RSS 227 projects tagged "Bioinformatics"

Download Website Updated 06 Jun 2001 Genpak

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Pop 38.57
Vit 2.96

Genpak is a small set of utilities designated to process DNA, RNA, and protein sequences in a very Un*x-like manner. This way, Genpak programs can be combined using pipes and redirections, as well as easily incorporated into CGI scripts. The utilities include a program for calculating GC content, Tm, translating DNA/RNA sequences into protein sequences, quick sequence retrieval, random sequence generation, and finding promoter sequences using a Hertz matrix.

Download Website Updated 24 Sep 2007 Ghemical

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Pop 149.57
Vit 6.70

Ghemical is a molecular modelling software package with some nice 3D visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). The geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms are included. Ghemical is written in C++, and hopefully offers a good framework for a generic freeware molecular modelling tool.

Download Website Updated 21 Nov 2011 GoFigure2

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Pop 45.83
Vit 41.33

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 Website Updated 08 Jul 2003 GraphPak for Qt

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Pop 39.37
Vit 1.00

GraphPak is a programming library of 2D and 3D charting objects for the Qt toolkit. It provides software developers with a set of C++ objects to easily create charts or graphs that aid in the visual presentation of technical and business data. This release includes Bar, Line, Pie, Ring, Area, Hi-Lo, Box and Whisker, and Polar charts. It is based on the KD Chart product from Klarälvdalens Datakonsult AB.

Download Website Updated 14 Feb 2008 HapCluster++

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Pop 24.12
Vit 4.62

HapCluster++ is a software package for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. HapCluster++ is a C++ implementation of the method described in the paper "Fine Mapping of Disease Genes via Haplotype Clustering" by E.R.B. Waldron, J.C. Whitaker, and D.J. Balding. Genetic Epidemiology. 30: 170–179. (2006).

Download Website Updated 17 Jun 2008 IU Parallel FastDNAML

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Pop 8.06
Vit 46.18

IU parallel fastDNAml is a program that infers evolutionary histories from genetic sequences, modified and extended from the serial version of fastDNAml to run in parallel on heterogeneous and widely distributed systems.

Download Website Updated 27 Jan 2006 ImageJ

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Pop 58.86
Vit 1.43

ImageJ is an image processing program inspired by NIH Image for the Macintosh. It can display, edit, analyze, process, save, and print 8-bit, 16-bit, and 32-bit images. There are modules for biology, astronomy, nuclear medicine, physics, and more. If you can take a picture of something, whether with a microscope, a telescope, an oscilloscope, an xray machine, or a scanner, then this program will let you enhance, manipulate, and measure the results.

No download Website Updated 17 Jun 2008 Indiana University CLSD Parser Scripts

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Pop 8.31
Vit 46.18

The Indiana University CLSD Parser Scripts are data ingest parsers for the Centralized Life Science Data service for use with IBM DiscoveryLink/DB2.

Download Website Updated 23 Aug 2005 Isotopic Pattern Calculator

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Pop 36.33
Vit 3.84

IPC (Isotopic Pattern Calculator) is a tool for mass spectrometry that calculates the isotopic distribution of a given chemical formula or peptide sequence. It uses gnuplot to visualize the results.

Download Website Updated 22 Sep 2006 JChemPaint

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Pop 172.07
Vit 9.11

JChemPaint is a program for drawing 2D chemical structures like those found in most chemistry textbooks.

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termit

A vte-based terminal emulator.

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fcmm

A fast concurrent memoization map.