228 projects tagged "Bioinformatics"

No download Website Updated 16 Mar 2006 CatDCD

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Pop 21.63
Vit 1.80

CatDCD functions much like the Unix "cat" command: it concatenates DCD files into a single DCD file. You can also use CatDCD to write only selected atoms to the final DCD file.

Download Website Updated 17 Dec 2007 Cell Electrophysiology Simulation Environment

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Pop 40.10
Vit 4.30

Cell Electrophysiology Simulation Environment is a framework to perform electrophysiological simulations. It can, for example, simulate cardiac myocyte electrical activity. It is useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations.

No download Website Updated 05 Aug 2010 CellProfiler

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Pop 23.02
Vit 2.11

CellProfiler is a system for analyzing cell images. It is designed for biologists without training in computer vision or programming to make quantitative measurements of cells in thousands of images automatically. It is implemented using Matlab, but compiled standalone versions are available.

Download No website Updated 09 Jul 2003 CgiBlast

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Pop 17.92
Vit 1.00

CgiBlast is a CGI interface to NCBI's Basic Local Alignment Search Tool, giving widespread access to the genetics search tool. It uses the CFour CgiParser library.

Download Website Updated 22 May 2011 Chemistry Development Kit

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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 30 Jan 2001 Clarrhmos

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Pop 31.14
Vit 1.00

Clarrhmos is a description language and simulator for myocardial structure and electrophysiology. Input to the program is a model file specifying types of cells, action potential shape, refractory period, 3D placement of the cells, relation of parameters to other functions, pacing, electrode placement. Output is a file describing depolarisation and repolarisation of the myocardium and electrograms. A graphic tool for interactive inspection of the output file is also included.

Download Website Updated 05 Jan 2004 Cluster Installation Finishing Scripts

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Pop 43.24
Vit 2.36

The Finishing Scripts for Cluster Installations handle specific post-installation configuration that might not be convienent nor possible using existing cluster installation methods. The usual installation process is used to build a reasonably configured node, and the system then reboots into normal mode, achieves network visibility, and executes the finishing script. The finishing script handles all of the finer details of installing packaged or non-packaged software, tweaking installation, setting host/net specific parameters/files, etc. It is controlled via a single, easily modified script.

Download Website Updated 07 Mar 2006 ClusterControl

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Pop 31.97
Vit 1.00

ClusterControl is a Web interface to simplify distributing and monitoring (bioinformatics) applications on Linux cluster systems. It is based on a modular concept that enables integration of command line oriented programs into the application framework of ClusterControl. The system enables integration of different applications accessed through one interface and executed on a distributed cluster system. It uses Apache, PHP, and OpenPBS or Sun Grid Engine.

Download Website Updated 28 Feb 2006 CoaSim

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Pop 42.31
Vit 5.96

CoaSim is a tool for simulating the coalescent process with recombination and gene conversion under the assumption of exponential population growth. It efficiently constructs the ancestral recombination graph for a given number of individuals and uses this to simulate samples of SNP and micro satellite haplotypes/genotypes. The generated sample can afterwards be separated in cases and controls, depending on the states of selected individual markers. The tool can accordingly also be used to construct cases and control data sets for association studies.

Download Website Updated 19 Apr 2006 DNALinux

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Pop 62.94
Vit 2.98

DNALinux is a live Linux distribution with bioinformatics software preloaded. It is for people who find it hard to install EMBOSS, Primer3, BLAST, and other bioinformatics software or who want to have a test system for class or demonstration purposes.

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Open Camera

A camera app for Android.

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mcl-edge

A command-line network analysis workbench.