Names on Nodes

automated application of biological nomenclature

About Names on Nodes

Names on Nodes is a web application that automatically applies biological nomenclature to datasets. Datasets may be uploaded as bioinformatics files (Nexus, etc.). Names on Nodes uses the definitions of names to apply them to phylogenetic hypotheses.

The basic principles which Names on Nodes uses were laid out in:

Currently Names on Nodes is in development. It is not yet known when it will be launched. Progress can be tracked at Mike Keesey's blog, A Three-Pound Monkey Brain.

Documentation

MathML Definitions

Names on Nodes uses MathML 2.0 to model nomenclatural definitions. To accomplish this, it relies on certain mathematical entities related to phylogeny and taxonomy. These are defined and discussed in the MathML Definitions document.

Entities

Although Names on Nodes will primarily store information in a database, it will also be capable of reading entity information from XML files. The XML format is laid out in the Entity Definitions document.

Open Source Code

The Names on Nodes source code (primarily Java, ActionScript, and MXML) has been moved to Google Code. It is not currently in clean condition, but if you would like to check it out you may do so at the following URL: http://code.google.com/p/namesonnodes

Demo Tools

Until Names on Nodes is complete, a series of small applications will be released online in order to showcase some of the functionality. These present an opportunity to test certain components before the final application is complete.

Nexus Viewer

Nexus Viewer opens Nexus files and displays the trees in them combined into a single phylogenetic network. (Note that this only works properly for Nexus files with rooted trees. For files without rooted trees, it will simply display a series of operational taxonomic units.) Click here.

Text Tree Maker

Text Tree Maker converts Newick tree strings into readable text cladograms. Click here.