Scalable online comparative genomics of mononucleosomes: A bigjob

Jack A. Smith, Melissa Romanus, Pradeep Kumar Mantha, Yaakoub El Khamra, Thomas C. Bishop, Shantenu Jha

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

Our goal is to develop workows for simulating arbitrary collections of mononucleosomes in atomic detail as an on demand analysis tool for online comparative genomics. The limiting factor is resource availability. The aim of this paper is to document and share our experiences in providing a general-purpose, easy-to-use and extensible solution for such computations. At the core it involves supporting the execution of high-throughput workloads of high-performance biomolecular simulations on one or more XSEDE machines. Although conceptually simple, it is still a difficult practical problem to solve, especially in a exible, robust, scalable manner. Specifically, we employ BigJob{ an interoperable Pilot-Job. The bulk of this paper is about our experience in executing a very large number of ensembles including the associated non-trivial data management problem. Our experience suggests that although a nascent and edgling technology, BigJob provides a exible and scalable Pilot-Job to support workloads that were hitherto not easy.

Original languageEnglish (US)
Title of host publicationProceedings of the XSEDE 2013 Conference
Subtitle of host publicationGateway to Discovery
DOIs
StatePublished - 2013
EventConference on Extreme Science and Engineering Discovery Environment, XSEDE 2013 - San Diego, CA, United States
Duration: Jul 22 2013Jul 25 2013

Publication series

NameACM International Conference Proceeding Series

Other

OtherConference on Extreme Science and Engineering Discovery Environment, XSEDE 2013
Country/TerritoryUnited States
CitySan Diego, CA
Period7/22/137/25/13

All Science Journal Classification (ASJC) codes

  • Software
  • Human-Computer Interaction
  • Computer Vision and Pattern Recognition
  • Computer Networks and Communications

Keywords

  • Bigjob
  • Chromatin
  • Comparative genomics
  • Computational workow
  • Distributed computing
  • HPC
  • Large scale
  • MD
  • NAMD
  • Nucleosome positioning
  • SAGA

Fingerprint

Dive into the research topics of 'Scalable online comparative genomics of mononucleosomes: A bigjob'. Together they form a unique fingerprint.

Cite this