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Beta
Nexplorer results page with Tree Of Life tree obtained from iTOL in circular format
Screenshot of SPARQL query interface Tree with Alignment data. The popup panel shows options to manipulate data Screenshot that shows the custom dataset interface in nexplorer3
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This software is provided free of charge by the National Institute of Allergy & Infectious Disease.


Nexplorer3

Web-Based application to manipulate character state data

Overview

Nexplorer3 is a web-based application for interactive browsing and manipulation of phylogenetic trees and character data (e.g., data from comparisons of aligned sequences or aligned morphological features), providing image-based manipulation and annotation of trees and data. In addition to the option to upload custom dataset, Nexplorer3 also provides hundreds of datasets for new users to try out.

The back end of Nexplorer3 uses a data model based directly on the Comparative Data Analysis Ontology (CDAO). This makes Nexplorer3 a ?semantic? or ontology-aware application that can be updated and expanded according to the underlying ontology. The ?front end? of Nexplorer3 has been developed using the latest Google Web toolkit (GWT). The CDAO ontology is handled using the Jena semantic framework.

The web interface of Nexplorer explorer has been developed using the latest Google Web toolkit (GWT) and the CDAO ontologies are handled using Jena semantic framework.

We are developing Nexplorer3 to serve two general types of uses

  • a standalone application for end-users who wish to upload, annotate, manipulate and share their own data sets
  • An adaptable front end for databases (e.g., TreeBase, PaVE) and other resources to provide access to character-data-and-trees, allowing end-users to query and view the content

Release

Nexplorer3 is currently released as a public beta. The NIAID OCICB Bioinformatics and Computational Biosciences Branch (BCBB) is currently evaluating accuracy, stability, and scaleability of Nexplorer3. Based on user feedback from our NIAID users, we are adding functionality. We welcome all potential users, including those outside NIAID, to submit bug reports and general feedback. Please report any problems as well as suggestions for improvement to here

Benefits & Features

  • Provides visual manipulation of phylogenetic and character state data
  • Uses data types defined in an extensible, open-source, external ontology (CDAO)
  • Provides option to make semantic queries on the input data using the SPARQL language
  • Helps user in selecting and organizing subset of data from the input data and save the output in comprehensible graphical format

Features planned or in progress

  • Interactive user annotation of rows, columns, or blocks of characters
  • Interaction history allowing roll-backs
  • Online resource model allowing data sharing with permissions

Credits


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