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.
Puggle is a desktop search engine that provides full text search over files, folders, music, photos, Web pages, and other data that are stored locally on your computer. Puggle is able to create many different indices, each with a different configuration. For example, you may have a different index for your music collection as well as your documents. Each of them can be used on demand, simply by loading it. Furthermore, Puggle supports indexing of portable devices, like USB flash drives or external hard disks. The index will be stored in the device, using relative paths, allowing you to search over the data very quickly on any computer.
Cyclone is a low-level network toolkit that provides support for HTTP 1.1 in an API very similar to the one implemented by the Tornado Web server. It has localization based on gettext with pluralization support, native support for XMLRPC and JSONRPC, native support for WebSockets (drafts 75 and 76), decent support for sending plain text or HTML email with TLS and attachments, built-in support for Redis, and support for HTTP authentication.