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An overview of biomedical platforms for managing research data

Vivek Navale, Denis von Kaeppler, Matthew McAuliffe
2021 Journal of Data, Information and Management  
Managing biomedical Big Data will require the development of strategies that can efficiently leverage public cloud computing resources.  ...  Several web-based platforms are available for researchers to access services and tools for biomedical research.  ...  Commercial biomedical platforms (e.g., DNAnexus) also provide a secure cloud computing environment for analyzing and integrating phenotypic, clinical, and genomic data (https://www.dnanexus.com/).  ... 
doi:10.1007/s42488-020-00040-0 fatcat:itiji5ifu5hjhhcjvtzwz6jq6e

Eleven quick tips for architecting biomedical informatics workflows with cloud computing

Brian S. Cole, Jason H. Moore, Francis Ouellette
2018 PLoS Computational Biology  
In this article, we present 11 quick tips for architecting biomedical informatics workflows on compute clouds, distilling knowledge gained from experience developing, operating, maintaining, and distributing  ...  This is a PLOS Computational Biology Education paper. PLOS Computational Biology | https://doi.  ...  Cloud computing providers often offer fully managed services for version-control hosting, allowing researchers, teams, and even whole institutions to maintain private collections of repositories without  ... 
doi:10.1371/journal.pcbi.1005994 pmid:29596416 pmcid:PMC5875741 fatcat:p4r7k2qqirh7xkfjvddaq53z44

Cloud computing applications for biomedical science: A perspective

Vivek Navale, Philip E. Bourne, Francis Ouellette
2018 PLoS Computational Biology  
Cloud computing offers users pay-as-you-go access to services such as hardware infrastructure, platforms, and software for solving common biomedical computational problems.  ...  For certain types of biomedical applications, cloud computing has emerged as an alternative to locally maintained traditional computing approaches.  ...  Sean Davis, Center for Cancer Research, National Cancer Institute; Ms. Andrea Norris, Director, Center for Information Technology; and Dr.  ... 
doi:10.1371/journal.pcbi.1006144 pmid:29902176 pmcid:PMC6002019 fatcat:wfvdmkpytnbfbih27knmldrcyy

Challenges and Solutions for Internet of Things Driven by IPv6

2016 KSII Transactions on Internet and Information Systems  
Two smart living applications, a biomedical application and a smart building application, are proposed.  ...  Based on the analytical results, the policy decision module processes the data in the device or in the cloud computing environment.  ...  In the IoT environment, sensing devices collect environmental information, which is transmitted via a network to the middleware or cloud for computing and management.  ... 
doi:10.3837/tiis.2016.02.001 fatcat:v6zdaxnqkjdclglsetfuwquwuy

Design and Application of Intelligent Cloud Dis-ease-Diagnostic System Based on Non-Coding Amino Acid Mass Spectrometry

Xingyuan Wang
2020 Biomedical Journal of Scientific & Technical Research  
Mass spectrogram contains a lot of information [7] . If we use computer image processing technology to process it, it is still at the level of analysis and processing.  ...  Then apply for cloud diagnosis service to cloud diagnosis service platform and pay for it, and then submit sample mass spectrum data. C.  ...  The operation process of cloud diagnosis service platform ( Figure 2 ) is as follows: A.  ... 
doi:10.26717/bjstr.2020.24.004001 fatcat:wlqlqnjh4zaypinty2kxoo3vka

Big Biomedical data as the key resource for discovery science

Arthur W Toga, Ian Foster, Carl Kesselman, Ravi Madduri, Kyle Chard, Eric W Deutsch, Nathan D Price, Gustavo Glusman, Benjamin D Heavner, Ivo D Dinov, Joseph Ames, John Van Horn (+2 others)
2015 JAMIA Journal of the American Medical Informatics Association  
We have prototyped integration with analysis services and biomedical digital asset management system 17 services to explore the ability to provide higher-level abstractions via a distributed data cloud  ...  What BDDS has done BDDS investigators have applied Globus services 16 to a range of biomedical domains, deploying and operating services that have been used to move and share imaging, genomic, and proteomic  ... 
doi:10.1093/jamia/ocv077 pmid:26198305 pmcid:PMC5009918 fatcat:mkyc2zhcsbahllwbj6yfo6jf2e

Enabling Large-Scale Biomedical Analysis in the Cloud

Ying-Chih Lin, Chin-Sheng Yu, Yen-Jen Lin
2013 BioMed Research International  
Recent progress in high-throughput instrumentations has led to an astonishing growth in both volume and complexity of biomedical data collected from various sources.  ...  Cloud computing is an alternative to crack the nut because it gives concurrent consideration to enable storage and high-performance computing on large-scale data.  ...  A solution to power the cloud infrastructure for digital imaging communication in medicine (DICOM) is introduced as a robust cloud-based service [38] .  ... 
doi:10.1155/2013/185679 pmid:24288665 pmcid:PMC3832998 fatcat:zi7vkjnqczbx3gydrgbdbbmwhe

Translational Biomedical Informatics in the Cloud: Present and Future

Jiajia Chen, Fuliang Qian, Wenying Yan, Bairong Shen
2013 BioMed Research International  
In this paper we demonstrated the utility and promise of cloud computing for tackling the big data problems.  ...  We also outline our vision that cloud computing could be an enabling tool to facilitate translational bioinformatics research.  ...  a niche for personalized cancer management.  ... 
doi:10.1155/2013/658925 pmid:23586054 pmcid:PMC3613081 fatcat:dmpe2jfwxvaoxoagpkhwu4gnnu

Data Lakes, Clouds and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data [article]

