The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
BANNER is a named entity recognition system intended primarily for biomedical text. It uses conditional random fields as the primary recognition engine and includes a wide survey of the best techniques described in recent literature.
An api for domain level interaction with SNOMED CT and an implementation based on a storage engine using a native SNOMED distribution stored in neo4j as a backend.
Trial Criteria Online Data Entry (trialCODE): a Java-based user interface that codifies eligibility requirements used to automate the screening of potential subjects to clinical trials. Used for caMATCH screening engine on BreastCancerTrials.org site.
Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.
Conrad is both a high performance Conditional Random Field engine which can be applied to a variety of machine learning problems and a specific set of models for gene prediction using semi-Markov CRFs.
Simulare is a simulation engine and application built on java. At first it'll simulate an aquarium but planned to evolve latter. One objective is a simple UI so everybody can use it. Imagine a fish farmer optimizing his production with this software! ;)
This projects intends to develop a complete distributed peer-to-peer environment
for running heuristic optimization, modelling, artificial life, etc applications. This involves a network engine, libraries and different user interfaces. All this in java.