RSS 227 projects tagged "Bioinformatics"

No download Website Updated 24 Aug 2005 Enki

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Pop 45.10
Vit 1.00

Enki is a fast 2D physics-based robot simulator. It is able to simulate cinematics, collisions, sensors, and cameras of robots on a flat surface. It also provides limited support for friction. It is able to simulate groups of robots hundreds of times faster than real-time on a modern desktop computer.

Download Website Updated 23 Aug 2005 ADF MAGE-ML Tool

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Pop 13.60
Vit 1.42

The aim of ADF MAGE-ML Tool is to provide a module for converting ADF files (a tab delimited file representing microarray design layout) into MAGE-ML format, and for generating an ADF from an array design described in MAGE-ML format. The module is build upon the ADF specifications and using MAGE-Stk APIs (Java). MIAME-compliance checking, a logging system, and integration of LifeScience Identifier (LSID) specifications are key components of the module. The module can be used via the command line or a graphical user interface.

Download Website Updated 23 Aug 2005 Isotopic Pattern Calculator

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Pop 36.06
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.

No download Website Updated 16 Aug 2005 BioCoRE

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Pop 49.93
Vit 3.03

BioCoRE is a collaborative work environment for biomedical research, research management, and training. It features easy-to-use tools, among them co-authoring papers and other documents, running applications on supercomputers, sharing molecular visualization over the Internet, notifying project team members of recent project changes by email, chatting, keeping a lab book, and other practical features.

Download Website Updated 18 Jul 2005 QDist

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Pop 34.09
Vit 4.60

The QDist package implements the O(n log^2 n) time method for computing the quartet distance between unrooted evolutionary trees.

Download Website Updated 09 Jul 2005 Fasta2SVG

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Pop 10.00
Vit 1.00

Fasta2SVG is a script that converts a fasta file containing a genomic DNA or protein sequence into an SVG vector graphic. It offers different modes for formatting alignments or simple sequences and various parameters such as color and size, which can be set on the command line.

Download Website Updated 29 Apr 2005 libmba

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Pop 190.33
Vit 4.64

The libmba package is a collection of mostly independent C modules potentially useful to any project. There are the usual ADTs including a linkedlist, hashmap, pool, stack, and varray, a flexible memory allocator, CSV parser, path canonicalization routine, I18N text abstraction, configuration file module, portable semaphores, condition variables, and more. The code is designed so that individual modules can be integrated into existing codebases rather than requiring the user to commit to the entire library. The code has no typedefs, few comments, and extensive man pages and HTML documentation.

Download Website Updated 27 Apr 2005 GENtle

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Pop 24.39
Vit 1.00

GENtle is bioinformatics software for everyday molecular biology tasks. It features DNA and amino acid sequence display and editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, primer design, virtual PCR, online database access, graph/spectra display, PHYLIP interface, and more.

Download Website Updated 14 Apr 2005 FinchTV

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Pop 33.09
Vit 2.35

FinchTV is a way to easily view and edit your DNA sequencer chromatogram data. It can display an entire trace in a scalable multi-pane view, and will also display quality values (when available). You can edit your base calls and save your data to a new chromatogram file for later use, select and copy sequence for use in other applications, and print your trace out to paper or a file. You also have the ability to search your sequence data using regular expressions or simple base queries, to view raw data from .ab1 files, and to reverse complement your sequence and traces.

Download No website Updated 30 Mar 2005 libGenome

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Pop 19.60
Vit 2.00

libGenome is a development library designed to make common operations on DNA and protein sequences easy. libGenome provides functionality to read and write sequence and annotation data in several file formats. It provides a common manipulation interface for sequence and annotation data in any supported file format. Some of the basic manipulation functionality offered by libGenome is concatenation, truncation, reverse complementation, and translation of sequences. It was intended to be used on genome size sequences and is optimized accordingly. This is a cross platform library written in ANSI C++ and is currently supported on any platform with gcc. Metrowerks CodeWarrior on Windows and Mac OS are also supported.

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validator.php

A script to automatically validate HTML code generated by a PHP script.

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DEMUX Framework

A Java framework for building modular, cross-platform applications.