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Shulei Sun,
Jing Chen,
Weizhong Li,
Ilkay Altintas, Abel W. Lin,
Steven Peltier,
Karen Stocks,
Eric E. Allen,
Mark H. Ellisman,
Jeffrey S. Grethe,
John Wooley
Nucleic Acids Research. 01/2011; 39:546-551.
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Ilkay Altintas, Abel W. Lin,
Jing Chen,
Chris Churas,
Madhusudan Gujral,
Shulei Sun,
Weizhong Li,
Ramil Manansala,
Mayya Sedova,
Jeffrey S. Grethe,
Mark H. Ellisman
01/2010
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ABSTRACT: The advent of “Grids,” or Grid computing, has led to a fundamental shift in the development of applications for managing and
performing computational or data-intensive analyses. A current challenge faced by the Grid community entails modeling the
work patterns of domain or bench scientists and providing robust solutions utilizing distributed infrastructures. These challenges
spawned efforts to develop “workflows” to manage programs and data on behalf of the end user. The technologies come from multiple
scientific fields, often with disparate definitions, and have unique advantages and disadvantages, depending on the nature
of the scientific process in which they are used. In this chapter, we argue that to maximize the impact of these efforts,
there is value in promoting the use of workflows within a tiered, hierarchical structure where each of these emerging workflow
pieces are interoperable. We present workflow models of the Telescience™ Project1 and BIRN2 architectures as frameworks that manage multiple tiers of workflows to provide tailored solutions for end-to-end scientific
processes.
12/2006: pages 109-125;
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Rajvikram Singh,
Nicholas Schwarz,
Nut Taesombut,
David Lee,
Byungil Jeong,
Luc Renambot, Abel W. Lin,
Ruth West,
Hiromu Otsuka,
Sei Naito,
Steven Peltier,
Maryann E. Martone,
Kazunori Nozaki,
Jason Leigh,
Mark H. Ellisman
Future Generation Comp. Syst. 01/2006; 22:1032-1039.
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First International Conference on e-Science and Grid Technologies (e-Science 2005), 5-8 December 2005, Melbourne, Australia; 01/2005
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18th IEEE Symposium on Computer-Based Medical Systems (CBMS 2005), 23-24 June 2005, Dublin, Ireland; 01/2005
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First International Conference on e-Science and Grid Technologies (e-Science 2005), 5-8 December 2005, Melbourne, Australia; 01/2005
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Toyokazu Akiyama,
Kazunori Nozaki,
Seiichi Kato,
Shinji Shimojo,
Steven Peltier, Abel W. Lin,
Tomas E. Molina,
George Yang,
David Lee,
Mark H. Ellisman,
Kiyokazu Yoshida,
Hirotaro Mori
5th International Symposium on Cluster Computing and the Grid (CCGrid 2005), 9-12 May, 2005, Cardiff, UK; 01/2005
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Future Generation Comp. Syst. 01/2003; 19:1031-1039.
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J. Parallel Distrib. Comput. 01/2003; 63:539-550.
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ABSTRACT: Electron tomography is a powerful tool for deriving three-dimensional (3D) structural information about biological systems within the spatial scale spanning and . With this technique, it is possible to derive detailed models of subcellular components such as organelles and synaptic complexes and to resolve the 3D distribution of their protein constituents in situ. While there continues to be progress towards the integration of high-performance computing technologies with traditional electron tomography processes, there is a significant need for more transparent integration with applications and to minimize the administrative overhead and complexity (resource administration, authentication, scheduling, data delivery) passed on to the non-computer scientist end user. Here we present the “Telescience Portal” (https://gridport.npaci.edu/Telescience) as an example of a fully integrated, web-based solution for performing end-to-end electron tomography. More than just a collection of individual applications, the Portal provides a transparent workflow, where simple intuitive interfaces for grid-enabled parallel computation, resource scheduling, remote instrumentation, advanced image processing and visualization, access to distributed/federated databases, and network-enabled data management and archival are tightly coupled within a secure environment which promotes increased collaboration between researchers. This tightly integrated Telescience system is a test-bed application for using grid resources to accelerate the throughput of data acquisition and processing, increase access to scarce and/or expensive instrumentation, and improve the accuracy of derived data products.
Journal of Parallel and Distributed Computing.
