BioJava aims to provide a comprehensive set of Java components for the rapid development of applications in Bioinformatics. It contains interfaces for representing Sequences, Features, and other important bioinformatics concepts. It can also read and write sequence data in a variety of common formats and communicate with Ensembl databases and with DAS and BioCorba servers.
Cactus is a general, modular, parallel environment for solving systems of partial differential equations. The code has been developed over many years by a large international collaboration of numerical relativity and computational science research groups and can be used to provide a portable platform for solving any system of partial differential equations.
SimSoup is a graphical artificial chemistry simulator for Linux and Windows. The program enables a chemistry to be defined in terms of molecule types and the possible interactions between them. A simulation run involves setting up a number of molecules of various molecule types in a reactor, and then allowing interactions to take place over a period of time. Interactions taking place in the reactor are shown on a graphical display. The motivation for development of the program is to enable investigations into the behaviour of networks, particularly in relation to 'metabolism first' theories of the origin of life, although the basic design supports modeling of any network in which interactions can take place between nodes. Currently, development has reached the prototype stage.
Asymptopia Flashcard System uses Motif and LaTeX to produce, manage, and use attractively formatted flashcards. You load some or all of your "collections" and set the timer for pop-up frequency. The GUI interface and "Collection Manager" make creating and modifying flashcards as simple as pushing a single button. A knowledge of LaTeX is only required when entering special symbols.
APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.
Powua is a parallel super-computer consisting of many processors that work simultaneously. The Powua client lets users access this high computing power from wherever they are, directly on their computer, through a simple Internet connection. If your preferred software is supported, you can start using it immediately in Powua and speed up all those processes that would otherwise occupy your processor for a long time. Powua subdivides your operation and distributes it to many processors simultaneously.
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.