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Building cyberinfrastructure for bioinformatics using service oriented architecture

W.W. Li, S. Krishnan, K. Mueller, K. Ichikawa, S. Date, S. Dallakyan, M. Sanner, C. Misleh, Zhaohui Ding, Xiaohui Wei, O. Tatebe, P.W. Arzberger
2006 Sixth IEEE International Symposium on Cluster Computing and the Grid (CCGRID'06)  
Cyberinfrastructure makes the development and deployment of bioinformatics applications easier by providing the framework and components that may be loosely coupled using service oriented architecture.  ...  The availability of this type of cyberinfrastructure suggests that new applications should be designed with the grid in mind, using service oriented architecture for interoperability and efficiency.  ...  This type of complex environment is best developed using the service oriented approach [19] . A. Service oriented approach The concept of service oriented architecture is not new.  ... 
doi:10.1109/ccgrid.2006.1630932 fatcat:bszkz5mfqzapbkl52mkynojxny

PIRE

S. M. Sadjadi, S. Chen, S. Graham, S. Luis, Y. Deng, B. Furht, P. Martinez, N. Bowen, J. Caraballo
2009 The Fifth Richard Tapia Celebration of Diversity in Computing Conference on Intellect, Initiatives, Insight, and Innovations - TAPIA '09  
such as meteorology, bioinformatics, and healthcare.  ...  This Partnership for International Research and Education (PIRE) is a 5-year long project funded by the National Science Foundation that aims to provide 196 international research and training experiences  ...  Its design draws from model-driven engineering [8, 9] , communication middleware [10] , and software virtualization and service-oriented architectures.  ... 
doi:10.1145/1565799.1565814 dblp:conf/tapia/SadjadiCGLDFMBC09 fatcat:emlqxepkqncffabex7vin6w3uy

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

Stephen A. Goff, Matthew Vaughn, Sheldon McKay, Eric Lyons, Ann E. Stapleton, Damian Gessler, Naim Matasci, Liya Wang, Matthew Hanlon, Andrew Lenards, Andy Muir, Nirav Merchant (+53 others)
2011 Frontiers in Plant Science  
The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for  ...  new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure  ...  for semantic web services use.  ... 
doi:10.3389/fpls.2011.00034 pmid:22645531 pmcid:PMC3355756 fatcat:nwkuqfhsorddrppjjzs6oz76ci

Trends in life science grid: from computing grid to knowledge grid

Akihiko Konagaya
2006 BMC Bioinformatics  
Data grid technologies are strong candidates for realizing "resourceome" for bioinformatics.  ...  Grid computing has great potential to become a standard cyberinfrastructure for life sciences which often require high-performance computing and large data handling which exceeds the computing capacity  ...  Acknowledgements The authors express special thanks for the member of the Open Bioinformatics Grid project and anonymous reviewers for their valuable discussion and useful comments for this manuscript.  ... 
doi:10.1186/1471-2105-7-s5-s10 pmid:17254294 pmcid:PMC1764466 fatcat:tlemqfzeljfdbaxa6gw5mid7f4

Service-Oriented Science

I. Foster
2005 Science  
Students and researchers must acquire new skills to build and use services. New cyberinfrastructure is required to host services, especially as demand increases.  ...  The term Bservice-oriented architecture[ refers to systems structured as networks of loosely coupled, communicating services (9) .  ...  Since its beginnings in the early 1990s, the Web has become an indispensable tool not just for the scientific world, but for the humanities, business, and recreation.  ... 
doi:10.1126/science.1110411 pmid:15879208 fatcat:e6ew3po7nzfwhc5gyhp4g6cqfi

Using a shared, remote cluster for teaching HPC

Clay Carley, Larry Sells, Brett McKinney, Chao Zhao, Henry Neeman
2013 2013 IEEE International Conference on Cluster Computing (CLUSTER)  
In the context of the Oklahoma Cyberinfrastructure Initiative, the University of Oklahoma has been providing its centrally managed clusters for use by courses statewide.  ...  This paper explores mechanisms for using this shared, remote resource for teaching, and advocates in favor of such use.  ...  Many bioinformatics and machine learning tools use specific file formats, requiring conversion; for example, PARF uses the Attribute-Relation File Format (ARFF) format, which was made popular by the Waikato  ... 
doi:10.1109/cluster.2013.6702630 dblp:conf/cluster/CarleySMZN13 fatcat:pxu3drp27nehnbwkq6c75ixxxi

A Service-Oriented Data Integration and Analysis Environment for In Silico Experiments and Bioinformatics Research

Xiaorong Xiang, Gregory Madey, Jeanne Romero-Severson
2007 2007 40th Annual Hawaii International Conference on System Sciences (HICSS'07)  
In this paper, we present a practical experiment of building a service-oriented system upon current web services technologies and bioinformatics middleware.  ...  Our evaluation demonstrates that a service-oriented architecture can accelerate scientific research, increase research productivity, and provide a new approach to doing science.  ...  With the service-oriented architecture, the same services can be used for different workflows, minimizing the need to create new services.  ... 
doi:10.1109/hicss.2007.33 dblp:conf/hicss/XiangMR07 fatcat:mjxqebq3cbdn3dwtc3w4wiygpy

The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences

Nirav Merchant, Eric Lyons, Stephen Goff, Matthew Vaughn, Doreen Ware, David Micklos, Parker Antin
2016 PLoS Biology  
The iPlant Collaborative provides life science research communities access to comprehensive, scalable, and cohesive computational infrastructure for data management; identity management; collaboration  ...  tools; and cloud, high-performance, high-throughput computing. iPlant provides training, learning material, and best practice resources to help all researchers make the best use of their data, expand their  ...  These projects have allowed iPlant to rapidly deploy and extend its cyberinfrastructure.  ... 
doi:10.1371/journal.pbio.1002342 pmid:26752627 pmcid:PMC4709069 fatcat:uwhpaj2ryvewlgfyljkx2sjdzm

