Open Source Java Scientific/Engineering Software - Page 20

DotPlot is an Eclipse plug-in to graphically compare word sequences of any type of text. Matches will be plotted as dots on a graph. Similarities in thousands of lines of text or code will result in typical textures and diagonals in the plot.

Platform independend, multithreaded fractal generator. Fine control over thread/CPU usage; unlimited precision; smooth/random/function coloring; supports color map files (over 1600 available); many image file formats. For any Java 1.5+ (32/64 Bit) VM.

GMOL is an application designed to visualize genome structure in 3D. It allows users to view the genome structure at multiple scales, including: global, chromosome, loci, fiber, nucleosome, and nucleotide. This software was built upon the pre-existing Jmol package by Prof. Cheng's group. The software is developed in Prof. Jianlin Cheng's Bioinformatics, Data Mining and Machine Learning Laboratory in the Computer Science Department at the University of Missouri - Columbia, USA. The project is supported by the National Science Foundation (grant no. DBI1149224). If you use GMOL in your research, please cite: Nowotny, Jackson, Avery Wells, Oluwatosin Oluwadare, Lingfei Xu, Renzhi Cao, Tuan Trieu, Chenfeng He, and Jianlin Cheng. "GMOL: an interactive tool for 3D genome structure visualization." Scientific reports 6 (2016): 20802.

GNU Gluco Control (GGC) is diabetes management application. It helps managing user's daily data, food data. Has graphs, statistics, printing, diabetes devices support (meter, pump, CGMS). It works on any platform supporting at least Java 5 (1.5). Our repo moved to GIT (click on tab Git Code), Lowest supported Java now is 1.8 and project code base is in process of redesign (updating libraries and ways how application is built and run). IMPORTANT: Project was moved to GitHub: https://github.com/andyrozman/ggc on 4th April 2024

GeomSS is a geometry modeling and scripting system in Java. Write scripts that create and analyze complex geometry including NURBS curves and surfaces. This is especially useful for tasks that must be repeated with small or parametric variations.

[EN] GraficoAR is a lightweight, pure Java application for 2D mathematical function plotting and real-time analysis. Built with Swing without heavy external libraries, it features a custom recursive parsing engine that respects operator precedence (+,-,*,/). Features: dynamic Cartesian graphing, adaptive grid zooming/labeling, numerical differentiation (plots the 1st derivative in blue), and definite integration (Riemann sums with text output and transparent blue geometric shading under the curve). Includes angle unit toggle (Rad/Deg) and a portable stand-alone version with bundled JRE. [IT] GraficoAR è un'app Java leggera per lo studio e il tracciamento di funzioni matematiche 2D. Sviluppata in Swing senza librerie esterne, usa un motore di parsing ricorsivo (+,-,*,/). Offre: grafici cartesiani dinamici, zoom con etichette assi adattive, calcolo della derivata (linea blu) e dell'integrale definito Supporta Gradi/Radianti.

JBioFramework (JBF) is a set of two different chemical separations simulations (2D Electrophoresis and Mass Spectrometry) that are frequently used in chemistry, biochemistry and proteomics research. It is written in the Java programming language and will run on any and all systems that have the JVM installed. As we continue to develop the software over the coming months/years and attempt to quantify the success of our efforts with testing and reviews, user input is very important. Please don't hesitate to review the software below or email Paul Craig [pac8612@rit.edu] with larger descriptions/bugs/feature ideas. Our next scheduled release will contain (in addition to 2DE and MassSpec) a 1D Electrophoresis simulation as well as a tab containing ChemAxon's MarvinSketch [http://www.chemaxon.com/products/marvin/] along with some improved functionality. It should be out shortly as we complete the creation and modification of a permanent domain for the project.

This project provides a java implementation of the Captcha project ( see http://www.captcha.net ). A CAPTCHA is a program that can generate and grade tests that: -Most humans can pass. -Current computer programs can't pass.

JCad is a project to create a fully function 2D CAD program written entirely in Java. It\\\'s Purpose is to create a cross platform smart 2D CAD program with Java2D/Swing.

JPlotter is an open source math plotter that can draw graphs of arbitrary mathematical functions. Some of the special features are plotting of the derivatives, area calculation, plotting of directional fields of differential equations and plotting of phase and amplitude graph of complex functions.

Statically integrated evaluation of the basic security (SIA method) based on the book of Wessolly and Erb, ISBN 3-87617-093-1

Jep is a Java package for parsing and evaluating mathematical expressions. It currently supports user defined variables, constants, and functions. The open-source Jep project was halted in favor of commercial development of version 3.0 upwards.

The new version is available at https://sourceforge.net/projects/ghawwasv4/

LogicAnalyzer is a framework as well as an application to operate a PC based logic analyzer. It's built using the Eclipse RCP and designed with extensibiliy in mind. Integrating new devices or creating completely new functionality is easy.

Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)

MetaMaster is a Java-based desktop application for defining, managing and manipulating metadata associated with a collection of data files or datasets (both locally and on the network) which are bundled together into "data packages". ANDS-funded

MCS is a tool that exploits the Monte Carlo method and, with a complex algorithm based on the PERT (Program Evaluation and Review Technique), it estimates a project's time. MCS is a opensource project and it was devolped by Java Programming Language.

Modern MATLAB-based modelling software for 13C metabolic flux analysis (MFA). Support available in Google group (https://groups.google.com/d/forum/13cmfa-openflux).

Opt4J is an open source Java-based framework for evolutionary computation. It contains a set of (multi-objective) optimization algorithms such as evolutionary algorithms (including SPEA2 and NSGA2), differential evolution, particle swarm optimization, and simulated annealing. The benchmarks that are included comprise ZDT, DTLZ, WFG, and the knapsack problem. The goal of Opt4J is to simplify the evolutionary optimization of user-defined problems as well as the implementation of arbitrary meta-heuristic optimization algorithms. For this purpose, Opt4J relies on a module-based implementation and offers a graphical user interface for the configuration as well as a visualization of the optimization process.

PFAAT is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. You can download PFAAT from http://pfaat.sourceforge.net/

Planning Tool is a tool developed by QualDev Group (Universidad de los Andes, Bogota, Colombia) created to support the planning process and to track project's activities for all the projects worked in the group.

SBSI (Systems Biology Software Infrastructure) is a suite of tools for systems biology, such as parallelized numerical algorithms, and a Java, Eclipse RCP based client for visualizing results, running simulations, and integrating SBML based plugins.

OpenSDC is a set of libraries that form a communication framework to facilitate the development of distributed systems of medical devices in high-acuity environments. It is based on the upcoming SDC standard, which is specified by the IEEE in IEEE Std 11073-20702-2016 (Point-of-care medical device communication Part 20702: Medical Devices Communication Profile for Web Services), IEEE Std 11073-10207-2017 (Point-of-care medical device communication Part 10207: Domain Information and Service Model for Service-Oriented Point-of-Care Medical Device Communication), and P11073-20701 (IEEE Draft Standard for Service-Oriented Medical Device Exchange Architecture & Protocol Binding). The SDC standard has the goal to meet increasing demand for medical device interoperability in an Integrated Clinical Environment (ICE), see also ASTM F2761-1:2009. OpenSDC is not intended to be used in clinical trials, clinical studies, or in clinical routine.

A neuroscientific knowledge management system for the published literature

VIKAMINE is a flexible environment for visual analytics, data mining and business intelligence - implemented in pure Java. It features several powerful visualization and mining methods, and can utilize background knowledge.