Open Source Java Scientific/Engineering Software - Page 25

The JUMP DB Query Plugin is an extension for the OpenJUMP GIS platform that allows OpenJUMP users to give arbitrary database queries to retrieve and display geographic feature sets. Spatial databases currently supported are PostGIS, Oracle Spatial, MySQL, and SpatiaLite.

JUnitConv is an universal Units of Measure Converter built as a Java Applet. It supports an unlimited number of Units Categories, Units of Measure and Multiplier Prefixes that could be customized using external text files.

Set of Java packages to apply Genetic Algorithms to any kind of problem. Various genetic operators are implemented and an example shows of how the system could be applied to digital circuit evolution.

Write VISA instrument drivers in Java for Windows and Linux. Maybe the best way to give a full description is to explain the history of this project. History: This instrument driver project is part of of a non open source data acquisition and analysis project used at Colorado School of Mines, JSeisLab. JSeisLab is a Java port of its predecessor "Spectrum Division for Windows" which is written in VB 6.0. Design: I created a 64-bit JNA wrapper with IVI's visa.h version 5.0 as input to JNAerator (https://github.com/nativelibs4java/JNAerator). Instrument drivers written in Java can use this wrapper. A 64-bit VISA library from either an instrument company (e.g. National Instruments, Tektronix) when running Windows or libvisa (http://www.librevisa.org) when running Linux needs to be installed .

Java Data Processing Project aims to manipulate text file containing scientific data such as time/intensity scan or spectrum. Jdpp provide large flexibility to read all possible time duration and date format. It is originally design to treat MS data.

A full math Java class library containing complex functions and algorithms such as cubic-spline interpolation, least squares, matrix computations. Eventually to make a web based interface to the library using JSP.

3d visualization of USGS Digital Elevation Models (DEM). Support for stereo visualization. Written in Java and Java3D

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.

This program provides for easy modification and viewing of SPICE circuit files. It will also read SPICE3 RAW format (as well as GnuCap) and create graphs of results through an interactive GUI. It supports waveform math, copying to clipboard, and saving.

The goal of this fractal renderer is to enable intricate images to be created with maximum control over the results. To this end, it supports multiple layers, many fractal types (including user – defined equations) and different ways of rendering.

The Koppen Climate Classifier is an open source software written in Java that classifies regional climate based on Koppen Climate Classification System. It classifies climate based on three types of inputs: temperature, precipitation and hemisphere. The Koppen Climate Classification is one of the most widely used climate classification systems. It was first published by a Russian German climatologist, Wladimir Koppen. This system is based on the concept that native vegetation is the best expression of climate.

A software tool enabling the user to browse through an image stack created by a confocal microscope. Points can be plotted through the stack, producing a digital 3D representation, which can be viewed in 3D and compared with other plots.

The LexGrid Editor is an Eclipse-based open source tool for authoring, viewing, and maintaining lexical resources that conform to a formal terminology model. Resources can be developed locally or viewed in context of a networked 'grid' of terminologies

Cap analysis of gene expression (CAGE) is a sequencing based technology to capture the 5’ ends of RNAs in a biological sample. After mapping, a CAGE peak on the genome indicates the position of an active transcriptional start site (TSS) and the number of reads correspond to its expression level. CAGE is prominently used in both the FANTOM and ENCODE project. MOIRAI is a compact yet flexible workflow system designed to carry out the main steps in data processing and analysis of CAGE data. MOIRAI has a graphical interface allowing wet-lab researchers to create, modify and run analysis workflows. Embedded within the workflows are graphical quality control indicators allowing users assess data quality and to quickly spot potential problems. MOIRAI package comes with three main workflows allowing users to map, annotate and perform an expression analysis over multiple samples.

MYRA is a collection of Ant Colony Optimization (ACO) algorithms for the data mining classification task. It includes popular rule induction and decision tree induction algorithms. The algorithms are ready to be used from the command line or can be easily called from your own Java code. They are build using a modular architecture, so they can be easily extended to incorporate different procedures and/or use different parameter values. This project is now hosted at: https://github.com/febo/myra

A Java application to request calibrated raster maps from compatible web based map servers, and then save the maps in OziExplorer (.map) format.

Create custom substitution matrices for BLAST protein search. Easy to use GUI based application.

Mavscript ermöglicht es in einem Textdokument Berechnungen durchzuführen. Die eigentliche Berechnung verarbeitet das Algebraprogramm Yacas (oder der Java-Interpreter BeanShell).

Metaquokka is a highly configurable xml editor, currently available as Gridsphere portlet. Besides the default format, there is suppoert for ESysXML, a simulation description scheme for a geodynamics framework. Supports Generic Mapping Tools rudimentary.

A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.

MoonPlanner is a Java calendar that allow to view moon's phases, moon's signs (constellations in which the moon is), and show the part of the plant corresponding to each sign (flower, fruit, leaf or root). For every calendar's day the user can attach notes (that are stored in a persistent database). At the startup the program will remind you if there will be notes for current day. Timezones and localizations (En, IT) are supported by the application. This calendar is usable between 1900 and 2020. This tool can be useful to plan gardening tasks or to view some astrology informations. References and requirements: - JRE/JDK version 1.5 or later must be installed on host computer. - UI are made using SWT by Eclipse (see http://www.eclipse.org/swt/). - The software uses AstroLib library version 1.1.5 provided by Mark Huss to calculate Moon's phases (http://mhuss.com/AstroLib.html). - The software uses Apache Derby 10.9.1.0 (http://db.apache.org/derby/) as embedded database.

(Former project name was Geo5.) It was never easier to share your position with friends. Just open http://jfellow.net/geo5/ and see you and your friends on a map. (http://jfellow.net/geo5/ is a test server. You can download and install your own server. It's open source.) - Build groups, all group members see each other automatically. - No registration, no installation, no spyware. - Advanced: Tracks, routing (planned). It's about privacy. Reclaim the internet from authorities and companies!

Myrtle is a simple programmable spreadsheet and statistical analysis software specifically designed for learning statistics. It provides the standard spreadsheet functionality one would expect like multiple tabbed sheets, relative and absolute row and column referencing in formulas, and a large catalog of built-in functions. Functions specific to logic and computer science, mathematics, probability, and statistics are available. Student's can easily create, customize, and update plots and graphical summaries of their analyses. Myrtle offers a unique bookmarking facility which allows students to create and reuse named references to their favorite cell ranges. This can help students focus attention on the important relationships among particular rows or columns of data. Myrtle's graphics and reporting features allow students to report back to their instructors their mastery of course content.

The project offers support for NTC thermistor calculations. The Steinhart-Hart equation is a mathematical model for these thermistors. Software to calculate the coefficients based on temp-resistance tables and functions allowing conversion are provided.

Nevada is a tool for interactive visualization of dynamic networks. Unlike other dynamic network visualization tools it's focussing on visualizations preserving the user's mental-map. Import of Pajek files is supported.