Open Source Java Information Analysis Software

ProM is the comprehensive, extensible framework for process mining. Process Mining deals with the a-posteriori analysis of (business) processes using enactment logs.

Converts Google Earth KML file to a CSV file, and vice versa. This enables you to plot all custom POIs with Google Earth first before transferring them into your Garmin GPS using the POI Loader.

The National Library of New Zealand's Metadata Extraction Tool automatically extracts preservation-related metadata from digital files, then output that metadata in XML formats. It can be used through a graphical user interface or command-line interface. Please take the latest code from 'https://github.com/DIA-NZ/Metadata-Extraction-Tool.git'. The code on source forge will not be updated henceforth as it is moved to github.

A set of tools (in Java) for working with next generation sequencing data in the SAM/BAM format. Note that development has moved to GitHub at https://github.com/broadinstitute/picard and support is available on the GATK forum at http://gatkforums.broadinstitute.org/categories/ask-the-team

A real-time graph plotter. While your application is computing and logging results to a CSV file using the LiveGraph Writer API, the plotter lets you visualise and monitor the results live - by instantly plotting charts and graphs of the data.

You can install the latest Eclipse plugin version from the update site https://javahexeditor.sourceforge.io/update or the Eclipse Marketplace https://marketplace.eclipse.org/content/java-hex-editor. Older versions of the Eclipse plugin are available via the update site for the version, e.g. https://javahexeditor.sourceforge.io/update/0.5.1 You can download the latest stand-alone version and older versions on the "Files" tab.

easyrec is a recommender system that aims for easy integration of recommendations into web applications. It has a web based admin tool, and its recommendation engine is accessible through a REST API, providing methods like 'other users also bought'

Tools for mass spectrometry, especially for protein mass spectrometry and proteomics: Quantification tools, converters for Applied Biosystems (Q Star and Q Trap), calculation of in-silico fragmentation spectra, converter for Mascot result files

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.

Blunder is an automated tool for analyzing chained exceptions in Java. It's usefull for classify, generate a customized error message and a list for possible solutions.

The Citizen Privacy Service is an asynchronous component using artificial intelligence capabilities including DL decidability and first order logic provenance that provide policy decision and policy enforcement points based on the US Privacy Act of 1974.

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

EDAS2 is a web-based environmental quality data management and decision support framework

Network software for annotation and quality control of distributed data. Supported by NSF: DBI 0646266 and NSF: DBI 0960535. http://wiki.filteredpush.org

FlexibleParser (Java) is currently formed by the following independent libraries/parts: - UnitParser. It allows to easily deal with a wide variety of situations involving units of measurement. - NumberParser. It provides a common framework for all the .NET numeric types. AUTHORSHIP & COPYRIGHT I, Alvaro Carballo Garcia (varocarbas), am the sole author of each single bit of this code. All the contents of this repository can be considered public domain. For more information about my copyright/authorship attribution ideas, visit https://customsolvers.com/copyright/. IMPORTANT NOTE This project is a mirror of the repository FlexibleParser_Java in my GitHub account (varocarbas). Both versions are fully synchronised and immediately updated with any change.

FormatCheck screens flat files looking for violations in the format of the data. It uses a set of XML files that define the rules for each file format. The Swing front-end allows the user to run the verification, view and print the errors.

The Genomic Diversity and Phenotype Data Model (GDPDM) captures molecular and phenotypic diversity data. MySQL databases are used to implement the schema. This project develops software tools (written in Java, Perl, etc.) associated with this model.

HadStat is service on the cloud, allow you to analysis the data on the cloud and return the result in nice graph,this service is free, you can redistribute it and/or modify it under the terms of the GNU General Public License. this service using many technologies , like Hadoop mapreduce, HTML, PHP, Web Service applications, linux server, java, eclipse IDE, with many indicators:Simple moving average (SMA),Exponential moving average (EMA),Smoothed simple moving average (SMMA),Linear weighted moving average (LWMA )on DATA from NYSE daily prices.....

K-automaton is a new parsing (syntactic analysis) machine isomorphous to language. Implemented in Java. Can generate Java code from grammars described in EBNF.

MACOW is a formal and scalable mandatory access implementation suitable on open worlds such as the provided on Semantic Web, Autonomic Computing and Coaltions and Federations scenarios. It is able to access control on distributed systems.

The aim of MIEX (Metadata and Information Extractor from small XML documents) is to create a wrapper for the Stanford Parser, to extract and store metadata (syntactic structures, relationships among words...) from simple XML documents.

The ProM Import Framework allows to extract process enactment event logs from a set of information systems. These can be exported in the MXML format, which is the standard event log data format for Process Mining analysis techniques.

Scan, the Semantic Content ANnotator, is a semantic pipeline that helps connecting information extraction tools to semantic database. UIMA-based, it allows easy plugin-writing: information extraction, ontology control, store in RDF Repositories.

Simple-Scrape is a simple web-scraping library that allows for programmatic access to HTML code. No further techniques are needed and the library is very compact and thus easy to use.

Some Java packages and projects to simplify working with Java. Addionaly some example sourcecode for using special technics in Java.