Robert L. Grossman
2018 arXiv   pre-print
Data commons collate data with cloud computing infrastructure and commonly used software services, tools and applications to create biomedical resources for the large-scale management, analysis, harmonization  ...  We review software platforms for managing, analyzing and sharing genomic data, with an emphasis on data commons, but also covering data ecosystems and data lakes.  ...  A working definition of a data cloud for biomedical data is a cloud computing platform [6] that manages and analyzes biomedical data and, usually, integrates the security and compliance required to work  ... 
arXiv:1809.01699v2 fatcat:wh2jq5nlenbapppiuthdxerccm

Data Lakes, Clouds, and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data

Robert L. Grossman
2019 Trends in Genetics  
Data commons collate data with cloud computing infrastructure and commonly used software services, tools, and applications to create biomedical resources for the large-scale management, analysis, harmonization  ...  We review software platforms for managing, analyzing, and sharing genomic data, with an emphasis on data commons, but also cover data ecosystems and data lakes.  ...  A working definition of a data cloud for biomedical data is a cloud computing platform [6] that manages and analyzes biomedical data and, usually, integrates the security and compliance required to work  ... 
doi:10.1016/j.tig.2018.12.006 pmid:30691868 pmcid:PMC6474403 fatcat:fi5wkfpotrf4lhdffvg6vxldqa

Cyclone: A Platform For Data Intensive Scientific Applications In Heterogeneous Multi-Cloud/Multi-Provider Environment

Yuri Demchenko, Miroslav Zivkiovic, Cees De Laat, Christophe Blanchet, Mohamed Bedri, Jean-François Gibrat, Oleg Lodygensky, Mathias Slawik, Ilke Zilci, Rob Branchat, Charles Loomis
2016 Zenodo  
This paper presents results of the ongoing development of the CYCLONE as a platform for scientific applications in heterogeneous multi-cloud/multi-provider environment.  ...  The paper provides information about selected use cases implementation using SlipStream cloud automation and management platform with application recipe example.  ...  Performing the analysis of collections of genomes requires large computing resources that can distributed over several computers, generally the computing nodes of a cluster.  ... 
doi:10.5281/zenodo.243122 fatcat:3u4evra2dffepfuqf7coblakqi

Cyclone: A Platform For Data Intensive Scientific Applications In Heterogeneous Multi-Cloud/Multi-Provider Environment

Yuri Demchenko, Miroslav Zikovich, Cess de Laat, Christophe Blanchet, Mohamed Bedri, Jean-François Gibrat, Oleg Lodygensky, Mathias Slawik, Ilke Zilci, Rob Branchat, Charles Loomis
2016 Zenodo  
This paper presents results of the ongoing development of the CYCLONE as a platform for scientific applications in heterogeneous multi-cloud/multi-provider environment.  ...  The paper provides information about selected use cases implementation using SlipStream cloud automation and management platform with application recipe example.  ...  Performing the analysis of collections of genomes requires large computing resources that can distributed over several computers, generally the computing nodes of a cluster.  ... 
doi:10.5281/zenodo.59160 fatcat:dxjh7l6ih5cvbhe5aweq3b5wfu

Cloud Computing in Healthcare and Biomedicine

Barbara Calabrese, Mario Cannataro
2015 Scalable Computing : Practice and Experience  
Cloud Computing offers large scalable computing and storage, data sharing, on-demand anytime and anywhere access to resources and applications, and it supports easy but powerful distributed computing models  ...  This paper reviews main cloud-based healthcare and biomedicine applications; with a special focus on healthcare, biomedicine and bioinformatics solutions and underlines main issues and problems related  ...  In [73] a cloud computing based Voice over IP (VoIP) service for diabetic patients self care management, is presented.  ... 
doi:10.12694/scpe.v16i1.1057 fatcat:k5s2o37zcrge5pvbwimhotbsca

Corbel Report On Models And Pilot Designs For Sustainable Scalable Cloud-Based Provision Of Data Access And Compute Across Infrastructures

Morris Swertz, Fleur Kelpin, David van Enckevort, Ilkka Lappalainen, Mikael Linden, Tommi Nyrönen, Petr Holub, Jan-Willem Boiten, Anna Leida Molder, Helen Parkinson
2017 Zenodo  
Task 3 in Work Package 6 addresses the secure data management and compute needs of service providers dealing with data that needs to be access controlled, for example human identifiable data such as genome  ...  As first deliverable we here report on models and pilot designs for sustainable scalable cloud-based provision of data and compute across infrastructures, providing guidance to BMS infrastructure development  ...  Services include local and federated data access modes for managed data, identity management for users and dataset owners, and access to/from secure computational (grid/cloud) environments in which to  ... 
doi:10.5281/zenodo.376279 fatcat:qrwc2azvjzgl5iqt6swa65bo2m

Telemedicine work station using computer communication network
IJARCCE - Computer and Communication Engineering

K. Gugan, R.G. Suresh Kumar, S. Saravanan
2015 IJARCCE  
This paper explains internet based Telemedicine workstation Setup Hybrid computing (Telemedicine computing, Cloud computing, Grid computing, Cluster computing) can be maintained complex Big Data storage  ...  Cloud computing Technology can be stored increasing large number of medical data and reduce 70% cost of server in Hospitals.  ...  ., R.G Suresh Kumar , Head of the Computer science department, Rajiv Gandhi college of Engineering and Technology, Puducherry, India. They Guide to Telemedicine base station of center.  ... 
doi:10.17148/ijarcce.2015.4185 fatcat:76flkxz5azerxd7qrbfraez6p4
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