Open Source Java Scientific/Engineering Software - Page 38

CERCA is an open-source research tool that supports the verification of bibliographic references in scientific manuscripts. It extracts references from PDF files and checks their existence and consistency against authoritative metadata sources, producing explainable diagnostics, audit logs, and reproducible reports. It is intended for: - Researchers performing final manuscript checks - Reviewers assessing reference consistency - Editors supporting editorial quality control - Meta-research and reproducibility workflows CERCA is an experimental tool. It does not replace manual verification. CERCA is a Java desktop application built with JavaFX. To run it, you need a JRE that includes JavaFX, such as Azul Zulu JRE. Developed by: Lidiany Cerqueira, PhD Computer Science Researcher

COHCAP (City of Hope CpG Island Analysis Pipeline, pronounced "co-cap") is an algorithm to analyze single-nucleotide resolution methylation data (Illumina 450k methylation array, targeted BS-Seq, etc.). Please note: 1) The SourceForge version of COHCAP is no longer being updated. Please see the GitHub version: https://github.com/cwarden45/COHCAP This was the source repository for the Bioconductor version, with some changes after the decision to only provide the code through GitHub. 2) In addition to the original NAR paper, please see the following links: Benchmarks: http://www.nature.com/protocolexchange/protocols/2965#/introduction Protocol Exchange Files: http://sourceforge.net/projects/cohcap/files/Protocol_Exchange_Example.zip 3) Custom Annotation Files (including EPIC Array): https://sourceforge.net/projects/cohcap/files/additional_Bioconductor_annotations.zip/download

CONMAP is a console program to aid in geobody connection analysis in geosciences. It accepts input and outpts results in GEO-EAS (GSLIB) format for easy interoperability with most geoscience softwares. To get help in usage, simply run the program without arguments. CONMAP is a Java 1.7 program. Open a command prompt, go to the directory where you download CONMAP.jar and enter the command "java -jar CONMAP.jar <arguments>" (without quotation marks) to run the program. Geobody detection itself runs pretty fast, with almost all execution time spent in file loading, parsing and saving. New features in version 2.0: geobody walk, vertical transitions count and mean thickness. See details running CONMAP without arguments.

CRAFTY is a large-scale ABM of land use change. It has been designed to allow efficient but powerful simulation of a wide range of land uses and the goods and services they produce. It is fully open-source and can be used without the need for any programming.

Continuous wavelet transform library

The information system (IS) “Cantharella: Pharmacochemical database of natural substances” share and sustain pharmacochemical data of all organisms collected for the study of their natural substances, with a controlled access via internet.

The aim of the cardiac atlas project is to establish a structural and functional atlas of the heart. This project is funded by the NIH grant and led by the University of Auckland, New Zealand.

CAVOR is an engine for building apps that involve both graphic and text/numeric data. Primarily GIS is the initial focus, but consider also CAD, CASE, project management (eg PERT charts), and others. Built-in scripting, C API, also supports Tcl and Java.

Cervelletto is a neural network simulator. It uses a new neural model based on biological, neurological and psychological studies. [it's not yet completed... just give me some weeks! sorry!]

A map/reduce based application for mapping short reads generated by the next-generation sequencing machines.

CoNet is a Cytoscape plugin that detects significant non-random patterns of co-occurrence (copresence and mutual exclusion) in incidence and abundance data. It has been designed with (microbial) ecological data in mind, but can be applied in general to infer relationships between objects observed in different samples (for example between genes present or absent across organisms).

CSBI is a component based framework that allows for inter-component data sharing and access. GINY is an Open Source Graph Library.

Conceptpower is an authority file service, which is based on WordNet 3.0 (http://wordnet.princeton.edu) and can be extended as needed. Each entry in Conceptpower is identified by an URI, which should be used to refer to a particular entry. Conceptpower has three parts: a public search function, a management component, and a basic REST interface. The public search function provides the user with basic search functionality. The management component provides a simple user management, and term management functionality (such as adding, editing, and deleting terms). The REST interface provides basic searching via a web service.

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.

A set of applications, utilities, and libraries used in conjunction with commodity hobby-grade radio controlled helicopters to create an aerial robotics platform.

CryptoDock is free multi-platform application written in Java that hosts various hash and modern cryptographic algorithms you can use to protect your sensitive data on your computer. Available cryptographic algorithms: 1. NLSE-1 2. One Time Pad 3. AES Available hashing algorithms: 1. MD5 2. SHA-1 3. SHA-256 4. SHA-512 IMPORTANT: In order to run CryptoDock you need to have Java installed on your computer. Java is free and can be downloaded from - http://www.java.com/

The Cylindrical Alignment App is the successor to Cylindrical BLAST Viewer. Similarly, it arranges search or other comparisons, against their "axis". Searches can be made by Basic Local Alignment Search Tool, ClustalW, or Gene Machine to name a few. This version does not require downloading or installing Java3D, and has more modern GUI features.

Eukaryotic gene expression is controlled through molecular logic circuits that combine regulatory signals of many different factors. Complexation of transcription factors and other regulatory proteins is a prevailing and highly conserved mechanism of signal integration within critical regulatory pathways and enable to infer controlled genes as well as the exerted regulatory mechanism. We developed DACO (domain-aware cohesiveness optimization), a novel algorithm that combines protein-protein interaction networks and domain-domain interaction networks with the cluster-quality metric cohesiveness. The metric is locally maximized on the holistic level of protein interactions while sophisticated connectivity constraints on the domain level are utilized to account for the exclusive and thus inherently combinatorial nature of the interactions within such assemblies. The original publication can be found on http://bioinformatics.oxfordjournals.org/content/30/17/i415 .

This project is a thesis (diploma) from the University of Applied Science Aalen. It contains a logic simulator for digital technique.

The DRS (Digital Replay System) is a desktop application for replaying and analysing combinations of video, audio, images, transcripts and computer log files in an integrated way.

ENES is a video game preservation initiative : we develop both hardware & software to extract data from video game cartridges such as NES. We do not provide roms through our website because of copyright.

The EURP OntoLookup is a CREOLE plugin for GATE http://www.gate.ac.uk/ which uses an OWL ontology for lookup. It has a very fast implementation based on a tree of hash maps.

EasyGIS simplifies GIS data management, sharing, and publishing. REST interfaces (json, html views). Lucene based FTS searches. Thematic maps, business cartography. Integration with external GIS data providers - Google, OSM.

moved to https://github.com/Mithos/Euclid/wiki

Experimental utilities in Java for geographic information and remote sensing in environmental science. Seagis is build on top of Geotools 2, which is an OpenGIS implementation. Some Seagis classes may move to Geotools 2 when (and if) they become mature e