Literature DB >> 20107625

HPC AND GRID COMPUTING FOR INTEGRATIVE BIOMEDICAL RESEARCH.

Tahsin Kurc1, Shannon Hastings, Vijay Kumar, Stephen Langella, Ashish Sharma, Tony Pan, Scott Oster, David Ervin, Justin Permar, Sivaramakrishnan Narayanan, Yolanda Gil, Ewa Deelman, Mary Hall, Joel Saltz.   

Abstract

Integrative biomedical research projects query, analyze, and integrate many different data types and make use of datasets obtained from measurements or simulations of structure and function at multiple biological scales. With the increasing availability of high-throughput and high-resolution instruments, the integrative biomedical research imposes many challenging requirements on software middleware systems. In this paper, we look at some of these requirements using example research pattern templates. We then discuss how middleware systems, which incorporate Grid and high-performance computing, could be employed to address the requirements.

Entities:  

Year:  2009        PMID: 20107625      PMCID: PMC2811341          DOI: 10.1177/1094342009106192

Source DB:  PubMed          Journal:  Int J High Perform Comput Appl        ISSN: 1094-3420            Impact factor:   1.942


  11 in total

1.  caCORE: a common infrastructure for cancer informatics.

Authors:  Peter A Covitz; Frank Hartel; Carl Schaefer; Sherri De Coronado; Gilberto Fragoso; Himanso Sahni; Scott Gustafson; Kenneth H Buetow
Journal:  Bioinformatics       Date:  2003-12-12       Impact factor: 6.937

2.  An Integrated Framework for Parameter-based Optimization of Scientific Workflows.

Authors:  Vijay S Kumar; P Sadayappan; Gaurang Mehta; Karan Vahi; Ewa Deelman; Varun Ratnakar; Jihie Kim; Yolanda Gil; Mary Hall; Tahsin Kurc; Joel Saltz
Journal:  Proc Int Symp High Perform Distrib Comput       Date:  2009

3.  caGrid 1.0: an enterprise Grid infrastructure for biomedical research.

Authors:  Scott Oster; Stephen Langella; Shannon Hastings; David Ervin; Ravi Madduri; Joshua Phillips; Tahsin Kurc; Frank Siebenlist; Peter Covitz; Krishnakant Shanbhag; Ian Foster; Joel Saltz
Journal:  J Am Med Inform Assoc       Date:  2007-12-20       Impact factor: 4.497

4.  Sharing data and analytical resources securely in a biomedical research Grid environment.

Authors:  Stephen Langella; Shannon Hastings; Scott Oster; Tony Pan; Ashish Sharma; Justin Permar; David Ervin; B Barla Cambazoglu; Tahsin Kurc; Joel Saltz
Journal:  J Am Med Inform Assoc       Date:  2008-02-28       Impact factor: 4.497

5.  Translational Research Design Templates, Grid Computing, and HPC.

Authors:  Joel Saltz; Scott Oster; Shannon Hastings; Stephen Langella; Renato Ferreira; Justin Permar; Ashish Sharma; David Ervin; Tony Pan; Umit Catalyurek; Tahsin Kurc
Journal:  IPDPS       Date:  2008-05-01

6.  e-Science, caGrid, and Translational Biomedical Research.

Authors:  Joel Saltz; Tahsin Kurc; Shannon Hastings; Stephen Langella; Scott Oster; David Ervin; Ashish Sharma; Tony Pan; Metin Gurcan; Justin Permar; Renato Ferreira; Philip Payne; Umit Catalyurek; Enrico Caserta; Gustavo Leone; Michael C Ostrowski; Ravi Madduri; Ian Foster; Subhashree Madhavan; Kenneth H Buetow; Krishnakant Shanbhag; Eliot Siegel
Journal:  Computer (Long Beach Calif)       Date:  2008-11       Impact factor: 2.683

7.  caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid.

Authors:  Joel Saltz; Scott Oster; Shannon Hastings; Stephen Langella; Tahsin Kurc; William Sanchez; Manav Kher; Arumani Manisundaram; Krishnakant Shanbhag; Peter Covitz
Journal:  Bioinformatics       Date:  2006-06-09       Impact factor: 6.937

8.  The caCORE Software Development Kit: streamlining construction of interoperable biomedical information services.

Authors:  Joshua Phillips; Ram Chilukuri; Gilberto Fragoso; Denise Warzel; Peter A Covitz
Journal:  BMC Med Inform Decis Mak       Date:  2006-01-06       Impact factor: 2.796

9.  Taverna: a tool for building and running workflows of services.

Authors:  Duncan Hull; Katy Wolstencroft; Robert Stevens; Carole Goble; Mathew R Pocock; Peter Li; Tom Oinn
Journal:  Nucleic Acids Res       Date:  2006-07-01       Impact factor: 16.971

10.  An application of a service-oriented system to support array annotation in custom chip design for epigenomic analysis.

Authors:  Junghee Han; Dustin Potter; Tahsin Kurc; Greg Singer; Pearlly S Yan; Sun Hao; Shannon Hastings; Stephen Langella; Scott Oster; Ramana V Davuluri; Tim H-M Huang; Joel H Saltz
Journal:  Cancer Inform       Date:  2008-04-10
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  1 in total

1.  geWorkbench: an open source platform for integrative genomics.

Authors:  Aris Floratos; Kenneth Smith; Zhou Ji; John Watkinson; Andrea Califano
Journal:  Bioinformatics       Date:  2010-05-28       Impact factor: 6.937

  1 in total

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