Open Source Java Data Visualization Software

Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other quantum chemistry programs. Files can be transferred directly from several databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple files can be loaded and compared. A rich scripting language and a well-developed web API allow easy customization of the user interface. Features include interactive animation and linear morphing. Jmol interfaces well with JSpecView for spectroscopy, JSME for 2D->3D conversion, POV-Ray for images, and CAD programs for 3D printing (VRML export).

TreeForm Syntax tree drawing software is a Linguistic Syntax/Semantics tree drawing editor. Designed for graphical n-ary tree drawing. Mac users can install the software through the new package, but must give authority through "System Preferences" > "Security & Privacy". Windows and Linux users can run the software through the JAR file directly. All users must have Java 8 or higher installed. https://java.com/en/download/

IMPORTANT NOTICE: This project has moved to GitHub: https://github.com/sarahtattersall/PIPE Releases will be posted here, but please check on GitHub for the most recent activity. Create, model and analyse Petri nets with a standards-compliant Petri net tool. PIPE2 is the active fork of the Platform Independent Petri net Editor project, which originated at Imperial College London.

This project has moved. Please follow the WWW link below.

Argunet is a client-server software for computer-supported argument visualization (CSAV). Reconstructed debates are visualized as argument maps and can be shared through the Argunet Server.

The virtual lab is a NASA-funded project to provide simulated instrumentation. ITG has developed a Virtual Microscope (Virtual SEM and LM) for viewing high-resolution, multi-dimensional image datasets. More info and data: http://virtual.itg.uiuc.edu

Image Restoration and Inpainting: MinGW/OpenGL/Visual c++/Java image processing enhancing/restoring/detecting/recovering image parts(Old painting cracks...) FastRestorarion, 2D (Un)Splitted Linear Solver, nonlinear solver: conjugate gradient,QuasiNewton

jFAST is a simple finite automata (FA) graphical simulation utility; it is designed to feature simple mechanisms for creating, editing, and simulating FA. jFAST is ideal for use by students, instructors, and self-guided explorers alike.

GATA is a graphic alignment tool for comparative sequence analysis. It makes use of BLAST to graphically align two DNA sequences, creating box- line- box representations of window scored local alignments. GATA also displays extensive GFF gene annotation.

JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.

MobileMath is a software written by using J2ME technolology. It turns mobile into calculator supporting many operations such as : evaluate expression, plotting, differentiate & integrate expression... It can run on any mobiles supporting Java.

A java based digital logic simulator, designed to be used as an educational tool. uses a GUI to allow users to quickly and easily create and visualise circuits from simple components. User can create custom components

A Visual Microcode Simulator for the Classroom

OrthoInspector is a new software system for orthology/paralogy analysis. Its purpose is to facilitate the installation and the maintenance of a database describing orthology/inparalogy relations and to provide tools to exploit these data.

A project to create an interactive, scientifically-accurate 3D model of the HIV virus. Particularly intended for use in education.

Java3D 3DS FileLoader for platforms supporting JDK1.4 and Java 3D Highly functional, multiplatform 3DS File format loader Supports: Heirarchical animation Cameras Point Lights Directional Lights Textures Smooth Groups and other features

Coding convenient Aero & Astro functions into one easy to use package. From rocket engine design, to flight and space dynamics.

Avenzoar is a one-year exploration of renal cell carcinoma morphology and its related single nucleotide polymorphisms (SNPa) as a method of automating diagnosis of cancer by using a computer-aided decision tree controlled by analytical statistics.

A Java program to enable users to comprehend the "Contraction and Convergence" model for reduction in carbon emissions as proposed by the Global Commons Institute. Intended primarily as a demo for government delegates at UN conferences

A cellulary Automata.

Visit the new site: https://citespace.podia.com CiteSpace generates interactive visualizations of structural and temporal patterns and trends of a scientific field. It facilitates a systematic review of a knowledge domain through an in-depth visual analytic process. It can process citation data from popular sources such as the Web of Science, Scopus, Dimensions, and the Lens. CiteSpace also supports basic visual analytic functions for datasets without citation-related information, for example, PubMed, CNKI, ProQuest Dissertations and Theses. CiteSpace reveals how a field of research has evolved, what intellectual turning points are evident along a critical path, and what topics have attracted attention. CiteSpace can be applied repeatedly so as to track the development of a field closely and extensively. The e-book How to Use CiteSpace explains the design principles and functions along with illustrative examples in more detail: https://leanpub.com/howtousecitespace

This is educational software whose purpose it is to clarify the workings of different clustering algorithms by visualising the clustering process in 2D space. This make many possible problems and advantages very clear.

Conzilla is a concept browser. It browses and edits 'context-maps', a construct similar to conceptual models, UML diagrams or mind-maps. Conzilla uses RDF to describe and distribute such models.

DarkMaps is a program that reads images and builds a 3D map from them.

This projects concentrates software for setting up a chemical dictionary website.