Open Source Java Scientific/Engineering Software - Page 54

CHIRIS (Canada Health Infoway Reference Implementation Suite) is a demonstration of Electronic Health Record (EHR) interoperability messaging created by Canada Health Infoway. The project demonstrates and proves Patient Registry interoperability messagin

CRFTagger: Conditional Random Fields Part-of-Speech (POS) Tagger for English. The model was trained on sections 01..24 of WSJ corpus and using section 00 as the development test set (accuracy of 97.00%). Tagging speed: 500 sentences/s.

The Cloud Research Simulation Toolkit (CReST) is a cloud computing simulation platform written in Java.

The CSV Transformer is a data processing tool which transforms .xml-Files to comma separated values. The CSV Transformer was created in a load and performance testing project, the use case was to be able to transform 2800 configuration files of a big banking application to a single .csv-File. With this single file it was possible to compare the whole configuration between two releases with the already available tool CSV Comparator. This enabled the team to verify if there were any changes that could have a potential performance impact.

Goal of our project CSX (City Stats X) is to program a generic interface to visualize and present social data about a city. We will present this on the example of the city of Linz in Austria.

CSparseJ is a Java port of CSparse: a Concise Sparse matrix package.

CallSim is a software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data. CallSim provides a final classification or rescue of a base/indel in reads, where putative variants have been identified via typical SNP/indel workflows. plots rendered by: JFreeChart library http://sourceforge.net/projects/jfreechart/

Carbon Effective Supply Chain Simulator (CESCS) is a software package for simulating green supply chain. A unique approach is taken to help achieve the optimal balance between carbon footprint, supply chain cost, service level, and product quality.

This SourceForge.net project serves as repository and distribution point for Carbon Five Open Source software and documentation.

Celeste is a tiny and simple Cellular Automata simulator written in Java. It is a command line application that writes an image of each simulation step. Celeste was designed to run Conway's Game of Life but other rulesets can be implemented as well. It is released under the extremely permissive WTFPL.

An integrated bioinformatics toolkit for analysis of ChIPseq data from the Illumina DNA sequencing platform. Includes filtering, quality control, simulation, peakfinding, visualization, and comparison of samples.

ChainBuilder ESB is Java Business Integration (JBI) compliant open source solution for use in Service Oriented Architecture (SOA) environments. ChainBuilder ESB's graphical integration enables new and older applications to easily enter into SOA.

Chameleon is a rule-based expert system to assist farmers in semi-arid areas to prevent bush encroachment. It runs as a web-application on a Tomcat server with MySQL and is based on the Mandarax library for deduction rules and its front-end, Oryx.

Generic directory service (for the EPICS tool set). Directory entries are channels with properties and tags. Applications can query a web service to retrieve channels based on wildcard matching on properties and tags, and manipulate the directory data. Code has been moved to GitHub at https://github.com/ChannelFinder

Chemical Calculator that can calculate various aspects of compounds. The programs main features are: * Get information about an element * Calculate the amount of moles of an element * Calculate the Empirical and Molecular formulas of a compound

Chemical Evaluation Framework (CEF) is a molecular structure based software to assist in hazard assessment. Download requires Java 6 update 1. Source code is contained in jar files. Download contains GSH reactivity plugin.

===== Project moved to https://github.com/fpetitjean/Chordalysis ===== Log-linear analysis is the statistical method used to capture multi-way relationships between variables. However, due to its exponential nature, previous approaches did not allow scale-up to more than a dozen variables. We present here Chordalysis, a log-linear analysis method for big data. Chordalysis exploits recent discoveries in graph theory by representing complex models as compositions of triangular structures, also known as chordal graphs. Chordalysis makes it possible to discover the structure of datasets with thousands of variables on a standard desktop computer. Associated papers at ICDM 2013, ICDM 2014 and SDM 2015 can be found at http://www.francois-petitjean.com/Research/ YourKit is supporting Chordalysis open source project with its full-featured Java Profiler. YourKit is the creator of innovative and intelligent tools for profiling Java and .NET applications. http://www.yourkit.com

CircuitSmith is to be a comprehensive electronic design package being developed in Java which will include schematic capture, printed circuit board layout and any other features which I (and hopefully others) can be bothered to program.

CloneAnalyzer is a tool for software quality analysis. It allows you to find, display and inspect clones, which are fragments of duplicated source code resulting from lack of proper reuse. It can be used as a plugin for Eclipse and on the command line.

CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.

Clown is a "clustering" framework. It allows you to cluster datasets (in ARFF) format using a number of different clustering algorithms.

Comprehensive Meta Prediction and Annotation Services for Proteins: The new all-in-one prediction tool that can be easily extended to include any SOAP/WSDL-enabled prediction servers. A concise user interface lets you use the results instantly.

Colloquium QDA is a tool for custom coding and analyzing qualitative ethnographic interviews. To run, make sure you first have JRE 8 or later installed (http://www.oracle.com/technetwork/java/javase/downloads/). Colloquium QDA is an open source cross-platform Java Swing app utilizing an embedded Java DB with Lucene integrated search.

The main purpose of CombiTagger is to read files generated by individual PoS taggers and use them to develop and evaluate combined taggers according to a given combination algorithm. http://aaai.org/ocs/index.php/FLAIRS/2009/paper/download/67/296

A program to calculate and create lists of possible variations (permutations) and selections (combinations) of a given set of elements. Creating the cartesian product of two sets is also possible.