22 projects tagged "Bioinformatics"
Updated 14 Feb 2012
VMD
| Pop | 132.66 |
|---|---|
| Vit | 17.06 |
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.
Updated 28 Oct 2011
BALLView
| Pop | 68.89 |
|---|---|
| Vit | 7.94 |
BALLView is an extensible viewer for bio-molecular structures. It provides all standard models and offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER, CHARMM, and MMFF94 force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, secondary structure calculation, molecular editing and docking. Since BALLView is based on BALL (the Biochemical ALgorithms Library), it is easily extensible on the level of C++ code. In addition, it provides a Python interface with Integrated Development Environment features to allow interactive rapid prototyping.
Updated 22 May 2011
Chemistry Development Kit
| Pop | 130.65 |
|---|---|
| Vit | 13.27 |
The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.
Updated 06 Apr 2011
Raster3D
| Pop | 52.25 |
|---|---|
| Vit | 4.24 |
Raster3D is a set of powerful tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm that is independent of any graphics hardware.
Updated 12 Mar 2011
Lush
| Pop | 147.09 |
|---|---|
| Vit | 6.20 |
Lush is a Lisp dialect with extensions for object-oriented and array-oriented programming. It is intended as a programming environment for prototyping numerically intensive applications. Unlike alternatives like Python or SciLab, Lush is designed for easy integration of existing C/C++/Fortran codes.
Updated 24 May 2010
OBSearch
| Pop | 42.54 |
|---|---|
| Vit | 3.09 |
OBSearch is a distributed similarity search index. It can (for example) match programs and help to detect Open Source/Libre license violations, find music that sounds like Sisters of Mercy, or match huge vectors of randomly generated integers just for fun.
Updated 20 Jun 2009
LSystems in PostScript
| Pop | 15.33 |
|---|---|
| Vit | 53.75 |
LSystems in PostScript is an L-system implemented entirely in the PostScript language. It can serve as an introduction to PostScript programming for nerds who are familiar with LSystems or as an introduction to L-systems for PostScript programers.
Updated 17 Apr 2009
R
| Pop | 466.48 |
|---|---|
| Vit | 13.77 |
R is a language and environment for statistical computing and graphics. It is similar to S, which was developed at Bell Laboratories by John Chambers et al. It provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc.). R is designed as a true computer language with control-flow constructions for iteration and alternation, and it allows users to add additional functionality by defining new functions. For computationally intensive tasks, Fortran and C code can be linked and called at run time.
Updated 11 Mar 2009
ploticus
| Pop | 290.62 |
|---|---|
| Vit | 8.04 |
PLOTICUS is a command line utility for creating bar, line, pie, boxplot, scatterplot, sweep, heatmap, vector, timeline, Venn diagrams, and other types of charts and plots. ploticus is good for automated or just-in-time graph generation. It handles date, time, and categorical data nicely, and has some basic statistical capabilities. It can output to GIF, PNG, SVG, SWF, JPEG, PostScript, EPS, and X11. You can use convenient preset options or create complex scripts with rich and detailed color and style operations.
Updated 29 Sep 2007
SoundRuler
| Pop | 53.79 |
|---|---|
| Vit | 2.21 |
SoundRuler is a tool for acoustic analysis, graphing, and teaching. It interactively recognizes and measures 35 temporal and spectral properties of each sound in a file. It also features several measurement, graphing, and didactic modules.
