226 projects tagged "Bioinformatics"
Updated 28 Oct 2011
BALLView
| Pop | 70.00 |
|---|---|
| Vit | 7.97 |
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 28 Oct 2011
NAMD
| Pop | 66.58 |
|---|---|
| Vit | 11.44 |
NAMD is a parallel, object-oriented molecular dynamics program designed for high-performance simulation of large biomolecular systems.
Updated 26 Oct 2011
E-Cell System
| Pop | 153.31 |
|---|---|
| Vit | 15.38 |
E-Cell System is an object-oriented software suite for modelling, simulation, and analysis of large scale complex systems such as biological cells. It allows many components, driven by multiple algorithms with different timescales, to coexist. The core library is written in C++ with a Python binding, and frontend software uses Python.
Updated 03 Oct 2011
openModeller
| Pop | 77.63 |
|---|---|
| Vit | 9.86 |
openModeller is a C++ framework providing tools and an API to model distribution patterns using a variety of algorithms. It can be used to predict species potential distribution based on a set of georeferenced occurrence points and a set of environmental layers.
Updated 22 May 2011
Chemistry Development Kit
| Pop | 132.82 |
|---|---|
| Vit | 13.31 |
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 14 Apr 2011
Scalable Assembler at Notre Dame
| Pop | 33.50 |
|---|---|
| Vit | 1.06 |
The Scalable Assembler at Notre Dame (SAND) replaces the early stages of the Celera Assembler with scalable versions that can run on collections of commodity computers. By harnessing clusters, clouds, grids, or just random machines in your office, many bioinformatics tasks can be reduced from weeks or months down to minutes or hours.
Updated 07 Apr 2011
JHeatChart
| Pop | 76.01 |
|---|---|
| Vit | 1.94 |
JHeatChart is a one class Java API for generating heat map charts that was created because very few charting APIs seem to contain the facility to create heat maps. It is not a full featured charting API and cannot be used to other charts. The generated charts are created as Java Image objects, which can be incorporated into a GUI or saved to a file.
Updated 06 Apr 2011
Raster3D
| Pop | 53.05 |
|---|---|
| Vit | 4.25 |
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 | 147.48 |
|---|---|
| Vit | 6.21 |
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 Feb 2011
PathVisio
| Pop | 74.74 |
|---|---|
| Vit | 4.21 |
PathVisio is a bioinformatics tool that lets you do everything with biological pathway diagrams. PathVisio helps you organize biological information and lets you present or publish that information easily. You can create and draw pathways, export them to many image formats, annotate them with links to online biological databases such as Ensembl, Entrez or HMDB, and add comments and literature references from pubmed. PathVisio also lets you sort through high-throughput experimental data in pathway context. This is a much more pleasant way to present data than just a large table. You can import microarray, proteomics or metabolomics data. PathVisio has a plugin interface that lets users customize it to new analysis types, new visualization methods, and new pathway formats. PathVisio is compatible with WikiPathways.
