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Java/XML toolkit for research using Bayesian networks and other graphical models of probability (exact and approximate inference, structure learning, etc.)
Mars Eva Computing Environment is a JMF, JINI project that is used to provide a collaborative mission planning & execution environment for furture teams on Mars. This effort is part of a simulation for the Mars Society of Australia.
TM4 is a suite of applications for managing and analyzing microarray data. TM4 provides data storage and tracking, image analysis, normalization, data filtering, clustering and statistical analysis capabilities. Includes MADAM, Spotfinder, MIDAS, and MeV.
Auth0 Token Vault handles secure token storage, exchange, and refresh for external providers so you don't have to build it yourself.
Rolling your own OAuth token storage can be a security liability. Token Vault securely stores access and refresh tokens from federated providers and handles exchange and renewal automatically. Connected accounts, refresh exchange, and privileged worker flows included.
Maple Tree is a Java based visualization tool used by researchers in the biological sciences to visualize and graphically browse the results of analyses of gene expression data collected from microarray experiments.
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! ;)
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EcoloSim is a Simulation Framework for simple spatial models in biology and ecology, in Java.
Typical problems are behavior of a herd of cattle, growth of microbe cells and other populations.
OntoCardio is an initiative to build ontologies for the legacy Cardio Database (Resource of bioinformation on cardiovascular diseases). SMI's Protege and its OWL plug-in has been adopted as the ontology construction and programming framework.
The Java Batch System (JBS) is a batch queueing system in the
tradition of NQS and PBS for internal (Java-based) and system batch
jobs. Stand-alone operation and integration with existing batch
queueing systems, initially OpenPBS, is supported.
Annotated Gel Markup Language is a simple markup language that is being proposed to markup data obtained by 2D gel electrophorosis.The goal of AGML is to enable proteomics research move into the browsing mode of searching through existing databases.
This project will develop cross-platform Java software for interfacing with EEG devices, specifically hardware developed by the OpenEEG project (http://openeeg.sourceforge.net/).
Sequence studio main package provides classes and interfaces for various kinds of sequence alignment. Differently from regular expressions it computes similarity with two initially unknown strings. Project page provides code generating applet.
GeNetDB, contraction of Genetic Network Database, is a bioinformatic platform destined to the study of genetic regulatory networks. It contains in one place the data and the way to study them, providing the user an access to all tools needed for his work
Network Visualization is a mature part of computer science that is enjoying a good deal of growth, partially fueled by Bioinformatics. Network is a synonym for Graph, and both refer to a collection of nodes and edges.
NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.
Anthill is a framework to support the design, implementation and evaluation of P2P applications based on ideas such as multi-agent and evolutionary programming borrowed from the complex adaptive systems area.
HmmSDK is a hidden Markov model (HMM) software development kit written in Java. It consists of core library of HMM functions (Forward-backward, Viterbi, and Baum-Welch algorithms) and toolkits for application development.
A Java program to parse chemical names using IUPAC nomenclature. The output can be either a visualisation of the molecule, or in a form for other programs to use (e.g. CML).
This tool integrates and enhances publicly available genome data from different sources into a local database. Using a web browser, scientists may view and query the data, keep persistent notes, and schedule batch services (such as BLAST) from NIH.