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).

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The JSpecView Project initially provided JAVA applets for the display of JCAMP-DX and AnIML/CML spectral files. The source and binary files are available via the Code (sourceforge SVN) and Files menu options. See the WIKI pages (Hosted Apps) for more detail. Beginning September 2018 all code changes are being handled via the Jmol Sourceforge page. The codes has been fully merged and JSmol the JavaScript/HTML5 version of Jmol now includes the non-Java version of JSpecView.

Scaffold Hunter is a JAVA-based software tool for the analysis of structure-related biochemical data. It enables generation of and navigation in a scaffold tree hierarchy annotated with various data.

An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).

Diagram (JGraph) driven simulator. Bondgraphs > nonlinear differantial system > plot: implemented for economics and ecology. Network analysis: emergy propagation implemented. Would also fit for electronics, mechanics, cost, GWP, footprint analysis.

Effectopedia is open knowledge aggregation and collaboration tool that provides a means of describing adverse outcome pathways in encyclopedic manner.

Gavrog stands for "Generation, Analysis and Visualization of Reticular Ornaments using Gavrog". It is a Java library together with a suite of interactive applications for the study of periodic net-like structures in space and their applications.

VMS Draw provides general utilities (e.g. normalization, conversion, and other manipulations of several spectra at the same time) and a flexible graphical user interface (GUI) for an easy use by non-specialists which allows a seamless flow of information between experimentally and theoretically oriented researchers. Finally, it permits effective interactions with other electronic structure codes [e.g., nuclear magnetic resonance (NMR), microwave] even if Gaussian 16 offers the widest set of methods for computational spectroscopy.

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.

4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.

Basic life is an application that desires to simulate basic life based on some basic chemistry/physics rules. This environment provides particles that can bond, vibrate, react, etc. in order to create basic cells

Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.

A Java program to parse chemical names using IUPAC nomenclature. The output can be either a visualisation of the molecule, or in a form for other programs to use (e.g. CML).

HPLC simulator is a web-based high-pressure liquid chromatography simulation. Adjust a wide range of chromatographic parameters and see their affect on retention times, column efficiency, backpressure, and more.

The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and source code repository can be found on https://jchempaint.github.io

A set of utilities for working with the GAMESS Computational packages. Written in java to maximize cross platform use

Jamberoo (former JMolEditor) is a library of algorithms for structural Computational Chemistry implemented in the Java programming language. The Jamberoo classes can be integrated into other Java applications.

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.

Jpowder, http://www.jpowder.org, is a Java viewer of powder diffraction data, and is a collaborative project between the ISIS Facility of the STFC and the E-Learning and Software Develepment Unit of the Kasem Bundit University.

Maui is the Maltcms User Interface, a rich client application for Chromatography-Mass Spectrometry and related research areas.

Modama is a new software project for processing and analysing 2d detector data (images) provided by any available detectors, mainly SAX and WAX.

The Molwind project aims at developing Open Source software to visualize relationships among molecular entities such as chemical structures on the basis of NASA WorldWind. Different levels of complexity get visible by zooming in areas of interest.

Predyketide is a stand-alone desktop application which provides a way to observe the resulting structure per elongation of the polyketide chain, and predict the most possible natural product structure. This tool can be helpful in the discovery of new drugs requiring lesser time and effort. The project uses the cdk v.1.5 and cdk-jchempaint-26.

A Java-based tool to visualize, integrate and analyze LC-MS/MS proteomics data.