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MULTI-X, a State-of-the-Art Cloud-Based Ecosystem for Biomedical Research

Milton Hoz de Vila, Rahman Attar, Marco Pereanez, Alejandro F. Frangi
2018 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
This cloud-based framework simplifies the logistical challenges of implementing data analytics and AI solutions by providing pre-configured environments with ad-hoc scalable computing resources and secure  ...  Beyond the complexity of executing dataintensive workflows over large-scale distributed data, the reproducibility of computed results is of paramount importance to validate scientific discoveries.  ...  Practical mechanisms must be implemented to facilitate the discovery and improve the leverage of these resources.  ... 
doi:10.1109/bibm.2018.8621317 dblp:conf/bibm/VilaAPF18 fatcat:x3wewucqjfbkvfzp3gfuzv426q

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop

Kathleen M. Jagodnik, Simon Koplev, Sherry L. Jenkins, Lucila Ohno-Machado, Benedict Paten, Stephan C. Schurer, Michel Dumontier, Ruben Verborgh, Alex Bui, Peipei Ping, Neil J. McKenna, Ravi Madduri (+2 others)
2017 Journal of Biomedical Informatics  
While such data hold significant promise for accelerating discovery, their use entails many challenges including: the need for adequate computational infrastructure, secure processes for data sharing and  ...  These are just some elements of a complex ecosystem that needs to be built to support the rapid accumulation of these data.  ...  facilitate a data ecosystem that will promote new discoveries through data reuse and data integration.  ... 
doi:10.1016/j.jbi.2017.05.006 pmid:28501646 pmcid:PMC5545976 fatcat:akpykof6sfeehcd2jhegji2pmi

CSE Software Ecosystems: Critical Instruments of Scientific Discovery

Lois Curfman McInnes, Michael Heroux, J. David Moulton, David Bernholdt, Xiaoye Li, Tim Scheibe, Ulrike Meier Yang, And All IDEAS Project Members
2017 Figshare  
Difficulties arise from the confluence of disruptive changes in computing architectures, new opportunities for greatly improved simulation capabilities, and demand for greater scientific reproducibility  ...  variety of technical and social issues in scientific software.  ...   PETSc: Suite of data structures and routines for the scalable solution of PDE-based applications.  ... 
doi:10.6084/m9.figshare.4708543.v2 fatcat:vxh5hbxnobf45h3kgn45ougef4

INTERVENTIONS FOR SCIENTIFIC AND ENTERPRISE APPLICATIONS BASED ON HIGH PERFORMANCE AND CLOUD COMPUTING

Kitty Ahuja .
2014 International Journal of Research in Engineering and Technology  
of a huge number of computers for executing large scale experiments.  ...  As enterprise applications are data centric, user friendly, complex, scalable and often require software packages, decision support systems, warehouse while scientific applications have need of the availability  ...  Computational and Data-Driven Sciences are the major pillars of scientific discovery in addition to experimental and theoretical sciences.  ... 
doi:10.15623/ijret.2014.0301070 fatcat:xxctnysnmfbsrlbgqq52ij7xp4

InterSCity: A Scalable Microservice-based Open Source Platform for Smart Cities

Arthur M. Del Esposte, Fabio Kon, Fabio M. Costa, Nelson Lago
2017 Proceedings of the 6th International Conference on Smart Cities and Green ICT Systems  
Smart City technologies emerge as a potential solution to tackle common problems in large urban centers by using city resources efficiently and providing quality services for citizens.  ...  We discuss how the microservice approach enables a flexible, extensible, and loosely coupled architecture and present experimental results demonstrating the scalability of the proposed platform.  ...  We also acknowledge the following developers for their contributions to the InterSCity platform source  ... 
doi:10.5220/0006306200350046 dblp:conf/smartgreens/EsposteKCL17 fatcat:7m6baugi5reqfaean7lghr6gge

A Study of Cloud Computing Based Model to Facilitate Collaborative Research

Rahul Wargad, Manimala Puri
2015 IJAEDU- International E-Journal of Advances in Education  
Cloud computing in Collaborative research can facilitate (a) Combined efforts of many good researchers for excellent outcomes, (b) Creativity, (c) Sharing experience of all researchers, (d) Get funding  ...  An attempt is made to explore the possible solutions to facilitate collaborative research with the help of Cloud computing technology in order to make certain vital observations to lay down conclusion.  ...  number of factors have contributed to a trend towards increased collaboration.  ... 
doi:10.18768/ijaedu.11531 fatcat:squm2e2lejcm3ppr7dqkeomb7a

DataFed: Towards Reproducible Research via Federated Data Management [article]

Dale Stansberry, Suhas Somnath, Jessica Breet, Gregory Shutt, Mallikarjun Shankar
2020 arXiv   pre-print
The increasingly collaborative, globalized nature of scientific research combined with the need to share data and the explosion in data volumes present an urgent need for a scientific data management system  ...  DataFed represents a step towards reproducible scientific research by enabling reliable staging of the correct data at the desired environment.  ...  and collaborative research, and facilitate data-driven scientific discovery.  ... 
arXiv:2004.03710v1 fatcat:y645uounzbcq3bdkkalrtqrdzm

Opportunities and Challenges in Running Scientific Workflows on the Cloud

Yong Zhao, Xubo Fei, Ioan Raicu, Shiyong Lu
2011 2011 International Conference on Cyber-Enabled Distributed Computing and Knowledge Discovery  
We coin the term "Cloud Workflow", to refer to the specification, execution, provenance tracking of large-scale scientific workflows, as well as the management of data and computing resources to enable  ...  Cloud computing; Scientific Workflow; Cloud workflow; Data Intensive Computing I.  ...  Scalability would be top concern for implementation of such a model.  ... 
doi:10.1109/cyberc.2011.80 dblp:conf/cyberc/ZhaoFRL11 fatcat:zlpe7p73lnh2jksgtnstvkafn4

