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BiobankCloud :
BiobankCloud : A platform for the secure storage, sharing, and processing of large biomedical data sets
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- Bessani, A. (author)
- Univ Lisbon, Fac Ciencias, LaSIGE, Lisbon, Portugal.
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- Brandt, J. (author)
- Humboldt Univ, Berlin, Germany.
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- Bux, M. (author)
- Humboldt Univ, Berlin, Germany.
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- Cogo, V. (author)
- Univ Lisbon, Fac Ciencias, LaSIGE, Lisbon, Portugal.
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- Dimitrova, L. (author)
- Charite, Berlin, Germany.
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- Dowling, Jim (author)
- KTH,Programvaruteknik och Datorsystem, SCS,KTH Royal Inst Technol, Stockholm, Sweden.
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- Gholami, Ali (author)
- KTH,KTH Royal Inst Technol, Stockholm, Sweden.
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- Hakimzadeh, Kamal (author)
- KTH,Programvaruteknik och Datorsystem, SCS,KTH Royal Inst Technol, Stockholm, Sweden.
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- Hummel, M. (author)
- Charite, Berlin, Germany.
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- Ismail, Mahmoud (author)
- KTH,Programvaruteknik och Datorsystem, SCS,KTH Royal Inst Technol, Stockholm, Sweden.
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- Laure, Erwin (author)
- KTH,Parallelldatorcentrum, PDC,High Performance Computing and Visualization (HPCViz),KTH Royal Inst Technol, Stockholm, Sweden.
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- Leser, U. (author)
- Humboldt Univ, Berlin, Germany.
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- Litton, J. -E (author)
- Karolinska Inst, Solna, Sweden.
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- Martinez, R. (author)
- Karolinska Inst, Solna, Sweden.
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- Niazi, Salman (author)
- KTH,Programvaruteknik och Datorsystem, SCS,KTH Royal Inst Technol, Stockholm, Sweden.
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- Reichel, Jane (author)
- Uppsala universitet,Centrum för forsknings- och bioetik
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- Zimmermann, K. (author)
- Charite, Berlin, Germany.
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Univ Lisbon, Fac Ciencias, LaSIGE, Lisbon, Portugal Humboldt Univ, Berlin, Germany. (creator_code:org_t)
- 2016-06-24
- 2016
- English.
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In: 1st International Workshop on Data Management and Analytics for Medicine and Healthcare, DMAH 2015 and Workshop on Big-Graphs Online Querying, Big-O(Q) 2015 held in conjunction with 41st International Conference on Very Large Data Bases, VLDB 2015. - Cham : Springer. - 9783319415758 - 9783319415765 ; , s. 89-105
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http://www.di.fc.ul....
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Subject headings
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- Biobanks store and catalog human biological material that is increasingly being digitized using next-generation sequencing (NGS). There is, however, a computational bottleneck, as existing software systems are not scalable and secure enough to store and process the incoming wave of genomic data from NGS machines. In the BiobankCloud project, we are building a Hadoop-based platform for the secure storage, sharing, and parallel processing of genomic data. We extended Hadoop to include support for multi-tenant studies, reduced storage requirements with erasure coding, and added support for extensible and consistent metadata. On top of Hadoop, we built a scalable scientific workflow engine featuring a proper workflow definition language focusing on simple integration and chaining of existing tools, adaptive scheduling on Apache Yarn, and support for iterative dataflows. Our platform also supports the secure sharing of data across different, distributed Hadoop clusters. The software is easily installed and comes with a user-friendly web interface for running, managing, and accessing data sets behind a secure 2-factor authentication. Initial tests have shown that the engine scales well to dozens of nodes. The entire system is open-source and includes pre-defined workflows for popular tasks in biomedical data analysis, such as variant identification, differential transcriptome analysis using RNA-Seq, and analysis of miRNA-Seq and ChIP-Seq data.
Subject headings
- TEKNIK OCH TEKNOLOGIER -- Industriell bioteknik -- Biomaterial (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Industrial Biotechnology -- Bio Materials (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Annan data- och informationsvetenskap (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Other Computer and Information Science (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Hälsovetenskap -- Medicinsk etik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Health Sciences -- Medical Ethics (hsv//eng)
Keyword
- Biological materials
- Data handling
- Engines
- Genes
- Information management
- Open source software
- Open systems
- RNA
- Storage (materials)
- Adaptive scheduling
- Biomedical data analysis
- Computational bottlenecks
- Next-generation sequencing
- Parallel processing
- Scientific workflow engines
- Storage requirements
- Transcriptome analysis
- Digital storage
Publication and Content Type
- ref (subject category)
- kon (subject category)
Find in a library
To the university's database
- By the author/editor
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Bessani, A.
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Brandt, J.
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Bux, M.
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Cogo, V.
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Dimitrova, L.
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Dowling, Jim
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show more...
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Gholami, Ali
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Hakimzadeh, Kama ...
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Hummel, M.
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Ismail, Mahmoud
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Laure, Erwin
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Leser, U.
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Litton, J. -E
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Martinez, R.
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Niazi, Salman
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Reichel, Jane
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Zimmermann, K.
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- About the subject
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- ENGINEERING AND TECHNOLOGY
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ENGINEERING AND ...
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and Industrial Biote ...
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and Bio Materials
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Computer and Inf ...
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and Other Computer a ...
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Health Sciences
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and Medical Ethics
- Articles in the publication
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1st Internationa ...
- By the university
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Royal Institute of Technology
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Uppsala University