CyVerse Austria—A Local, Collaborative Cyberinfrastructure

Konrad Lang, Sarah Stryeck, David Bodruzic, Manfred Stepponat, Slave Trajanoski, Ursula Winkler, Stefanie Lindstaedt
2020 Mathematical and Computational Applications  
and hosting relevant tools, including analytics software to ensure reproducible analytics using Docker technology for the researchers taking part in the initiative.  ...  The initiative CyVerse US from the University of Arizona, US, supports all processes from data generation, management, sharing and collaboration to analytics.  ...  Integrated Rule-Oriented Data Systems (iRODS) Deployment The integrated rule-oriented data system (iRODS) is a central building block of CAT and enables federated data storage between different storage  ... 
doi:10.3390/mca25020038 fatcat:ihd7ier5irextfgnxrkaedmhyy

Portals for collaborative research communities: two distinguished case studies

Ibrahim Elsayed, Gregory Madey, Peter Brezany
2010 Concurrency and Computation  
VectorBase at its core is a scientific database that focuses on search, data mining and offers multiple integrated bioinformatics tools for analyzing and browsing genomic and related data.  ...  These services include e-mail, electronic chat, issue trackers, voice and video over IP, a project management wiki, a documentation wiki, and teleconferencing for groups  ...  ACKNOWLEDGEMENTS We thank Sandra Gesing and Jano van Hemert for inviting us to contribute to this Special Issue  ... 
doi:10.1002/cpe.1685 fatcat:4f7ja2vxq5hj7ectrxstl4osr4

iMicrobe: Tools and data-dreaiven discovery platform for the microbiome sciences

Ken Youens-Clark, Matt Bomhoff, Alise J Ponsero, Elisha M Wood-Charlson, Joshua Lynch, Illyoung Choi, John H Hartman, Bonnie L Hurwitz
2019 GigaScience  
, and (3) use and publish bioinformatics tools that run on highly scalable computing resources.  ...  Findings The iMicrobe platform brings together analysis tools and microbiome datasets by leveraging National Science Foundation–supported cyberinfrastructure and computing resources from CyVerse, Agave  ...  This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant No. ACI-1548562.  ... 
doi:10.1093/gigascience/giz083 pmid:31289831 pmcid:PMC6615980 fatcat:cq4cvvg5mjfr3fzbtvt2yangwq

CAMERA: A Community Resource for Metagenomics

Rekha Seshadri, Saul A Kravitz, Larry Smarr, Paul Gilna, Marvin Frazier
2007 PLoS Biology  
Citation: Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M (2007) CAMERA: A community resource for metagenomics. PLoS Biol 5(3): e75.  ...  Craig Venter Institute for their assistance in preparing the manuscript. Funding.  ...  The authors acknowledge funding from the Gordon and Betty Moore Foundation to the California Institute for Telecommunications and Information Technology at the University of California, San Diego, and  ... 
doi:10.1371/journal.pbio.0050075 pmid:17355175 pmcid:PMC1821059 fatcat:c323majirzdljpjvlpri7iqaui

Louisiana: a model for advancing regional e-Research through cyberinfrastructure

D. S. Katz, G. Allen, R. Cortez, C. Cruz-Neira, R. Gottumukkala, Z. D. Greenwood, L. Guice, S. Jha, R. Kolluru, T. Kosar, L. Leger, H. Liu (+8 others)
2009 Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences  
Louisiana researchers and universities are leading a concentrated, collaborative effort to advance statewide e-Research through a new cyberinfrastructure: computing systems, data storage systems, advanced  ...  The PetaShare architecture.  ...  Additionally, SAGA has been interfaced with Cactus applications ( Jha et al. 2007 to use information services and other advanced cyberinfrastructure features.  ... 
doi:10.1098/rsta.2009.0037 pmid:19451102 pmcid:PMC3268211 fatcat:pqfowoapcrckvcil75spwlxcrm

Self-Repairing Computers

Armando Fox, David Patterson
2003 Scientific American  
In this article, we review several of our activities in these areas: service architectures for Chemical Informatics; Web 2.0 approaches for managing real-time data from online experiments; management and  ...  Web 2.0 is briefly summarized as building upon network-enabled, stateless services with simple message formats and message exchange patterns to build rich client interfaces, mashups (custom, composite,  ...  One of our primary activities has been to build a service-oriented computing framework, implementing Web Services using the CDK and other libraries.  ... 
doi:10.1038/scientificamerican0603-54 fatcat:vaanc2oiyjc2tc7bus6wkfoine

Large scale data analytics on clouds

Geoffrey C. Fox
2012 Proceedings of the fourth international workshop on Cloud data management - CloudDB '12  
Clouds with cheaper, greener, easier to use IT for (some) applications are growing in importance.  ...  The multicore chip architecture is reawakening parallel computing while it and GPGPU's (even more cores) are behind Exascale initiatives, which will continue drive to high end with a simulation orientation  ...  Fox, and Tom Furlani, Design of an Accounting and Metric-based Cloud-shifting and Cloud-seeding framework for Federated Clouds and Bare-metal Intensive Computing for Bioinformatics.  ... 
doi:10.1145/2390021.2390026 dblp:conf/cikm/Fox12 fatcat:b2jgwzdhhrdxtpci5xnxqqzy6u
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