OUP accepted manuscript

2017 Briefings in Bioinformatics  
We untangle the parameters for selecting a preferable solution for bioinformatics research with Md.  ...  Rezaul Karim is a PhD researcher at Semantics in eHealth and Life Sciences with expertise in the development of computational resources for the analysis and visualization of ribosome profiling (RiboSeq  ...  and João Bosco Jares for helping them in drawing the Figure 2 .  ... 
doi:10.1093/bib/bbx039 pmid:28419324 pmcid:PMC6169675 fatcat:xsdfepwqmnb7pgkmnep2ifn2wi

Architecture-aware Algorithms and Software for Peta and Exascale Computing

Jack Dongarra
2011 2011 IEEE International Parallel & Distributed Processing Symposium  
• Future architectures targeted toward good HPL performance will not be a good match for most applications.  ...  anticipated.ØFacilitating mathematical optimization and uncertainty quantification for exascale discovery, design, and decision making.9.  ...  Interconnect technology: § Increasing the performance and energy efficiency of data movement.  ... 
doi:10.1109/ipdps.2011.419 dblp:conf/ipps/Dongarra11 fatcat:3minwqg5ojbaxnhgi5c3rv53g4

Towards A Methodology and Framework for Workflow-Driven Team Science [article]

Ilkay Altintas, Shweta Purawat, Daniel Crawl, Alok Singh, Kyle Marcus
2019 arXiv   pre-print
Scientific workflows are powerful tools for management of scalable experiments, often composed of complex tasks running on distributed resources.  ...  We also present a conceptual design towards the development of methodologies and tools for effective workflow-driven collaborations, namely the PPoDS methodology and the SmartFlows Toolkit for smart utilization  ...  The authors would also like to thank Workflows for Data Science (WorDS) Center of Excellence team members Mai Nguyen and Volkan Vural for their participation in the discussions leading to this paper.  ... 
arXiv:1903.01403v1 fatcat:ubbe6qk5kfb77erhetvp25jele

Toward Interoperable Cyberinfrastructure: Common Descriptions for Computational Resources and Applications

Joe Stubbs, Suresh Marru, Daniel Mejia, Daniel S. Katz, Kyle Chard, Maytal Dahan, Marlon Pierce, Michael Zentner
2020 Practice and Experience in Advanced Research Computing  
We sketch a solution to the problem of a common description and catalog of resources: we describe an approach to implementing a resource registry for use by the community and discuss potential approaches  ...  The user-facing components of the Cyberinfrastructure (CI) ecosystem, science gateways and scientific workflow systems, share a common need of interfacing with physical resources (storage systems and execution  ...  While we ultimately strive for interoperability at the scientific application level, finding a solution for uniform resources is a necessary precursor.  ... 
doi:10.1145/3311790.3400848 dblp:conf/xsede/StubbsM0KCDPZ20 fatcat:miwvy4mecfflpcpreoldu3kwle

Towards a Scalable Architecture for Smart Villages: The Discovery Phase

Vijaya Kumar Murty, Sukarmina Singh Shankar
2020 Sustainability  
The spread and quantum of this daunting challenge calls for a scalable solution.The aim of the 'Scalable Architecture for Smart Villages' project is to contribute to an eective solutionwhich addresses  ...  In this paper we outline the discoveryphase, which will lay the foundation for developing our framework of scalable smart villages.The Discovery Phase is a research process where the community learns about  ...  Conflicts of Interest: The authors declare no conflict of interest, the funders had no role in the design of the study, in the collection, analyses, or interpretation of data, in the writing of the manuscript  ... 
doi:10.3390/su12187580 fatcat:2rdqz6obqbg2jpg3hxbpdjhlka

Knowledge generation using satellite earth observations to support sustainable development goals (SDG): A use case on Land degradation

Gregory Giuliani, Paolo Mazzetti, Mattia Santoro, Stefano Nativi, Joost Van Bemmelen, Guido Colangeli, Anthony Lehmann
2020 International Journal of Applied Earth Observation and Geoinformation  
The authors would like to thank the Swiss Federal Office for the Environment (FOEN) for their financial support to the Swiss Data Cube.  ...  of Zurich and the Swiss Federal Institute for Forest, Snow and Landscape Research WSL.  ...  Harmonized discovery of and access to heterogeneous resources (e.g. data) from different systems • Publication of scientific workflows connecting data and models • Execution of scientific workflows based  ... 
doi:10.1016/j.jag.2020.102068 fatcat:qj5tinajovcybjg4cl5akxgfre

A Seeded Cloud Approach to Health Cyberinfrastructure: Preliminary Architecture Design and Case Applications

Chaitan Baru, Nathan Botts, Thomas Horan, Kevin Patrick, Sue S. Feldman
2012 2012 45th Hawaii International Conference on System Sciences  
The expected volume of information and users -including many with only basic skills in data handling and analysis of such systems -also demands an elastic solution.  ...  Applications in public health and health services require access to a range of heterogeneous data, from environmental information in a region, to population-level data across regions, to more closely held  ...  Thank you to the reviewers for their suggestions that helped to make this a stronger paper. References  ... 
doi:10.1109/hicss.2012.82 dblp:conf/hicss/BaruBHPF12 fatcat:oxtrpgsx2vgapne3g4pmuoeshm
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