228 projects tagged "Bioinformatics"

Download Website Updated 21 Nov 2011 GoFigure2

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Pop 40.60
Vit 41.79

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.

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.

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.

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 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 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.

No download Website Updated 28 Jan 2009 Electronic Support for Public Health

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Pop 12.53
Vit 44.11

ESP is a secure, automated system that analyzes electronic medical record (EMR) data to identify and report patients with notifiable diseases to the Massachusetts Department of Public Health. The growing use of electronic medical record systems (EMRs) permits efficient re-use of data already being collected by clinicians during routine private practice, offering an unparalleled opportunity to improve public health practice. Information held in EMR systems includes diagnoses, procedures, laboratory test, and treatment information, as well as patient demographic data. This software permits secure, simple, and robust messaging from electronic medical record systems to public health authorities.

Download Website Updated 02 Dec 2009 Bio2RDF

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Pop 28.35
Vit 2.50

The Bio2RDF software is a package which resolves bio2rdf.org semantic Web identifiers corresponding to bioinformatics data and knowledge bases into RDF files which can be consumed by any generic RDF processor.

Download Website Updated 10 Mar 2010 The Digital Seed Vault

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Pop 42.67
Vit 3.10

The Digital Seed Vault is a seed stock database mainly developed for researchers in the plant sciences. It can also be used by people who handle a lot of different seeds, e.g. garden enthusiasts, seed breeders, or seed producers.

Download Website Updated 04 Aug 2008 EPoS

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Pop 11.66
Vit 1.42

EPoS is a modular software framework for phylogenetic analysis and visualization. EPoS combines a powerful graphical user interface with a plugin system that allows simple integration of new algorithms, visualizations, and data structures. EPoS currently supports distance based tree construction from multiple sequence alignments and distance matrices as well as different algorithms to create consensus trees and supertrees. EPoS also integrates a tree visualization module that can be used to compare two trees and export visualizations.

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Open Camera

A camera app for Android.

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mcl-edge

A command-line network analysis workbench.