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Ilkay Altintas,
Jing Chen,
Mayya Sedova,
Amarnath Gupta,
Shulei Sun, Abel W. Lin,
Madhusudan Gujral,
Manish K. Anand,
Weizhong Li,
Jeffrey S. Grethe,
Mark Ellisman
[show abstract]
[hide abstract]
ABSTRACT: Community Cyber infrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) is an eScience project to enable the microbial ecology community in managing the challenges of metagenomics analysis. CAMERA supports extensive metadata based data acquisition and access, as well as execution of metagenomics experiments through standard and customized scientific workflows. Users can use a wide range of community analysis tools to select and invoke integrated annotation of genomic datasets. Users can also search and sort information based on selected metadata over the underlying semantic database. We present the semantic data model of CAMERA and its integration with scientific workflow execution information. We also describe how this model is used to interlink related workflows, where outputs of previous workflow executions can be used as inputs by subsequent workflow executions. We demonstrate the effectiveness of our model and approach through scenarios built on currently supported CAMERA workflows and analysis.
2010 Sixth IEEE International Conference on e-Science Workshops.
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[show abstract]
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ABSTRACT: Electron tomography is a powerful technique for deriving 3D structural information from biological specimens. As advanced instrumentation, networking, and grid computing are applied to electron tomography and biological sciences in general, much work is needed to integrate and coordinate these advanced technologies in a transparent way to deliver them to the end user. The Telescience Portal (http://gridport.npaci.edu/Telescience) is a web-based solution for end-to-end electron tomography that centralizes applications and seamlessly interfaces with the grid to accelerate the throughput of data results. In this paper we will describe the architecture and design of the Telescience Portal in the context of our experiences leading up to and including the iGrid2002 workshop. We will examine the lessons learned in developing the production Telescience environment, leveraging a successful international collaboration with groups in Japan and Taiwan, building end-to-end native IPv6 networks across continents, and examining IPv6 enabled mechanisms for transferring large data from two unique, remotely accessible high performance scientific instruments. Traditional computer science communities develop next generation technologies. Applications like Telescience drive these next generation technologies into production quality applications for everyday research needs.
Future Generation Computer Systems.
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Rajvikram Singh,
Nicholas Schwarz,
Nut Taesombut,
David Lee,
Byungil Jeong,
Luc Renambot, Abel W. Lin,
Ruth West,
Hiromu Otsuka,
Sei Naito,
Steven T. Peltier,
Maryann E. Martone,
Kazunori Nozaki,
Jason Leigh,
Mark H. Ellisman
[show abstract]
[hide abstract]
ABSTRACT: At iGrid 2005 we demonstrated the transparent operation of a biology experiment on a test-bed of globally distributed visualization, storage, computational, and network resources. These resources were bundled into a unified platform by utilizing dynamic lambda allocation, high bandwidth protocols for optical networks, a Distributed Virtual Computer (DVC) [N. Taesombut, A. Chien, Distributed Virtual Computer (DVC): Simplifying the development of high performance grid applications, in: Proceedings of the Workshop on Grids and Advanced Networks, GAN 04, Chicago, IL, April 2004 (held in conjunction with the IEEE Cluster Computing and the Grid (CCGrid2004) Conference)], and applications running over the Scalable Adaptive Graphics Environment (SAGE) [L. Renambot, A. Rao, R. Singh, B. Jeong, N. Krishnaprasad, V. Vishwanath, V. Chandrasekhar, N. Schwarz, A. Spale, C. Zhang, G. Goldman, J. Leigh, A. Johnson, SAGE: The Scalable Adaptive Graphics Environment, in: Proceedings of WACE 2004, 23–24 September 2004, Nice, France, 2004]. Using these layered technologies we ran a multi-scale correlated microscopy experiment [M.E. Maryann, T.J. Deerinck, N. Yamada, E. Bushong, H. Ellisman Mark, Correlated 3D light and electron microscopy: Use of high voltage electron microscopy and electron tomography for imaging large biological structures, Journal of Histotechnology 23 (3) (2000) 261–270], where biologists imaged samples with scales ranging from 20X to 5000X in progressively increasing magnification. This allows the scientists to zoom in from entire complex systems such as a rat cerebellum to individual spiny dendrites. The images used spanned multiple modalities of imaging and specimen preparation, thus providing context at every level and allowing the scientists to better understand the biological structures. This demonstration attempts to define an infrastructure based on OptIPuter components which would aid the development and design of collaborative scientific experiments, applications and test-beds and allow the biologists to effectively use the high resolution real estate of tiled displays.
Future Generation Computer Systems.
