Open Source Java Scientific/Engineering Software - Page 12

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.

It uses two different solutions: - placing of circles closest to the center from the largest to smallest, see brianshaler on github https://github.com/brianshaler/Circle-Packing-in-Processing - simulation "real" world with use of a Java Physics Engine JBox2D, see http://www.jbox2d.org

Official site: https://fudaa-project.atlassian.net/wiki/spaces/FUDAA/overview Sources moved to GitLab: https://gitlab.com/fudaa

ICE is a simple mathematical calculator with very useful shortcuts for Engineer: works natively with tolerance, can run Monte Carlo analysis, uses engineer notation, includes most of the day by day functions used by engineers.

A basic and easy java program to make black and white identikit drawing ,with a library of face elements that you can also modify and expand without limit !Source code available. Also available a very rough base for a 3D construction of the face.

LAMINA (Leaf shApe deterMINAtion) is a tool to provide classical measures of leaf shape (blade dimensions) and size (area) as well as measures that indicate asymmetry in leaf shape and measures of herbivory damage (missing leaf area).

Lucon is a user friendly graphical concordancer. It runs on UTF-8 text and xml files and it allows to search for a sole word, for terms, for words at a certain distance and it displays the contexts of the searched terms.

TextMarker is now developed and hosted at Apache UIMA (http://uima.apache.org/textmarker.html). TextMarker is a UIMA-based tool for information extraction and more. The full featured editor of the rule language and the build process of UIMA descriptors are complemented with components for visualization, explanation, testing and rule learning.

Thea, Tools for High-throughput Experiment Analysis, is an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base.

You can install the latest Eclipse plugin version from the update site https://javahexeditor.sourceforge.io/update or the Eclipse Marketplace https://marketplace.eclipse.org/content/java-hex-editor. Older versions of the Eclipse plugin are available via the update site for the version, e.g. https://javahexeditor.sourceforge.io/update/0.5.1 You can download the latest stand-alone version and older versions on the "Files" tab.

The Antigen Variability ANAlyzer (AVANA) tool uses information entropy to measure variability in protein sequence alignments. It also compares alignments using mutual information, identifying the mutations that characterize specific sequence sets.

Researchers, Mathematicians and Enthusiasts. Download "Billiards Everything" to discover new periodic billiard paths, an unresolved problem from 1775! Download "Billiards Covers" to see the most current list of periodic paths in triangles. Follow "The Great Periodic Path Hunt" at gwtokarsky.github.io for the latest news. Email tokarsky@ualberta.ca for feedback.

CompuCell3D is a software framework for multimodel simulations of biocomplexity problems. It has been developed as an ongoing project for the Interdisciplinary Center for the Study of Biocomplexity at the university of Notre Dame.

Crystalsim is a simple freeware program with a neat graphical user interface for X-ray diffraction (XRD) data analysis . It can simulates all possible {hkl} planes data for the selected crystal. Crystallographic Information File (.cif) can also be used. Analyze both powder diffraction and single crystal data . Indexed at International Union of Crystallography (IUCR). Crystalline lattice parameters such as ‘a’, ‘b’, ‘c’ as well as interfacial angles such as alpha, beta, gamma can also be entered manually. Processed data can be saved as .csv file format. Designed by M Kanagasabapathy, Assistant Professor, Department of Chemistry, Rajus' College, Affiliated to Madurai Kamaraj University Rajapalayam (TN) India email: rrcmks(at)gmail.com

This program is an offline and stand-alone Java application which simulates the Enigma encryption machine that was used during World War II.

Entity recognition and normalization software for biomedical text

This project is the development of a Selection Tool primarely used in ImageJ and possibly in GIMP. It is based in LiveWire and SNAKES methods and will firstly be used in IVUS (intravascular ultra sound) images.

Graphical front-end for GNU Octave. Edit formulas in mathematical notation. Uses Octave (Matlab clone) as a math engine.

Parallel Iterative Deconvolution is a multithreaded ImageJ plugin for iterative image deblurring.

RunCC is a new kind of parsergenerator that generates parsers and lexers at runtime. Source generation is only optional. It features the absence of any cryptography. Although intended for small languages, it comes with Java and XML example parsers.

ScapeToad is an easy to use application for the cartogram creation. Cartograms are deformed maps where the polygon size is proportional to a given statistical value. ScapeToad reads and writes Shapefiles. See <https://github.com/christiankaiser/ScapeToad> for the latest version of the code.

This open package aimed to addresses frequency distribution, run-chart, X-chart, R-chart, X-bar and S-chart, R-bar and R-chart, X and MR-chart, standard deviation, Control limits, Process Capability, p and np type charts, c and u type charts.

TomoJ is an ImageJ plug-in for tomographic reconstruction. It was designed for electron tomography, however any acquisition with parallel beam should work. TomoJ proposes the preprocessing and the registration of tilt-series prior to 3D reconstructions (WBP, ART, SIRT, OS-SART, compressed sensing). TomoJ is written in Java, the computations are multithreaded and reconstruction can be performed on CPU or GPU (OpenCL). registration is described in: Journal of Structural Biology: X. 2020, Volume 4. "Improvements on marker-free images alignment for electron tomography" C.O.S. Sorzano et al. https://doi.org/10.1016/j.yjsbx.2020.100037. BMC Bioinformatics. 2009 Apr 27;10:124."Marker-free image registration of electron tomography tilt-series." C.O.S. Sorzano et al. reconstruction part was described in: BMC Bioinformatics. 2007 Aug 6;8:288. "TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy."Messaoudi C et al

A 3D wind tunnel simulator created in 2008 by a group of COMP314 students at The University of Waikato. The user is able to insert objects into the windtunnel and view a (very) rough simulation of the wind flowing around it. View the Wiki for detailed instructions on how to use it. Created by: Sam Sarjant, Kias Hafiz, David Spooner, Sam McIntosh, Kieran Ryan, Yong Chun Fu