Bioinformatics and Clouds

Project Details

Project Lead
John Conery 
Project Manager
John Conery 
Project Members
David Ozog, Tom Conlin, Chris Hoge, Nathan Dunn, William Voorhees, Raihan Masud, Elijah Hamovitz, Victor Hanson-Smith, Nafisa Chowdhury, Sohan Akolkar, Jason Sydes, Peter Batzel, Holly Arnold  
Supporting Experts
Saliya Ekanayake, Yang Ruan  
Institution
University of Oregon, Center for Ecology and Evolutionary Biology  
Discipline
Computer Science (401) 

Abstract

We will explore the use of cloud computing technology for several labs in the Center for Ecology and Evolutionary Biology, in particular groups doing large scale phylogenetic inference and clustering of short sequence reads.

Intellectual Merit

Exploratory

Broader Impacts

We are in the process of installing a local cloud on the UO campus, and would like to get a head start on creating and using VMs.

Scale of Use

A few VMs for experiments, 1 TB to test storage provisioning and access

Results

The goal for our project was to give systems adminstrators and bioinformatics researchers at the University of Oregon some experience with provisioning and launching virtual machines in a cloud computing environment in preparation for our transition to a private cloud to be set up here on campus.

Our group members have been moderately successful.  All were able to run the FutureGrid tutorial and learn how to launch a VM and log into it once it was running.  A few were able to get beyond that step, uploading QIIME and other VM images.  One member reported success with installing software, but found the latency too high to run any sort of interactive software.  Interest in using FG began to wane as (a) we decided to use OpenStack instead of Eucalyptus or Nimbus and (b) more of our systems administrators time needed to be directed toward installing and configuring our system.

Overall this has been a very positive experience, and many of the ideas behind how the FG portal is structured will influence how we try to manage the user experience here.  I would like to keep this project going and continue to use it as a "sandbox" for new students and potentially for some of the research I plan to work on in the near future.