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.
Berkeley DB XML is a native XML database engine for use within your product. Made available as a C++ library with language bindings for Java, Perl, Python, PHP, and Tcl, it integrates directly into your application (it is not a standalone database server). It provides XQuery access into a database of document containers. XML documents are stored and indexed in their native format using Berkeley DB as the transactional database engine.
Redet is a tool for developing and executing regular expressions using any of more than 50 search programs, editors, and programming languages, intended both for developing regular expressions for use elsewhere and as a search tool in its own right. For each program in each locale, a palette showing the available constructs is provided. The properties of each program are determined by runtime tests, which guarantees that they will be correct for the program version and locale. Additional features include persistent history, extensive help, a variety of character entry tools, and the ability to change locale while running. Redet is highly configurable and fully supports Unicode.
GenomePixelizer 2D plotter (or genoPix2D) generates images (actually interactive canvases) of genomic similarity dot plots in which each "dot" indicates similarity between a pair of genes. Diagonal runs of dots generally indicate collinearity (or synteny) in the genomic regions being compared. The program can compare large (chromosome-scale or even eukaryotic genome-scale) genomic regions, and can produce PostScript output of the dot plots. Images on a genoPix2D canvas are not static. They are interactive, and every dot (element) is associated with corresponding gene annotations that are searchable by gene ID or keyword.