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.
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.
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.
Nazooke! Client lets people track their friends, vehicles, animals, or other things. Nazooke! Client sends the user's position in defined intervals to a remote server which will show the user's position on a map. The Nazooke! Client uses any Java GPS enabled device or any Windows Mobile 5 device. A port of this software aims to run on small specific devices that allow vehicle tracking, child tracking, or animal tracking.
Python Web Graph Generator is a threaded Web graph (Power law random graph) generator. It can generate a synthetic Web graph of about one million nodes in a few minutes on a desktop machine. It supports both directed and undirected graphs. It implements a threaded variant of the RMAT algorithm. A little tweak can produce graphs representing social networks or community networks. It can also output connected components in a graph.