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Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets

Allison P Heath, Matthew Greenway, Raymond Powell, Jonathan Spring, Rafael Suarez, David Hanley, Chai Bandlamudi, Megan E McNerney, Kevin P White, Robert L Grossman
2014 JAMIA Journal of the American Medical Informatics Association  
and sharing large genomics datasets Bionimbus: a cloud for managing, analyzing http://jamia.bmj.com/content/early/2014/01/24/amiajnl-2013-002155.full.html Updated information and services can be found  ...  CONCLUSION We have described the architecture and some typical use cases of the cloud-based Bionimbus system, which is designed for managing, analyzing, and sharing large genomics datasets in a secure  ...  OBJECTIVE This paper describes the Bionimbus Protected Data Cloud (PDC), an open-source cloud-based infrastructure for managing, analyzing, and sharing large amounts of genomics and phenotypic data in  ... 
doi:10.1136/amiajnl-2013-002155 pmid:24464852 pmcid:PMC4215034 fatcat:x5mcted7hfaqhd2kjbb72wszaq

A Case for Data Commons: Toward Data Science as a Service

Robert L. Grossman, Allison Heath, Mark Murphy, Maria Patterson, Walt Wells
2016 Computing in science & engineering (Print)  
Data commons collocate data, storage, and computing infrastructure with core services and commonly used tools and applications for managing, analyzing, and sharing data to create an interoperable resource  ...  cloud that the nonprofit Open Commons Consortium (OCC) has managed and operated since 2009. 1 One of the distinguishing characteristics of the OSDC is that it interoperates with a data commons containing  ...  Acknowledgments This material is based in part on work supported by the US National Science Foundation under grant numbers OISE 1129076, CISE 1127316, and CISE 1251201 and by National Institutes of Health  ... 
doi:10.1109/mcse.2016.92 pmid:29033693 pmcid:PMC5636009 fatcat:b22jtota5jesnka232cvg6gj7e

A Case for Data Commons: Towards Data Science as a Service [article]

Robert L. Grossman, Allison Heath, Mark Murphy, Maria Patterson and Walt Wells
2016 arXiv   pre-print
Across these case studies, several common requirements emerge, including the need for persistent digital identifier and metadata services, APIs, data portability, pay for compute capabilities, and data  ...  Though many challenges, including sustainability and developing appropriate standards remain, interoperable data commons bring us one step closer to effective Data Science as Service for the scientific  ...  , Inc. through contracts 14X050 and 13XS021 / HHSN261200800001E.  ... 
arXiv:1604.02608v1 fatcat:5xzjknntpncadmuc2klkly742u

Genomics as a service: A joint computing and networking perspective

G. Reali, M. Femminella, E. Nunzi, D. Valocchi
2018 Computer Networks  
In more detail, we analyze the main genomic processing applications, and classify not only the main computing alternatives to run genomics workflows in either a local machine or a distributed cloud environment  ...  It emerges that virtualization, both in computing and networking, is the key for a successful large-scale exploitation of genomic data, by pushing ahead the adoption of the GaaS paradigm.  ...  for managing, analyzing, transporting, and sharing large genomics datasets in a secure and compliant fashion [23] .  ... 
doi:10.1016/j.comnet.2018.08.005 fatcat:w562rwbavnax7pbtairhtnadje

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

Robert L. Grossman
2018 arXiv   pre-print
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.  ...  Over the past few years, data commons have been used to analyze, harmonize and share large scale genomics datasets. Data ecosystems can be built by interoperating multiple data commons.  ...  First, the size of the datasets is too large for all but the largest research organizations to manage and analyze.  ... 
arXiv:1809.01699v2 fatcat:wh2jq5nlenbapppiuthdxerccm

Parallel computing in genomic research: advances and applications

Daniel de Oliveira, Kary Ocaña
2015 Advances and Applications in Bioinformatics and Chemistry  
Parallelism techniques and high-performance computing (HPC) environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data.  ...  This article brings a systematic review of literature that surveys the most recently published research involving genomics and parallel computing.  ...  Author contributions All authors contributed toward data analysis, drafting and revising the paper and agree to be accountable for all aspects of the work.  ... 
doi:10.2147/aabc.s64482 pmid:26604801 pmcid:PMC4655901 fatcat:qyslams5evftjm7euma5vg2rtq

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

Robert L. Grossman
2019 Trends in Genetics  
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.  ...  Over the past few years, data commons have been used to analyze, harmonize, and share large-scale genomics datasets. Data ecosystems can be built by interoperating multiple data commons.  ...  Containers are designed to be run in different types of computing environments with no changes Data cloud A data cloud is a cloud computing platform for managing, analyzing, and sharing datasets Data  ... 
doi:10.1016/j.tig.2018.12.006 pmid:30691868 pmcid:PMC6474403 fatcat:fi5wkfpotrf4lhdffvg6vxldqa

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  ...  For instance, medical imaging is producing large datasets of biomedical images, while omics sciences, such as genomics, proteomics and interactomics, are producing large datasets of experimental data.  ... 
doi:10.12694/scpe.v16i1.1057 fatcat:k5s2o37zcrge5pvbwimhotbsca

