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Maximum entropy is a powerful method for constructing statistical models of classification tasks, such as part of speech tagging in Natural Language Processing. Several example applications using maxent can be found in the OpenNLP Tools Library.
EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
Anna is lightweight Java framework to build pipeline systems of any kind.
It will take care of recurrent needs such as dependency management, data serialisation and synchronization as well as parallelization of execution.
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Wikipedia Concept Association Map (WCAM) is new approach for textual knowledge representation and understanding. All concepts and associations are stored in a graph database for better performance and easy distribution.
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.
vMAGIC is a Java-API which helps creating VHDL generators and analyzers. vMAGIC comprises three parts: 1st a VHDL'93 compliant parser, 2nd a programming model to easily create and modify VHDL constructs, and 3rd a VHDL Writer to generate code.
Elly is a reasoner for entailment and satisfiability checking of ELP knowledge-bases. It is written in java and relies on the IRIS Datalog reasoner (https://sourceforge.net/projects/iris-reasoner) for its implementation.
The Evolutionary Environment Simulator (EvESimulator) is an agent-based economy simulation framework which provides a broader view on evolutionary aspects within a Digital Business Ecosystem.
Decimal floating point library in Java. Provides decimal floating point math for Java via a clean, easy to understand implementation. Much easier to use than Big Decimal, nearly IEEE-854 compliant. Compatible with J2ME, so it can be used on PDAs/phon
netcdf-tools is a set of tools for creating netCDF files. It supports command line use on both Windows and Unix as well as use directly as a Java library. Written by CSIRO Australia and funded by the ANDS Australian Research Data Commons Project
A Java application used in whole genome analysis to display SNPs in a genomic context. Supplementary data is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.
Example-based Modeling (EMO) is an tool to create data models, with examples, using a web interface. You interactively create a web-accessible database of models and samples for those models. A white paper describes the underlying assumptions.