Open Source BSD 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).

The SourceForge OpenRasMol project is an adjunct to the RasMol and OpenrasMol project at http://rasmol.org. It is hoped that the SourceForge OpenRasMol project will provide a convenient focal point for active collaborative contributions.

Java Treeview - An Open Source, Extensible Viewer for Microarray Data in the PCL or CDT format

BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.

MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection

MicroArray Genome Imaging and Clustering Tool (MAGIC tool) is a platform-independant java program for analyzing MicroArray data (.tiff scans & .txt godlists) via graphs and clustering operations (including QT-clustering). http://www.bio.davidson.edu/magic

This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.

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

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).

Molecular Graphics and Dynamics. Molecular model builder. Part of the Ascalaph Designer http://sourceforge.net/projects/asc-designer/ project. Windows & Linux.

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.

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.

CQRlib is an ANSI C implementation of a utility library for quaternion arithmetic and quaternion rotation math.

VANTED - Visualization and Analysis of NeTworks containing Experimental Data At SourceForge the VANTED development history is preserved, only limited amount of development will proceed here. Please head on to the most recent developments, which can be observed at www.vanted.org.

3D viewer which arranges BLAST hits and other bioinformatics-related alignments in a rotating, cylindrical display. Feedback appreciated. NOTE: requires Java3d installation. Superceded by Cylindrical Alignment App

A small Java program for reading, analysing, viewing and animating the data from an EEG machine during a psychology experiment.

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.

3D medical image platform for visualization and image processing. Segmentation with Levels sets. Surface reconstruction with marching Cubes, texture Mapping and Raycasting,DICOM support. Integration environment for VTK, ITK and vtkInria3D under wxWidgets

A Java software for 3D visualization of graphs/networks. It implements many graph layout algorithms (such as force-directed methods), graph generators (such as scale-free networks) and graph modifiers. Most functions can be accessed through its GUI.

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.

As of 2018-06-28, this project has moved to https://github.com/AdamaJava. This copy of the code will remain but all new code updates and releases will be from the new site. Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the wiki: http://sourceforge.net/p/adamajava/wiki/Home/

Arcadia is a light-weight, cross-platform, C++ desktop application designed for visualizing biological networks such as metabolic pathways.

Acre calculates growing-space or stand-density of trees and creats pictures of it. It can also be used to calculate weighted Voronoi-Diagrams (splits up an area to the neares point or to the point with the greatest influence at a certain place).

A Java application used in whole genome analysis to display SNPs in a genomic context. Supplementary data is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.

BINViz(Bidirectional Interactive Network Visualization) is a JavaScript library for network and graph visualization. The goal of this tool is to provide a better way to visualize complex graphical models and the underlying data in a web-based environ