RSS 51 projects tagged "Bioinformatics"

Download Website Updated 26 Dec 2012 massXpert mass spectrometry package

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Pop 215.17
Vit 16.60

The massXpert software package is a mass spectrometry environment for linear (bio-)polymers. It inherits all the innovations of GNU polyxmass. It allows the detailed definition of new polymer chemistries in the XpertDef module. These chemistry definitions are then used in the desktop calculator-like mass calculator (XpertCalc) and in the sophisticated polymer sequence editor and (bio-)chemical/mass spectrometric simulations module (XpertEdit). Available simulations include polymer and monomer chemical modifications, polymer sequence cleavage, gas-phase fragmentation, m/z ratio calculations, and more.

Download Website Updated 14 Feb 2012 VMD

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Pop 130.67
Vit 13.43

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

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Pop 17.55
Vit 3.32

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

Download Website Updated 28 Oct 2011 BALLView

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Pop 62.72
Vit 6.69

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

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Pop 59.51
Vit 9.37

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

Download Website Updated 22 May 2011 Chemistry Development Kit

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Pop 113.73
Vit 11.45

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 No website Updated 24 Feb 2011 Bioinformatics Benchmark System

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Pop 28.55
Vit 1.00

The Bioinformatics Benchmark System is an attempt to build a reasonable testing framework, tests, and data, to enable end users and vendors to probe the performance of their systems. It is not trying to be the last word in informatics benchmarking, as there are simply too many codes, tests, data sets, and databases. The goal is to create a core of tests that all may download and use to probe specific elements of system performance. The end goal is to enable a pluggable set of tests, including the core tests, so that performance data may be gathered.

No download Website Updated 07 Dec 2010 BALL

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Pop 43.47
Vit 3.56

The Biochemical ALgorithms Library (BALL) is a framework for rapid application development in molecular modeling and structural bioinformatics. BALL provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, NMR shift prediction, and visualization. Its extensibility results from an object-oriented and generic programming approach.

Download Website Updated 22 Jul 2010 COPASI

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Pop 26.00
Vit 3.12

COPASI is a software application for modeling and simulation of biochemical networks. The software package has a GUI that lets users define biochemical network models by entering chemical reactions and kinetic equations. A powerful simulation engine can then perform simulations of the dynamics of the networks and carry out many different computational analyses. COPASI can simulate dynamics using either an ODE approach or a stochastic chemical kinetics approach (Gillespie-type algorithms).

No download Website Updated 22 Mar 2010 Ascalaph

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Pop 22.16
Vit 38.60

Ascalaph is a general purpose 3D graphical molecular modeling suite that performs molecular mechanics and molecular dynamics simulations as well as quantum mechanics calculations.

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ChaiScript

An embedded scripting language for C++.

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MUltihost SSH Wrapper

Broadcasts commands over SSH to multiple hosts.