The Design of a Community Science Cloud: The Open Science Data Cloud Perspective

Robert L. Grossman, Matthew Greenway, Allison P. Heath, Ray Powell, Rafael D. Suarez, Walt Wells, Kevin White, Malcolm Atkinson, Iraklis Klampanos, Heidi L. Alvarez, Christine Harvey, Joe J. Mambretti
2012 2012 SC Companion: High Performance Computing, Networking Storage and Analysis  
The goal of the OSDC is to provide petabyte-scale data cloud infrastructure and related services for scientists working with large quantities of data.  ...  In this paper we describe the design, and implementation of the Open Science Data Cloud, or OSDC.  ...  An OSDC project called Bionimbus (www.bionimbus.org) has developed a cloud-based infrastructure for managing, analyzing, archiving, and sharing large genomic datases.  ... 
doi:10.1109/sc.companion.2012.127 dblp:conf/sc/GrossmanGHPSWWAKAHM12 fatcat:hxlb5kykave43kq2aa3quqo6wm

The Design of a Community Science Cloud: The Open Science Data Cloud Perspective [article]

Robert L. Grossman, Matthew Greenway, Allison P. Heath, Ray Powell, Rafael D. Suarez, Walt Wells, Kevin White, Malcolm Atkinson, Iraklis Klampanos, Heidi L. Alvarez, Christine Harvey, Joe J. Mambretti
2016 arXiv   pre-print
The goal of the OSDC is to provide petabyte-scale data cloud infrastructure and related services for scientists working with large quantities of data.  ...  In this paper we describe the design, and implementation of the Open Science Data Cloud, or OSDC.  ...  This work also used the Open Cloud Consortium's OCC-Y Cluster, which was donated by Yahoo! Inc.  ... 
arXiv:1601.00323v1 fatcat:wq63cbcnljbcnbxeimubqimlwe

Public–Private Partnerships in Cloud-Computing Services in the Context of Genomic Research

Palmira Granados Moreno, Yann Joly, Bartha Maria Knoppers
2017 Frontiers in Medicine  
With the advancement of technology and of the area of genomics, these partnerships also focus on large-scale genomic research projects that aim to advance the understanding of diseases that have a genetic  ...  Organized as PPP and employing cloud-computing services, the three projects have advanced quickly and are likely to be important sources of research and development for future personalized medicine.  ...  TCGA created a pipeline to collect, select, and analyze human tissues on a very large scale.  ... 
doi:10.3389/fmed.2017.00003 pmid:28164085 pmcid:PMC5247451 fatcat:6hdziyv3ffdddlfzlzbnwpibru

The medical science DMZ: a network design pattern for data-intensive medical science

Sean Peisert, Eli Dart, William Barnett, Edward Balas, James Cuff, Robert L Grossman, Ari Berman, Anurag Shankar, Brian Tierney
2017 JAMIA Journal of the American Medical Informatics Association  
Results: We describe a "Medical Science DMZ" concept as an option for secure, high-volume transport of large, sensitive datasets between research institutions over national research networks, and give  ...  The ability to store and compute using these data must therefore be addressed by a combination of local, national, and industry resources that exchange large datasets.  ...  Bionimbus protected data cloud and data commons architecture Over the past 4 years, the University of Chicago, in collaboration with the not-for-profit Open Cloud Consortium, has developed and operated  ... 
doi:10.1093/jamia/ocx104 pmid:29040639 fatcat:jdk3uuz27bfqffu6nffh6otnra

Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments [article]

Christina K. Yung, Brian D. O'Connor, Sergei Yakneen, Junjun Zhang, Kyle Ellrott, Kortine Kleinheinz, Naoki Miyoshi, Keiran M. Raine, Romina Royo, Gordon B. Saksena, Matthias Schlesner, Solomon I. Shorser (+14 others)
2017 bioRxiv   pre-print
portable software for uniform alignment, variant calling, artifact filtering and variant merging; performed the analysis in a geographically and technologically disparate collection of compute environments  ...  The International Cancer Genome Consortium (ICGC)'s Pan-Cancer Analysis of Whole Genomes (PCAWG) project aimed to categorize somatic and germline variations in both coding and non-coding regions in over  ...  To date, this is the largest whole genome cancer dataset analyzed in a consistent and uniform way.  ... 
doi:10.1101/161638 fatcat:lgpfe77jmbf6bnljteztvqla5i

Genomics big data hybrid depositories architecture to unlock precision medicine: a conceptual framework

Ummul H. Mohamad, Mohamad T. Ijab, Rabiah A. Kadir
2018 International Journal of Engineering & Technology  
the genomics-based precision medicine and the architectural design for the development of hybrid depositories as the initial step to bridge the gap towards precision medicine.  ...  processing engine and decision support, to carry out their purpose of merging the genomics data with the healthcare data.  ...  Cloud collaboration platform Besides that, Cancer Genomics Cloud Pilot, a project by NCI, aimed to improve cancer genomics data sharing by enabling researchers to incorporate their own datasets and tools  ... 
doi:10.14419/ijet.v7i4.16893 fatcat:4lgua7ixtbcxhhcwvenadbc2va

2019-July_CFDE_AssessmentReport.pdf

C. Titus Brown, Amanda Charbonneau, Owen White
2019 Figshare  
July 2019 Assessment Report for the Common Fund Data Ecosystem.  ...  Acknowledgements We are grateful to Brian Osbourne and Brian O'Connor for their assistance in preparation of this document.  ...  Many members of the CFDE tech team participated in data gathering; in particular we would like to cite Lee Liming for his review of the report and assistance with data collection, as well as Theresa Hodges  ... 
doi:10.6084/m9.figshare.9588374 fatcat:o6kr3ku2eff2tlnv6uep7eotbm
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