The Globus Galaxies platform: Delivering science gateways as a service

Concurrency and Computation: Practice and Experience

Volumn 27, Issue 16, 2015, Pages 4344-4360

  Madduri, Ravi ^a   Chard, Kyle ^a   Chard, Ryan ^b   Lacinski, Lukasz ^a   Rodriguez, Alex ^a   Sulakhe, Dinanath ^a   Kelly, David ^a   Dave, Utpal ^a   Foster, Ian ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b VICTORIA UNIVERSITY OF WELLINGTON   (New Zealand)

Author keywords

Cloud Computing; HPC; Science Gateways

Indexed keywords

APPLICATION PROGRAMS; CLOUD COMPUTING; DATA TRANSFER; GALAXIES; INFORMATION MANAGEMENT; METADATA; PLATFORM AS A SERVICE (PAAS); USER EXPERIENCE;

APPLICATION HOSTING; CLOUD INFRASTRUCTURES; DESIGN AND IMPLEMENTATIONS; DOMAIN INDEPENDENTS; SCIENCE APPLICATIONS; SCIENCE GATEWAY; SCIENTIFIC SOFTWARES; WORKFLOW EXECUTION;

GATEWAYS (COMPUTER NETWORKS);

EID: 84944919479     PISSN: 15320626     EISSN: 15320634     Source Type: Journal    
DOI: 10.1002/cpe.3486     Document Type: Article

References (29)

1. Foster I,. Service-oriented science. Science 2005; 308 (5723): 814-817.
2. Rion Dooley MV, Dan S, Steve T, Edwin S,. Software-as-a-service: the iPlant Foundation API. In 5th IEEE Workshop on Many-Task Computing on Grids and Supercomputers (MTAGS). Salt Lake City: Utah, 2012.
3. Foster I,. Globus online: accelerating and democratizing science through cloud-based services. IEEE Internet Computing 2011 (May/June); 15: 70-73.
4. McLennan MK, Kennell R,. HUBzero: a platform for dissemination and collaboration in computational science and engineering. Computing in Science & Engineering 2010; 12 (2): 48-53.
5. Marru S, et al,. Apache Airavata: a framework for distributed applications and computational workflows. In Proceedings of the 2011 ACM Workshop on Gateway Computing Environments. ACM: Seattle, Washington, USA, 2011; 21-28.
6. Lifka D, Foster I, Mehringer S, Parashar M, Redfern P, Stewart C, Tuecke S, XSEDE Cloud Survey Report.
7. Madduri, RK, et al,. Experiences building Globus Genomics: a next-generation sequencing analysis service using Galaxy, Globus Online and Amazon Web Services. Concurrency-Practice and Experience, 2013.
8. Goecks J, Nekrutenko A, Taylor J,. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology 2010; 11 (8): R86.
9. Allen B, et al,. Software as a service for data scientists. Communications of the ACM 2012; 55 (2): 81-88.
10. Ananthakrishnan R, et al,. Globus Nexus: an identity, profile, and group management platform for science gateways and other collaborative science applications. In Science Gateway Institute Workshop, co-located with IEEE Cluster. IEEE: Indianapolis, IN, 2013; 1-3.
11. Wilde M, et al,. Parallel scripting for applications at the petascale and beyond. IEEE Computer 2009; 42 (11): 50-60.
12. Litzkow MJ, Livny M, Mutka MW,. Condor-a hunter of idle workstations. In 8th International Conference on Distributed Computing Systems, 1988; 104-111.
13. Amazon. Amazon Web Services; Available from: http://www.aws.amazon.com [Accessed 21 January 2015].
14. Bo L, et al,. Deploying bioinformatics workflows on clouds with Galaxy and Globus Provision. In High Performance Computing, Networking, Storage and Analysis (SCC), 2012 SC Companion. IEEE Computer Society: Washington, DC, USA Salt Lake City, Utah, 2012; 1087-1095.
15. Hupp S,. REAN Cloud partners with Globus Genomics to scale genomics research with HIPAA compliance: Available from: http://tickerreport.com/press-releases/384283/rean-cloud-partners-with-globus-genomics-to-scale-genomics-research-with-hipaa-compliance/ [Accessed 21 January 2015]
16. Trubetskoy V, et al,. Consensus genotyper for exome sequencing (CGES): improving the quality of exome variant genotypes. Bioinformatics 2015; 31 (2): 187-93.
17. Krampis K, et al,. Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community. BMC Bioinformatics 2012; 13: 42.
18. Winslow RL, et al,. The cardiovascular research grid project. AMIA Summits Transl Sci Proc, 2011.
19. Goldberger AL, et al,. Physiobank, physiotoolkit, and physionet components of a new research resource for complex physiologic signals. Am Heart Assoc. 101 (23): e215-e220 0009-7322.
20. Granite S,. Waveform ECG. 2014; Available from: http://cvrgrid.org/tools/waveform-ecg [Accessed 21 January 2015]
21. Post AR, et al,. Temporal abstraction-based clinical phenotyping with Eureka!. AMIA Annual Symposium Proceedings 2013; 2013: 1160-1169.
22. Montella RB, et al,. FACE-IT: a science gateway for food security research. In 9th Gateway Computing Environments Workshop. IEEE: New Orleans, 2014; 42-46.
23. Chard K, et al,. A cloud-based image analysis gateway for traumatic brain injury research. In Proceedings of the 9th Gateway Computing Environments Workshop. IEEE Press: New Orleans, Louisiana, 2014; 13-16.
24. Chard R, et al,. PDACS: a portal for data analysis services for cosmological simulations. In Proceedings of the 9th Gateway Computing Environments Workshop. IEEE Press: New Orleans, Louisiana, 2014; 30-33.
25. Cholia S, Skinner D, Boverhof J,. NEWT: A RESTful service for building high performance computing web applications. In Gateway Computing Environments Workshop (GCE). IEEE Press: New Orleans, LA, 2010; 1-11.
26. Ming M, Humphrey M,. A Performance Study on the VM Startup Time in Proceedings of the 5th IEEE International Conference on Cloud Computing (CLOUD). 2012.
27. Afgan E, et al,. Harnessing cloud computing with Galaxy Cloud. Nat Biotech 2011; 29 (11): 972-974.
28. Czajkowski K, et al,. A resource management architecture for metacomputing systems. In Job Scheduling Strategies for Parallel Processing. Springer: Florida, USA, 1998; 62-82.
29. Altinay C, et al,. High-Performance Scientific Computing for the Masses: Developing Secure Grid Portals for Scientific Workflows in Proceedings of the 6th IEEE International Conference on e-Science (e-Science). 2010.