octopus is a program aimed at the ab initio virtual experimentation on a hopefully ever increasing range of systems types. Electrons are describe quantum-mechanically within the Density-Functional Theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the Pseudopotential approximation.
iloog is a Gentoo-based live CD targeted mainly at students and scientists. It features UnionFS filesystem support that enables you to write everywhere on the LiveCD and install extra packages, a graphical X environment through the Fluxbox window manager, many programming editors and IDEs, and a plethora of scientific applications, including Octave, Namd, Merlin, and full (La)TeX support.
Math::GSL is a Perl API to the GNU Scientific Library, which contains a large set of tools for writing scientific computing applications, like statistical distributions, special functions, random number generators, linear algebra, numeric integration/derivatives, FFTs, wavelets, and much more.
Zeobuilder is a user-friendly GUI toolkit for the construction of advanced molecular models. It is extensible via a plugin framework and contains several advanced tools for building, aligning, manipulating, and analyzing molecular structures. It describes a molecular model with a hierarchical data-structure of reference frames. This facilitates operations on models at different levels of detail.
QuBit is a library to support quantum superpositions in C++. This allows each variable of the CQuBit type to hold a number of different values at the same time. Normal mathematical operations can be performed on a QuBit, but they affect every value in the QuBit, at the same time. Binary operations on two QuBits cause a result based on every possible outcome.
pyXSD maps XML and XSD (XML Schema) files into Python, checks the XML against the schema, and transforms XML documents according to user-specified Python classes. There is a framework to make these transformation classes easy to write. The program uses a simple, pythonic, non-DOM interface with the XML tree structure.
spsim is a simple yet realistic diffraction pattern simulator for single particle diffraction experiments, as those made possible with the advent of XFELs. It takes a PDB as input and outputs noise-free and realistic diffraction patterns according to the experimental conditions chosen by the user.