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.
GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.
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.
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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.
E-BioFlow enables the scientists to design workflow using three different perspectives: control flow, data flow and resource perspective. The workflow tool is based on the Yawl engine and has support for BioMOBY and WSDL services and Perl and R scripts.
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.
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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.