Biomedical case studies in data intensive computing

Geoffrey Fox; Xiaohong Qiu; Scott Beason; Jong Choi; Jaliya Ekanayake; Thilina Gunarathne; Mina Rho; Haixu Tang; Neil Devadasan; Gilbert Liu

doi:10.1007/978-3-642-10665-1_2

Biomedical case studies in data intensive computing

Geoffrey Fox, Xiaohong Qiu, Scott Beason, Jong Choi, Jaliya Ekanayake, Thilina Gunarathne, Mina Rho, Haixu Tang, Neil Devadasan, Gilbert Liu

Discrete Algorithms

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

19 Scopus citations

Abstract

Many areas of science are seeing a data deluge coming from new instruments, myriads of sensors and exponential growth in electronic records. We take two examples - one the analysis of gene sequence data (35339 Alu sequences) and other a study of medical information (over 100,000 patient records) in Indianapolis and their relationship to Geographic and Information System and Census data available for 635 Census Blocks in Indianapolis. We look at initial processing (such as Smith Waterman dissimilarities), clustering (using robust deterministic annealing) and Multi Dimensional Scaling to map high dimension data to 3D for convenient visualization. We show how scaling pipelines can be produced that can be implemented using either cloud technologies or MPI which are compared. This study illustrates challenges in integrating data exploration tools with a variety of different architectural requirements and natural programming models. We present preliminary results for end to end study of two complete applications.

Original language	English
Title of host publication	Cloud Computing - First International Conference, CloudCom 2009, Proceedings
Pages	2-18
Number of pages	17
DOIs	https://doi.org/10.1007/978-3-642-10665-1_2
State	Published - 2009
Event	1st International Conference on Cloud Computing, CloudCom 2009 - Beijing, China Duration: Dec 1 2009 → Dec 4 2009

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	5931 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	1st International Conference on Cloud Computing, CloudCom 2009
Country/Territory	China
City	Beijing
Period	12/1/09 → 12/4/09

Keywords

Clouds
Clustering
Dryad
Hadoop
MapReduce
MPI
Sequencing

Access to Document

10.1007/978-3-642-10665-1_2

Cite this

Fox, G., Qiu, X., Beason, S., Choi, J., Ekanayake, J., Gunarathne, T., Rho, M., Tang, H., Devadasan, N., & Liu, G. (2009). Biomedical case studies in data intensive computing. In Cloud Computing - First International Conference, CloudCom 2009, Proceedings (pp. 2-18). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5931 LNCS). https://doi.org/10.1007/978-3-642-10665-1_2

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title = "Biomedical case studies in data intensive computing",

abstract = "Many areas of science are seeing a data deluge coming from new instruments, myriads of sensors and exponential growth in electronic records. We take two examples - one the analysis of gene sequence data (35339 Alu sequences) and other a study of medical information (over 100,000 patient records) in Indianapolis and their relationship to Geographic and Information System and Census data available for 635 Census Blocks in Indianapolis. We look at initial processing (such as Smith Waterman dissimilarities), clustering (using robust deterministic annealing) and Multi Dimensional Scaling to map high dimension data to 3D for convenient visualization. We show how scaling pipelines can be produced that can be implemented using either cloud technologies or MPI which are compared. This study illustrates challenges in integrating data exploration tools with a variety of different architectural requirements and natural programming models. We present preliminary results for end to end study of two complete applications.",

keywords = "Clouds, Clustering, Dryad, Hadoop, MapReduce, MPI, Sequencing",

author = "Geoffrey Fox and Xiaohong Qiu and Scott Beason and Jong Choi and Jaliya Ekanayake and Thilina Gunarathne and Mina Rho and Haixu Tang and Neil Devadasan and Gilbert Liu",

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Fox, G, Qiu, X, Beason, S, Choi, J, Ekanayake, J, Gunarathne, T, Rho, M, Tang, H, Devadasan, N & Liu, G 2009, Biomedical case studies in data intensive computing. in Cloud Computing - First International Conference, CloudCom 2009, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 5931 LNCS, pp. 2-18, 1st International Conference on Cloud Computing, CloudCom 2009, Beijing, China, 12/1/09. https://doi.org/10.1007/978-3-642-10665-1_2

Biomedical case studies in data intensive computing. / Fox, Geoffrey; Qiu, Xiaohong; Beason, Scott et al.
Cloud Computing - First International Conference, CloudCom 2009, Proceedings. 2009. p. 2-18 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5931 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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Fox G, Qiu X, Beason S, Choi J, Ekanayake J, Gunarathne T et al. Biomedical case studies in data intensive computing. In Cloud Computing - First International Conference, CloudCom 2009, Proceedings. 2009. p. 2-18. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-642-10665-1_2

Biomedical case studies in data intensive computing

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Keywords

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