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.
PrIMETV is a program that can visualize tree-within-tree phenomena such as gene/species tree reconciliations. Output can be given in a range of formats, including PostScript, Fig, and SVG. Thus, it is possible to easily edit the final illustration in many available drawing programs. PrIMETV can also directly manipulate important attributes such as color and layout policy.
Optimization Algorithm Toolkit is a workbench and toolkit for developing, evaluating, and playing with classical and state-of-the-art optimization algorithms on standard benchmark problem domains. It includes reference algorithm implementations, graphing, visualizations, and much more.
The chemical-mime-data package is a collection of data files to add support for various chemical MIME types on Linux/Unix desktops, such as KDE and GNOME. Chemical MIME types were proposed in 1995, though it seems they have never been registered with IANA. But they are widely used, and the project's aim is to support these important but unofficial MIME types. Initial data was taken from "The Chemical MIME Home Page" of Henry Rzepa.
ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. It is not a gene prediction program, nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity.
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.