RSS 52 projects tagged "Bioinformatics"

No download Website Updated 02 Nov 2004 Cactus

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Pop 152.45
Vit 3.46

Cactus is a general, modular, parallel environment for solving systems of partial differential equations. The code has been developed over many years by a large international collaboration of numerical relativity and computational science research groups and can be used to provide a portable platform for solving any system of partial differential equations.

Download Website Updated 01 Oct 2006 Jmol

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Pop 199.53
Vit 8.19

Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.

Download Website Updated 14 Feb 2012 VMD

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Pop 129.52
Vit 13.42

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 Website Updated 17 Oct 2004 Artemis

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Pop 19.36
Vit 2.00

Artemis is a DNA sequence viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. It can read and write complete EMBL and GENBANK database entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK, or GFF format.

Download Website Updated 22 May 2011 Chemistry Development Kit

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Pop 111.28
Vit 11.44

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 10 Jul 2009 Open Babel

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Pop 97.95
Vit 5.30

Open Babel is a community-driven scientific project including both cross-platform programs and a developer library designed to support molecular modeling, chemistry, and many related areas, including interconversion of file formats and data.

Download Website Updated 16 Jul 2007 Biomolecule Toolkit

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Pop 31.86
Vit 3.24

The Biomolecule Toolkit is an Open Source library for the structural modeling of biological macromolecules. The toolkit provides a C++ interface for common tasks in computational structural biology, to facilitate the development of molecular modeling, design, and analysis tools.

Download Website Updated 12 Mar 2011 Lush

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Pop 127.21
Vit 5.43

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.

Download Website Updated 24 Jul 2003 Swiss-PdbViewer

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Pop 21.54
Vit 1.78

Swiss-PdbViewer is an application that provides a user friendly interface for analyzing several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and to compare their active sites or any other relevant parts. Amino acid mutations, H- bonds, angles, and distances between atoms are easy to obtain with the intuitive graphic and menu interface.

No download Website Updated 01 Feb 2003 PubCrawler

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Pop 16.73
Vit 1.00

PubCrawler is a script for an "alerting" service which scans daily updates to the NCBI Medline (PubMed) and GenBank databases. When PubCrawler is run daily, the results can keep scientists informed of the current contents of Medline and GenBank by listing new database entries that match their research interests.

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Efax-gtk

A GUI frontend for the efax fax program.

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ChaosEsque Anthology

A first person shooter with extended options.