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[Computational-biology] Bioverse version 2.0

Michal Guerquin michalg at gmail.com
Thu Jul 20 15:19:40 EST 2006


I'd like to drop a note about Bioverse. We've been working on it for
many years and have recently reached "2.0" status.


In brief, the Bioverse provides a framework for exploring the
relationships among the molecular, genomic, proteomic, systems, and
organismal worlds.

Presently we house information about almost 500,000 proteins across 54
organisms. Each protein, or molecule, is described in terms of its
sequence, structure, and functions, as well its relationships to other
molecules molecules in terms of interactions and similarity. The
available information is compiled from experimental sources and also
from predictions made using a variety of computational methods,
including those developed by the Samudrala group.  You can read more
about this on the website.

The data and these relationships are viewable with a web browser or an
RPC interface.

Using the web interface, you can search for molecules by entering text
strings that match names, functional annotations, or sequences.
Clicking on a found molecule will reveal an initial view that can have
various sections expanded to reveal more detailed information.

With the RPC interface you can write an application to display our data
in a way that is convenient for you.  The RPC server offers it's data
in XML-RPC form, so you can access it from most programming language


In fact, the Bioverse web application (written in Javascript and
utilizing various "AJAX" techniques for content rendering) queries the
XML-RPC server directly for all its data needs. We are working on
finishing an improvement to Integrator, a tool for graphically
exploring protein interaction networks, which also uses the XML-RPC

We encourage you to check it out and give us your feedback. Write us at
bioverse at compbio.washington.edu or start a thread on the Bioverse
Google group:


Thanks, we hope to hear from you!

The Bioverse Team

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