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Knime (http://www.knime.org) nodes for sequence bioinformatics. Sequime is an eclipse plug-in for the KNIME data mining platform, providing additional nodes for reading, processing and visualizing sequence information.
Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.
Enrich and query corpora in the TEI-XML vocabulary. CorpusReader manage very large corpora and corpora containing milestone annotation. It provides tools for enriching corpora with output of linguistic parsers, and for extracting quantitative information
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Cougar Squared is a new Java library for machine learning and data mining research, supporting research needs of the community. It is written by researchers for researchers. It extends the WEKA and YALE machine learning frameworks.
The system searches synonyms (and related words) in Wikipedia. WikIDF generates index database of Wikipedia (for Russian, English, and German). The continuation of this project is "wikokit" at code.google.com
Feating constructs a classification ensemble comprising a set of local models. It is effective at reducing the error of both stable and unstable learners, including SVM. For details see the paper at http://dx.doi.org/10.1007/s10994-010-5224-5.
Executable program that measures sizes and other properties of colonies arrayed in a grid format (intended for 768, 384, or 96 colonies on agar plates) from jpeg images
Data mining tool for sequences (e.g. trajectories on a map, visited web pages, etc.) that creates a succinct description of the sequences, given a taxonomy (e.g. regions and sub-regions in the map, categories and sub-categories of pages, etc.).
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The NITE XML Toolkit supports the creation, analysis, and browsing of annotated multimodal, text, or spoken language corpora, and represents both timing and rich linguistic structure. It contains libraries for developers and some end user tools.
Siafu simulates individual agents and their context, from home to city-wide scenarios. As a developer, you use the API to write your simulation for the purposes of data-set generation, test or visualization, optionally hooking it to your own application.
Regexp testing tool allows to apply group of regexps to huge arrays of data (millions or so) in order to investigate search or search/replacement possibilities of regexp group.
library for capturing, storing and visualizing timeseries data
The JTimeSeries has moved to github
Please go to https://github.com/JTimeSeries/jtimeseries
The SourceForge copy has not been maintained since Sep 2012
A java library to assist with capturing and storing timeseries data/metrics. Provides facilities to publish timeseries data across a network, a lightweight server to persist series data, and client user interface components for real time visualization
Ontea - Pattern based Semantic Annotation Platform. Ontea search or create semantic meta data from text or documents using pattern based approaches. Implementation currently includes regular expressions (regex) patterns
JGraph is the most powerful, lightweight, feature-rich, and thoroughly documented open-source graph component available for Java. See the project homepage at www.jgraph.com for information and downloads.
A lyrical analysis and classification tool focused specifically on rhyming style in rap lyrics. Functions include phonetic transcription, rhyme visualization, and rapper classification.
Contextor is a light-weight simple-to-use Java based library to help developers and researchers working with the general concept of a resource; as examples, resources can be text resources, web resources, images and videos.
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.
A graph persistence framework and associated toolkits based on a navigational query style. A default persistence engine is included for storing graph objects and properties into simple relational tables but the actual storage model is pluggable.
Open data mining platform. Provides common architecture for algorithms of various types. Efficient processing of arbitrarily large volumes of data thanks to data streaming. Weka and Rseslib partially integrated. (www.debellor.org)
Ex-Crawler is divided into 3 subprojects (Crawler Daemon, distributed gui Client, (web) search engine) which together provide a flexible and powerful search engine supporting distributed computing. More informations: http://ex-crawler.sourceforge.net