228 projects tagged "Bioinformatics"

Download Website Updated 27 Sep 2007 Fast Genetic Algorithm

Screenshot
Pop 118.64
Vit 4.55

FGA (Fast Genetic Algorithm) is a simple yet powerful implementation of genetic algorithms. The library provides many variants of crossover and selection procedures, and a parallel version of the algorithm is included.

Download Website Updated 22 Sep 2006 spsim

Screenshot
Pop 17.23
Vit 1.00

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.

Download Website Updated 22 Jan 2008 Adun

Screenshot
Pop 24.70
Vit 2.91

Adun is an extensible biomolecular simulation program that includes data management and analysis capabilities.

Download Website Updated 04 May 2007 PrIMETV

Screenshot
Pop 14.76
Vit 1.80

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.

No download Website Updated 24 Oct 2006 ParFE

Screenshot
Pop 14.00
Vit 52.66

parFE is fully-parallel high-performance finite element code targeted to the modeling of trabecular bones in humans. It employs scalable multigrid solvers for efficient solutions on massively parallel computers.

Download Website Updated 10 Sep 2007 Optimization Algorithm Toolkit

Screenshot
Pop 35.28
Vit 2.36

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.

No download Website Updated 21 Dec 2006 Bird Weights

Screenshot
Pop 9.59
Vit 1.00

birdweights is a package of scripts to analyze data from an automated system for the measurement of mass and identification of birds at perches.

Download Website Updated 04 Feb 2007 chemical-mime-data

Screenshot
Pop 13.11
Vit 1.42

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.

Download Website Updated 28 Mar 2007 ESTScan

Screenshot
Pop 14.90
Vit 1.42

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.

No download Website Updated 24 Feb 2007 APBS

Screenshot
Pop 23.62
Vit 51.48

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.

Screenshot

Project Spotlight

Open Camera

A camera app for Android.

Screenshot

Project Spotlight

mcl-edge

A command-line network analysis workbench.