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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  ...  In this paper, we present MULTI-X, a cross-domain research-oriented platform, designed for collaborative and reproducible science.  ...  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  ...  This report reviews highlights from a two-day meeting involving the BD2K CFPWG to provide insights on trends and considerations in advancing Big Data science for biomedical research in the United States  ...  Data Science training events, Data Science Distinguished Seminar Series, and Frontiers in Data Science Lecture Series to contribute toward this part of the BD2K initiative.  ... 
doi:10.1016/j.jbi.2017.05.006 pmid:28501646 pmcid:PMC5545976 fatcat:akpykof6sfeehcd2jhegji2pmi

Building an effective Semantic Web for health care and the life sciences

Michel Dumontier
2010 Semantic Web Journal  
Health Care and the Life Sciences (HCLS) are at the leading edge of applying advanced information technologies for the purpose of knowledge management and knowledge discovery.  ...  While current focus has been on data, the provisioning of semantic web services, such that they may be automatically discovered to answer a question, will be an essential component of deploying Semantic  ...  Lin kedLifeData 4 Ontologies consists of a diverse array of life science datasets provisioned through cluster-based data warehouse solution using the commercial BigOW LIM engine.  ... 
doi:10.3233/sw-2010-0018 fatcat:m3pcjcvq3nerljd54bhjasg6my

Cover feature - Toward internet distributed computing

M. Milenkovic, S.H. Robinson, R.C. Knauerhase, D. Barkai, S. Garg, V. Tewari, T.A. Anderson, M. Bowman
2003 Computer  
Intel P u b l i s h e d b y t h e I E E E C o m p u t e r S o c i e t y C O V E R F E A T U R E The confluence of Web services, peer-to-peer systems, and grid computing provides the foundation for Internet  ...  Pierce for numerous discussions of network service layering and a minimal set of useful abstractions. We also thank Lenitra M. Clay for struggling to make our prose more readable.  ...  Improved scalability and performance result largely from the preference for use of local resources.  ... 
doi:10.1109/mc.2003.1198235 fatcat:tvcck7n32jh3foue4s2adup744

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  
a foundation of a community CSE software ecosystem, use these best practices and software to achieve science advances (e.g., in subsurface flow with hydrological and biogeochemical recycling), and engage  ...  Difficulties arise from the confluence of disruptive changes in computing architectures, new opportunities for greatly improved simulation capabilities, and demand for greater scientific reproducibility  ...   PETSc: Suite of data structures and routines for the scalable solution of PDE-based applications.  ... 
doi:10.6084/m9.figshare.4708543.v2 fatcat:vxh5hbxnobf45h3kgn45ougef4

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

Is P2P the unique solution for knowledge-rich collaboration working environments?

Isidro Laso Ballesteros
2005 14th IEEE International Workshops on Enabling Technologies: Infrastructure for Collaborative Enterprise (WETICE'05)  
, -Discovery of peers, resources and services, -Management of shared control and data among peers.  ...  -grid for number-crunching (imulation, finance and science) -Other kind of utility-like services: seamless connectivity Conclusion • P2P technologies are the best solution for a Peer economy. • P2P might  ... 
doi:10.1109/wetice.2005.42 dblp:conf/wetice/Ballesteros05a fatcat:wgl7v37owzfmtbvrkoooyztkua

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.  ...  While cloud computing is a model for enabling convenient, on-demand network access to a shared pool of configurable computing resources (e.g., networks, servers, storage, applications, and services) that  ...  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

Architecture-aware Algorithms and Software for Peta and Exascale Computing

Jack Dongarra
2011 2011 IEEE International Parallel & Distributed Processing Symposium  
Exascale Algorithms: Ø Reformulating science problems and refactoring their solution algorithms for exascale systems. 8. Algorithms for discovery, design, and decision:  ...  Exascale Algorithms: Ø Reformulating science problems and refactoring their solution algorithms for exascale systems. 8. Algorithms for discovery, design, and decision: 5.  ...  Interconnect technology: § Increasing the performance and energy efficiency of data movement.  ... 
doi:10.1109/ipdps.2011.419 dblp:conf/ipps/Dongarra11 fatcat:3minwqg5ojbaxnhgi5c3rv53g4

Global Health Innovation Technology Models

Kimberly Harding
2016 Nanobiomedicine  
In addition, there is a reinvigorated global movement towards clinical trial policy harmonization and acceptance of imported, de-identified clinical data sets for cross-trial analysis.  ...  The focus of PIP is to provide a framework for a sustainable clinical innovation model, supported by collaborative partnerships, to achieve new heights in drug discoveries and healthcare solutions [9]  ... 
doi:10.5772/62921 pmid:29942382 pmcid:PMC5998271 fatcat:pova6jp3s5dpve2sjpdpwz33zy

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  ...  To address this problem, we propose a roadmap for improving interoperability across CI components, and we sketch a solution to the challenge of resource description and discovery: a centralized, uniform  ... 
doi:10.1145/3311790.3400848 dblp:conf/xsede/StubbsM0KCDPZ20 fatcat:miwvy4mecfflpcpreoldu3kwle

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

Towards a Dynamic Scalable IoT Computing Platform Architecture

Desoky Abdelqawy, Amr Kamel, Soha Makady
2020 International Journal of Advanced Computer Science and Applications  
subtle task. (2) Providing a scalable solution without altering the end user privacy (e.g., through the use of cloud platforms) is hard to achieve. (3) Handling IoT Applications reliability as well as  ...  A novel scalable dynamic computing platform architecture is proposed to address such limitations and provide simultaneous support for five non-functional requirements.  ...  scalable dynamic resource discovery, (2) reliability (3) Real Time support and (4) privacy.  ... 
doi:10.14569/ijacsa.2020.0110282 fatcat:7tlw6htgrbgxhh6xdrcelifvyq

Resource Optimisation in IoT Cloud Systems by Using Matchmaking and Self-management Principles [chapter]

Martin Serrano, Danh Le-Phuoc, Maciej Zaremba, Alex Galis, Sami Bhiri, Manfred Hauswirth
2013 Lecture Notes in Computer Science  
IoT Cloud systems provide scalable capacity and dynamic behaviour control of virtual infrastructures for running applications, services and processes.  ...  For our IoT Cloud data management solution we utilize performance metrics expressed with linked data in order to integrate monitored performance data and end user profile information (via linked data relations  ...  That is not the necessary case for IoT, in some situations a collaborative solution of Cloud vendors might be the optimal Cloud implementation in terms of cost, scalability and key performance indicators  ... 
doi:10.1007/978-3-642-38082-2_11 fatcat:cgqiysdweffefcsqexqm7roiwq

OUP accepted manuscript

2017 Briefings in Bioinformatics  
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  ...  We untangle the parameters for selecting a preferable solution for bioinformatics research with Md.  ...  Funding The Science Foundation Ireland (grant number SFI/12/RC/ 2289).  ... 
doi:10.1093/bib/bbx039 pmid:28419324 pmcid:PMC6169675 fatcat:xsdfepwqmnb7pgkmnep2ifn2wi
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