228 projects tagged "Bioinformatics"

Download Website Updated 14 Feb 2012 VMD

Screenshot
Pop 134.44
Vit 13.15

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.

Download No website Updated 13 Feb 2012 Mychem

Screenshot
Pop 16.73
Vit 3.27

Mychem is an extension that provides a set of functions that permit you to handle chemical data within a MySQL database.

Download Website Updated 21 Nov 2011 GoFigure2

Screenshot
Pop 40.60
Vit 41.79

GoFigure2 is a cross-platform application for visualization, processing, and analysis of out-of-core multidimensional microscopy data (5D data sets). Users can visualize images, segment cells in 3d, track cells through time, and detect cell divisions to generate lineages. Results are stored in a MySQL database back-end. Once data has been processed, cell-based object features are quantified and can be used for sorting, color-coding, analysis, or exported to external tools. GoFigure2 was developed for biology research including studying the development of embryos (zebrafish and mouse), synthetic biology (signaling), and for drug screening.

No download No website Updated 31 Oct 2011 ODES

Screenshot
Pop 12.00
Vit 30.68

ODES is a pthreads parallelized exact algorithm to enumerate all maximal sub-graphs of a graph that exceed a specified cutoff density of at least 1/2, even if they overlap.

Download Website Updated 28 Oct 2011 BALLView

Screenshot
Pop 61.25
Vit 6.59

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.

Download Website Updated 28 Oct 2011 NAMD

Screenshot
Pop 62.75
Vit 9.20

NAMD is a parallel, object-oriented molecular dynamics program designed for high-performance simulation of large biomolecular systems.

Download Website Updated 26 Oct 2011 E-Cell System

Screenshot
Pop 129.90
Vit 12.44

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.

Download Website Updated 22 May 2011 Chemistry Development Kit

Screenshot
Pop 110.36
Vit 11.29

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.

Download Website Updated 14 Apr 2011 Scalable Assembler at Notre Dame

Screenshot
Pop 21.35
Vit 1.04

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.

Download Website Updated 07 Apr 2011 JHeatChart

Screenshot
Pop 68.64
Vit 1.88

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.

Screenshot

Project Spotlight

Open Camera

A camera app for Android.

Screenshot

Project Spotlight

mcl-edge

A command-line network analysis workbench.