Bioinformatics and Clouds
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 Impact
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.
Use of FutureGrid
testbed for evaluating feasibility of cloud
Scale Of Use
A few VMs for experiments, 1 TB to test storage provisioning and access
Publications
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.
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.
FG-26
John Conery
University of Oregon
Active
Project Members
Chris Hoge
David Ozog
Elijah Hamovitz
Holly Arnold
Jason Sydes
Nafisa Chowdhury
Nathan Dunn
Peter Batzel
Raihan Masud
Sohan Akolkar
Tom Conlin
Victor Hanson-Smith
William Voorhees
FutureGrid Experts
Saliya Ekanayake
Yang Ruan
Futuregrid is a resource provider for