programming logic, RML pages can also use external Java classes and embedded JPython and BeanShell scripts for a higher level of control. Features of the IDRS include user-based security, data connection pooling for use by both the central IDRS system and by individual reports, and multiple databases to be used for each report and JSP.
libGlass is a scalable set of components that can be used by applications to perform distributed computing. Applications are built by reusing the available components as needed. One of the major goals of Glass is to be a user-friendly framework, not only suitable for new applications, but also for legacy code. This is an important feature, as most available solutions for distributed computing require a substantial amount of rewrite of legacy code.
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.