228 projects tagged "Bioinformatics"

Download Website Updated 27 Sep 2009 Bioperl

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Pop 101.02
Vit 7.98

Bioperl is set of Perl Modules for bioinformatics. It contains objects for Sequences, features on Sequences, and other important bioinformatics attributes.

Download Website Updated 14 Jul 2009 mkESA

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Pop 31.30
Vit 1.75

mkESA is a program for constructing enhanced suffix arrays (ESAs) from biological sequence data. The program is based on an implementation of Manzini's lightweight Deep-Shallow algorithm, which can also utilize multiple CPUs/cores for extra performance. The generated output is compatible with the output of mkvtree from the Vmatch package.

Download No website Updated 10 Jul 2009 SPADE

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Pop 33.59
Vit 42.22

The Structural Proteomics Application Development Environment (SPADE) provides a community suite for developing and sharing protein structure and sequence tools. It includes a custom molecular viewer, sequence alignment editor, many reusable tools, and a chemical probing suite to support experimental verification of predicted structural models.

Download Website Updated 10 Jul 2009 Open Babel

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Pop 94.98
Vit 5.27

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 09 Jul 2009 libfid

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Pop 26.78
Vit 1.43

The Full-text Index Data structure library, libfid for short, is a portable software library for accessing indexed data through a simple C interface. It implements, among others, functions for reading indexed data from files, and for performing common operations such as fast string matching. Easy alphabet handling for mapping between printable and binary alphabets is integrated from the ground up. Currently, the enhanced suffix array is the only full-text index data structure supported. A very simplistic program for constructing enhanced suffix arrays is included.

No download Website Updated 26 Jun 2009 CESE Plus

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Pop 19.21
Vit 42.40

CESE Plus is a software platform designed to perform a wide array of cell electrophysiology simulations. It is a universal simulation environment supporting multitude of cell models and systems, including cardiac atrial, ventricular and SA node models, neuronal models, and more. CESE Plus is an enhanced commercial version of the CESE platform. These enhancements include full support for Mac OS X; a split display for comparison of multiple simulated data traces; data import and export between MS Excel, Axon text files, and ASCII tables; powerful cursors to select regions of interest and perform online measurements and statisical analysis; VirtuClamp to simulate voltage clamp and current clamp protocols; improved equation solvers with greater accuracy; and full commercial support.

No download Website Updated 20 Jun 2009 LSystems in PostScript

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Pop 10.86
Vit 57.09

LSystems in PostScript is an L-system implemented entirely in the PostScript language. It can serve as an introduction to PostScript programming for nerds who are familiar with LSystems or as an introduction to L-systems for PostScript programers.

Download Website Updated 17 Apr 2009 R

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Pop 454.99
Vit 12.74

R is a language and environment for statistical computing and graphics. It is similar to S, which was developed at Bell Laboratories by John Chambers et al. It provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc.). R is designed as a true computer language with control-flow constructions for iteration and alternation, and it allows users to add additional functionality by defining new functions. For computationally intensive tasks, Fortran and C code can be linked and called at run time.

Download Website Updated 11 Mar 2009 ploticus

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Pop 289.24
Vit 7.48

PLOTICUS is a command line utility for creating bar, line, pie, boxplot, scatterplot, sweep, heatmap, vector, timeline, Venn diagrams, and other types of charts and plots. ploticus is good for automated or just-in-time graph generation. It handles date, time, and categorical data nicely, and has some basic statistical capabilities. It can output to GIF, PNG, SVG, SWF, JPEG, PostScript, EPS, and X11. You can use convenient preset options or create complex scripts with rich and detailed color and style operations.

No download Website Updated 06 Feb 2009 Evolving Games for Unnatural Intelligence

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Pop 12.00
Vit 44.01

Evolving Games for Unnatural Intelligence is a Java package for unsupervised machine learning based on Evolutionary Game Theory on directed graphs. It is able to segment data without any previuos information on the number of segments. It has no GUI, but implements generalizations of the original method proposed by Li, Chen, He and Jiang in the arxiv paper "A Novel Clustering Algorithm Based Upon Games on Evolving Network", published on 30 Dec 2008.

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Open Camera

A camera app for Android.

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mcl-edge

A command-line network analysis workbench.