Augmented Syntax Diagrams (ASDs) provide a way to represent grammars of natural languages as directed graphs. Nodes represent instances (or usages) of words and phrase types in a language such as English. Edges link nodes together to indicate how instances of words and phrase types can follow one another to make up phrases, clauses, and sentences in the language.
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.
Erudite is an application for training and testing back propogation neural networks using the ANNeML (Artifical Neural Network Markup Language) XML format. It supports testing and training neural nets with CSV files and has support for randomized training sets, optional adapting learning rate, sigmoid or hyperbolic tangent transfer functions, optional bias and weight adjustment locking, and more.
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.