white_dune is a graphical VRML97/X3DV editor, simple NURBS/Superformula 3D modeller, animation tool, and VRML97/X3DV commandline compiler in development. VRML97 (Virtual Reality Modeling Language) is the ISO standard for displaying 3D data over the Web via browser plugins ("HTML for realtime 3D"). X3DV is the direct successor of VRML97. VRML97 and X3DV have support for animation, real-time interaction, and multimedia (images, movies, and sounds). white_dune can read, create, and display VRML97/X3DV files and let the user change the scenegraph/fields. It also has support for stereoscopic view via "quadbuffer"-capable stereo visuals, and support for 3D input devices like a joystick, spaceball, or magnetic tracker.
GNU TeXmacs is a free wysiwyw (what you see is what you want) editing platform with special features for scientists. The software aims to provide a unified and user friendly framework for editing structured documents with different types of content: text, mathematics, graphics, interactive content. TeXmacs can also be used as an interface to many external systems for computer algebra, numerical analysis, and statistics. New presentation styles can be written by the user and new features can be added to the editor using Scheme.
BRL-CAD is a powerful constructive solid geometry solid modeling system that includes an interactive geometry editor, ray-tracing support for rendering and geometric analysis, path-tracing for realistic image synthesis, network distributed framebuffer support, and image and signal-processing tools.
Genius is an arbitrary precision integer and multiple precision floating point calculator. It includes its own programming language similar in some aspects to C, bc, or Pascal. It can deal with rational numbers and complex numbers. It has matrix support as well. It uses the gmp library so it is very fast for calculations of large numbers. It has a command line and a GNOME interface. The GNOME interface supports plotting functions and 3D surfaces.
SaVi is satellite visualization software that lets you create, run, examine, and modify satellite orbits in two and three dimensions. Simulations of Iridium, Globalstar, Galileo, GPS, and other satellite constellations are included. SaVi requires Tcl and Tk on a system with Unix libraries. SaVi works well with the 3D renderer Geomview. Geomview is optional, though recommended for its 3D rendering capabilities.
ROOT is an OO framework for large-scale scientific data analysis and data mining. It contains an efficient hierarchical OO database, a C++ interpreter, advanced statistical analysis, visualization, introspection, documentation, networking, and GUI classes. The command/scripting language is C++, and large scripts can be compiled and dynamically linked in. Using the PROOF (Parallel ROOT Facility) extension, large databases can be analyzed in parallel. The system runs on all known POSIX platforms, Windows, and MacOS X.
OpenVRML is a VRML and X3D browser plug-in and C++ toolkit for incorporating VRML/X3D support into applications. It provides VRML97 and Classic VRML X3D parsers, a runtime, and an OpenGL renderer as C++ libraries. The renderer is fully separate from the runtime library so that users can also provide their own renderer. The OpenVRML browser is provided as a D-Bus service, and is embeddable in host applications using XEmbed. The distribution provides both a stand-alone host and a host that runs as a Mozilla plug-in.
VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD uses OpenGL and OpenGL Programmable Shading Language for high performance rendering of large structures.
The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.