228 projects tagged "Bioinformatics"

Download Website Updated 21 May 2014 mcl-edge

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Pop 199.68
Vit 93.68

MCL-edge is an integrated command-line driven workbench for large scale network analysis. It includes programs for the computation of shortest paths, diameter, clustering coefficient, betweenness centrality, and network shuffles. A module for loading and analyzing gene expression data as a network is provided. The MCL algorithm is a fast and highly scalable cluster algorithm for networks based on stochastic flow. The flow process employed by the algorithm is mathematically sound and intrinsically tied to cluster structure, which is revealed as the imprint left by the process. The threaded implementation has handled networks with millions of nodes within hours and is widely used in the fields of bioinformatics, graph clustering, and network analysis.

Download Website Updated 13 May 2014 Wandora

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Pop 376.65
Vit 69.84

Wandora is a general purpose data extraction, management, and publishing application based on Topic Maps and Java. Wandora has a graphical user interface, layered presentation of knowledge, several data storage options, rich data extraction, import and export capabilities, and an embedded HTTP server that enables dynamic publication of Topic Maps. Wandora is well suited for rapid ontology construction and knowledge mashups.

Download No website Updated 25 Feb 2001 dnacgr

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Pop 14.00
Vit 69.57

dnacgr is a program to visualise patterns in DNA and RNA by using Chaos Game representation. It shows the probability of bases and sequences, and can read .fasta and .seq format files. dnacgr can be used for genome analysis, and it reads millions of bases from files in seconds. It runs on the console, and requires SVGAlib. It prints to a file in PNG format.

Download Website Updated 07 Nov 2001 OmniGene

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Pop 12.73
Vit 67.71

OmniGene is a bioinformatics solution with a user interface inspired by Ensembl, middleware capable of connecting to disparate datasources, and a translation facility for common biological file formats.

No download Website Updated 19 Feb 2002 SLRI Bioinformatics Workshop

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Pop 11.45
Vit 66.94

The Samuel Lunenfeld Research Institute (SLRI) Bioinformatics Toolkit is a mainly C-based cross-platform toolkit for dealing with biological information, especially protein structure/function information. It is based on the NCBI Toolkit.

Download No website Updated 08 Oct 2003 NeoBio

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Pop 12.96
Vit 62.33

NeoBio is a Java class library of computational biology algorithms. The current version consists mainly of pairwise sequence alignment algorithms, such as the classical dynamic programming methods of Needleman and Wunsch (global alignment) and Smith and Waterman (local alignment). A more efficient approach, due to M. Crochemore, G. Landau, and M. Ziv-Ukelson (2002) is also available. All sequence alignment algorithms support simple scoring schemesm as well as substitution matrices such as standard BLOSUM and PAM matrices with constant (linear) gap penalty functions only. Future versions may contain related algorithms such as multiple sequence alignment, database search and protein structure prediction. NeoBio also also provides simple GUI and command line based tools to run the sequence alignment algorithms on DNA and protein sequences.

Download Website Updated 24 Dec 2003 Yawn: Yet Another W* Network

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Pop 24.60
Vit 61.71

Yawn (Yet Another {Weird | Wacky | Witty | Wonderful | W*} Network) is a Java framework for training and testing neural networks independently from the neural model and the test environment being used. The models implemented so far are AppART, GasART, fuzzy ARTMAP, and Multi-Layer Perceptron (MLP).

Download Website Updated 03 Aug 2004 Fingerprint-POC

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Pop 23.45
Vit 59.87

Fingerprint-POC is a fingerprint matching application using the Phase-Only Corelation method.

Download Website Updated 08 Nov 2004 open SPEAR

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Pop 9.06
Vit 59.06

open SPEAR stands for open Simulator of Physical Environment for Agents Research. It is a C++ library designed to build an efficient multi-agents and robotics simulation. The main audience for this project is the robotics/artificial life community.

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.

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Open Camera

A camera app for Android.

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mcl-edge

A command-line network analysis workbench.