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Training the Trainers:

High-Performance Computing Tutorial for Computational Science Professionals Collaborating with Biologists

Meeting dates: March 16-18, 2009

Tutorial description
This NIMBioS High Performance Computing (HPC) Tutorial focused on disseminating the tools necessary for organizations and individuals to leverage computational resources for research at the interface of biological/computational/mathematical research. Knowledgeable computational science individuals who may be HPC novices were invited to attend with the goal of enhancing their institutions' capabilities to leverage HPC resources.

Topics:
TeraGrid resources
Visualization and storage
Queue and submission management
Constraints and benefits of different parallelization approaches
Computational biology resources
MATLAB distributed computing toolbox
Case studies in use of HPC in computational/integrative biology

Leadership Team:
Michael Berry, Dept. of Electrical Engineering and Computer Science, UTK
Jim Ferguson, National Institute for Computational Sciences, UTK/ORNL
Mike Langston, Dept. of Electrical Engineering and Computer Science, UTK

Evaluation report (PDF)

Products

Publications

Abu-Khzam FN, Fernau H, Langston MA, Lee-Cultura S, Stege U. 2011. Charge and reduce: A fixed-parameter algorithm for string-to-string correction. Discrete Optimization, 8(1):41-49. [Online]

Abu-Khzam FN, Fernau H, Langston MA, Lee-Cultura S, Stege U. 2010. A fixed-parameter algorithm for string-to-string correction. Published Collection, Proceedings of Computing: the Australasian Theory Symposium, Brisbane, Australia.

Presentations (alphabetically, in reverse chronological order)

Abu-Khzam FN, Fernau H, Langston MA, Lee-Cultura S, Stege U. 2010. A fixed-parameter algorithm for string-to-string correction. Proceedings of Computing: the Australasian Theory Symposium, Brisbane, Australia.

Langston M. June 2009. Generating exact solutions to difficult combinatorial problems on extremely large graphs using out-of-core techniques. TeraGrid 09, Arlington, VA.

Langston M. June 2009. High-throughput computation can help identify key molecular problems on extremely large graphs using out-of-core techniques. Invited talk, Congress of the European Academy of Allergology and Clinical Immunology, Warsaw, Poland.

Langston M, et al. May 2009. Characterizing the gut microbiome in relation to host intestinal mRNA in collaborative cross progenitors. Research presentations at Complex Trait Community Annual Meeting, Manchester, UK.

Langston M, et al. May 2009. Extracting and validating gene-phenotype association networks using the ontological discovery environment. Research presentations at Complex Trait Community Annual Meeting, Manchester, UK.

Education

Banks D. 2011-2012. Undergraduate Course Offering: COSC 462 Parallel Programming. University of Tennessee, Knoxville, TN.

Software, Data, and/or Websites

Berry M, Day J, Franklin M, Ganusov V, Koessler D, Martin J, Reardon C, Rempe C, Srinivasan S. 2012. Online Tutorial: Python for Biologists. [Online]


A goal of NIMBioS is to enhance the cadre of researchers capable of interdisciplinary efforts across mathematics and biology. As part of this goal, NIMBioS is committed to promoting diversity in all its activities. Diversity is considered in all its aspects, social and scientific, including gender, ethnicity, scientific field, career stage, geography and type of home institution. Questions regarding diversity issues should be directed to Dr. Ernest Brothers, the NIMBioS Associate Director for Diversity Enhancement (diversity@nimbios.org). You can read more about our Diversity Plan on our NIMBioS Policies web page. The NIMBioS building is fully handicapped accessible.


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NSF logo. NIMBioS is sponsored by the National Science Foundation through NSF Award #DBI-1300426, with additional support from The University of Tennessee, Knoxville. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
 
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