Course: Testbed for Metagenomics

Project Information

Microbiology, Immunology, and Virology (611) 

The use of high performance computing resources within microbiology and molecular biology is still foreign to many students and researchers. A course in which these skills will be taught will be undertaken in 2014, however prior to this a testbed experiment must be run to ensure that the course is run smoothly, and the software used within the course can be implemented effectively on FutureGrid resources. A test of two months of FutureGrid resources will be used to evaluate the ability of an experienced user and a new user to the system to successfully navigate FutureGrid, launching and running of virtual machines, and the transfer of completed class material to and from FutureGrid.

Intellectual Merit

This test will educate a new user in the use of FutureGrid and allow for a course in 16S analysis to take place at the University of Oklahoma.

Broader Impacts

This test will provide the gateway for a course at the University of Oklahoma which will allow more researchers to understand and use federated academic grids to their advantage, further democratizing the mass sequencing efforts currently underway.

Project Contact

Project Lead
Blake Stamps (bstamps) 
Project Manager
Blake Stamps (bstamps) 
Project Members
Bradley Stevenson  

Resource Requirements

Hardware Systems
  • india (IBM iDataPlex at IU)
  • sierra (IBM iDataPlex at SDSC)
  • xray (Cray XM5 at IU)
  • bravo (large memory machine at IU)
Use of FutureGrid

This proposal will be used to educate myself and the professor in charge of the course on proper usage of FutureGrid resources and in the implementation of QIIME within a VM on futuregrid resources prior to the course beginning in January, at which point another request will be made to access FutureGrid.

Scale of Use

A few VMs as a testbed for QIIME for one to two months.

Project Timeline

09/18/2013 - 11:59