Open Source Java Scientific/Engineering Software - Page 26

gSky Digest is a system tray desktop application that presents astronomy events calculated for your home location. Currently it comes with detailed information about the Sun, the Moon and 7 planets. See Project Web Site for more details.

This is a fork of the jamod Modbus library, taken at version 1.2.1, released under the Apache 2 license, as contained in the SVN repository for that project. The goal of the j2mod project is to produce a more fully functioning Modbus(tm) communication library based on the Java programming language. It is the intention that this be an actively developed project, accepting submissions from professional software engineers with experience in Modbus Master and Slave development.

Optical Design Software for optical systems comprised of light sources, lenses, apertures, prisms, imagers, photometers, etc. Simulate light through the system and compute images and intensities at various locations in the design.

jQuantum is a Java program to simulate a quantum computer, to design quantum circuits, and to visualize the execution of quantum algorithms. Another main purpose, however, is to create images in your head, and thereby - understanding.

Mimosa is a modeling and simulation platform, covering the process from building conceptual models to running the simulations. The specification uses ontologies and an extensible set of formalisms for the dynamics. The simulation kernel is based on DEVS.

JDash is a dead, but ECUTracker is alive and well. A 100% rewrite for mobile devices.

Octave development environment built upon Eclipse's Dynamic Languages Toolkit (http://www.eclipse.org/dltk/). Distributed as an Update site for Eclipse 3.7 Indigo and Indigo-based package for several platforms. Supports search, autocompletion, launching scripts, interactive console, debug and integrated plotting on Octave versions 3.2.x, 3.4.x and 3.6.x. The current goal is to make it running out-of-box on multiple platforms. Currently only Linux and Windows are supported. Mac support is possible. The project needs a maintainer for Mac version, since I don't have Mac to build Octclipse and test it on this platform. Also, it is worth to support Eclipse 4.0 Juno with DLTK 4.

ALTER is a web-based tool to transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats.

Active Networking provides a framework in which executable code within data packets can execute upon intermediate network nodes. The goal of this research is to develop active networks that are capable of predicting their own behavior and to use this ca

This is a project which aims to create a theorical model for trajectories of airsoft bb's, and to compute them.

APP for Android 3.1 or greater to implement a CNC Controller that send orders using USB port to Arduino Mega 2560 R3 board to control 3 stepper motor to have a real CNC mill /// APP para Android 3.1 o superior para implementar un Controlador de CNC que envia ordenes usando el puerto USB a la placa Arduino Mega 2560 R3 para controlar 3 motores paso a paso para tener una fresadora de CNC real.

Artificial Intelligence (AI) evolves musical instruments you play with the mouse from small blocks of Java code that operate on numbers, each block designed to keep all numbers in range -1 to 1 if they started in that range, and combinations of these evolved codes running 44100 times per second for high quality 44.1 khz audio. You can also write the Java code into its window. Uses Javassist internal compiler on the new Java code assembled by renaming variables to overlap eachother and reordering, copying, and removing blocks of code. Listen to the recorded music in files section of sourceforge or try it for yourself. This branched into my other projects: GigaLineCompile, JSelfModify, JSoundCard, and Human AI Net as I got more into the AI and systems side of things and explored vision research as a better user interface to network minds together through the Internet. Someday I will bring it all together in a shared space on the Internet.

Modified version of AutoGrow, autogrow.ucsd.edu/ , with a mutation script added in the class files, and a global change of the defined mutation point from Hydrogen atoms to Calphas, to allow placement of Amino Acids. Deposited are 3 versions, used for my PhD Thesis. These allow for mutation of short 2-15 amino acid peptides, and associated screening of these using AutoDock or AutoDock Vina, allowing for 8 CPU systems to screen 10K peptides a day or 1-2K with flexible residues added in. A detailed method for determining the peptide ligand for any sequenced and modeled T cell receptor will be published and link added at some point. These scripts are written quickly in a couple weeks to meet a task and could be re-written more eloquently. I may or may not work on this project again, the goal would be to introduce amino acids into any protein in openCL to allow automated design on GPU's.Limits-The standard PDB codes used slightly modified, proline not at angles, peptide shld be linear,

Autoplot is an interactive browser for data on the web. Give Autoplot a URL or local file name and it creates a sensible plot of the data. Autoplot allows you to interactively browse data stored in ascii, .cdf, netcdf, and many other formats. Autoplot's source has been moved to GitHub. Thanks to SourceForge for many years of hosting!

Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)

The BE-Calculator is a Java application, written to ease the average diabetic's life. It currently only calculates how many I.U. you have to inject, but aims at providing a full, multilingual diabetic's diary. This project has been superseded by GGC!

Uses MathSciNet to search for bibtex references. The matching references can then be edited and added to a local file. For information on how to use this software please consult the wiki. Requires a MathSciNet subscription.

The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.

CEGA is a highly extendable layout plugin for Cytoscape based on an Evolutionary Algorithm. In contrast to other layout algorithms, CEGA lets users decide which features are important for the visualization of their graphs.

CIG-P is a higher order visualization tool for AP-MS which generates intuitive circular diagrams for visually appealing final representation of AP-MS data. CIG-P can be used to compare a) different AP-MS datasets of various baits or b) a particular bait under various perturbations (lenticular section CIG-P). The output of CIG-P is a simple and intuitively easy to grasp visualization of a complex dataset. Publication: CIG-P: Cicular Interaction Graph for Proteomics http://www.biomedcentral.com/1471-2105/15/344/ Previously known as PIVOT (Protein Interaction Visualization and Observation Tool)

CLIMS is a Laboratory Information Management System for protein Crystallography that features a novel graphical interface to a relational database. CLIMS has been reviewed as one of the top two LIMS for crystallographers by CCP4.

CamBA is a Linux package for statistical analysis, by script/GUI, of neuroimaging data (fMRI/sMRI), developed at the Brain Mapping Unit, University of Cambridge. Non-parametric permutation-based statistics. Input images: 4D NiFTI files, output: HTML/

Calculation of camshafts - allows to define a camshaft profile on the set trajectory which should provide the given mechanism. The trajectory can be set graphically, co-ordinates or function.

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).

Combean is a Java framework for mathematical structures and optimization algorithms. Through a set of Java interfaces and JavaBeans-based config, Combean glues optimization codes together - leading to more interoperable, adaptable and flexible solutions.