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Petabyte-scale innovations at the European Nucleotide Archive
2009
Nucleic Acids Research
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The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/embl), comprising the EMBL Nucleotide Sequence Database and the Ensembl Trace Archive, has identified challenges in the storage, movement, analysis ...
Dramatic increases in the throughput of nucleotide sequencing machines, and the promise of ever greater performance, have thrust bioinformatics into the era of petabyte-scale data sets. ...
Ensembl Trace Archive, lies therefore at the forefront of the European focus for petabyte-scale data strategies. ...
doi:10.1093/nar/gkn765
pmid:18978013
pmcid:PMC2686451
fatcat:xzwl3cvkjnarxbbbowzbnhazpi
The European Bioinformatics Institute in 2017: data coordination and integration
2017
Nucleic Acids Research
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The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https ...
Submissions continue to increase exponentially: our data storage has doubled in less than two years to 120 petabytes. ...
ChEBI (3), ChEMBL (4), the European Genome-phenome Archive (EGA) (5), the European Nucleotide Archive (ENA) (6), Ensembl (7), Ensembl Genomes (8), Europe PMC (9), IntAct (as part of the IMEx Consortium ...
doi:10.1093/nar/gkx1154
pmid:29186510
pmcid:PMC5753251
fatcat:ubzlegb2kjcltbtdftwsh6mlja
Genomic big data hitting the storage bottleneck
2018
EMBnet journal
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Scientific community experiences the data crisis era, where, out of the box solutions may ease the typical research workflow, until technological development meets the needs of Bioinformatics. ...
The motivation for sequencing has fallen behind. Sometimes, the time that is spent to solve storage space problems is longer than the one dedicated to collect and analyse data. ...
using advanced personalized models and advanced interventions", co-funded by the European Commission under the Horizon 2020 research and innovation programme. ...
pmid:29782620
pmcid:PMC5958914
fatcat:ix3epgyfxfdorl5jnuvxuyi7ri
Genomic big data hitting the storage bottleneck
2018
EMBnet journal
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Scientific community experiences the data crisis era, where, out of the box solutions may ease the typical research workflow, until technological development meets the needs of Bioinformatics. ...
The motivation for sequencing has fallen behind. Sometimes, the time that is spent to solve storage space problems is longer than the one dedicated to collect and analyse data. ...
using advanced personalized models and advanced interventions", co-funded by the European Commission under the Horizon 2020 research and innovation programme. ...
doi:10.14806/ej.24.0.910
fatcat:eq4iqnbcifgpbabkszpskwd6pq
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA
2013
Nature
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of their cost-efficiency for large-scale information archival 9 . ...
In all, the five files were represented by a total of 153,335 strings of DNA, each comprising 117 nucleotides (nt). ...
In our experiment (megabyte scale) the encoding scheme is 88% efficient; Fig. 2a indicates that efficiency remains .70% for data storage on petabyte (PB, 10 15 bytes) scales and .65% on exabyte (EB, ...
doi:10.1038/nature11875
pmid:23354052
pmcid:PMC3672958
fatcat:ss4dzlmtrfdt3hkl75gwvq3ulu
CNSA: a data repository for archiving omics data
2020
Database: The Journal of Biological Databases and Curation
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six objects, namely Project, Sample, Experiment, Run, Assembly and Variation at present. ...
Here, relying on China National GeneBank (CNGB), we present CNGB Sequence Archive (CNSA) for archiving omics data, including raw sequencing data and its further analyzed results which are organized into ...
Acknowledgements We gratefully thank other colleagues in the CNGB who helped to create and maintain the CNSA. ...
doi:10.1093/database/baaa055
pmid:32705130
fatcat:sgmpgg3fnze2pdyokgsfm2ngau
Data Storage in DNA
2014
International Journal of Electrical Energy
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An urgent need for a proper medium for information archival and retrieval purposes arises. ...
The analyzed data from the researches reveals that just four grams of DNA can store all the information that the world produces in a year. ...
ACKNOWLEDGMENTS We are grateful to the management of BITS Pilani for allowing us to publish the technical review paper. ...
doi:10.12720/ijoee.2.2.119-124
fatcat:zbintbzsqndhxdhxkp3asdlqce
Unlocking Big Data for better health
2017
Nature Biotechnology
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European Nucleotide Archive The ENA provides globally comprehensive primary data repositories for nucleotide sequencing information. ...
Support from the UK Government's Large Facilities Capital Fund.
Compressed nucleotide sequence data: 2.58 petabytes stored (compare to 1.8 petabytes in 2013). ...
doi:10.1038/nbt.3918
pmid:28700551
fatcat:oqiurm5cgzec7lfenvjvlemxoy
Big Data Initiatives
2014
Zenodo
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computational models relevant to the life sciences
• Chemical Entities of Biological Interest (ChEBI) -database and ontology of molecular
entities
• European Nucleotide Archive (ENA) -resource of nucleotide ...
CERN Worldwide LHC Computing Grid The European Centre for Nuclear Research has been at the forefront of computing innovations since its foundation in 1954. ...
Finally, the analysis has also resulted in some specific ideas about the potential externalities that may result from the large-scale deployment of big data, as well as some initial evidence about how ...
doi:10.5281/zenodo.49165
fatcat:kztedlrb3zh57ksuesfbbaluqu
Biodiversity Community Integrated Knowledge Library (BiCIKL)
2022
Research Ideas and Outcomes
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through provision of access to data, associated tools and services at each separate stage of and along the entire research cycle. ...
BiCIKL is an European Union Horizon 2020 project that will initiate and build a new European starting community of key research infrastructures, establishing open science practices in the domain of biodiversity ...
He worked as scientific researcher at the University of Amsterdam, Netherlands Institute for Sea Research, the Alfred Wegener Institute for Polar Research, and as managing director at ETI Biodiversity ...
doi:10.3897/rio.8.e81136
fatcat:4owwssl7zzfzna6likizigcv7u
News section
2003
Briefings in Bioinformatics
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Collaboration with the
Macromolecular Structure Database
(MSD) 15 at the European Bioinformatics
Institute (EBI) 16 is already underway and
will lead in due course to the
incorporation within the ...
Gonzalez E-mail: dgonzalez@charter.net California Institute of Technology, the University of Illinois at Urbana-Champaign, Manchester University, CERN (European Organization for Nuclear Research), the ...
doi:10.1093/bib/4.1.91
pmid:12715837
fatcat:nyzdvbct45h6ngxkumzaoraife
Patterns of database citation in articles and patents indicate long-term scientific and industry value of biological data resources
2016
F1000Research
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Data from open access biomolecular data resources, such as the European Nucleotide Archive and the Protein Data Bank are extensively reused within life science research for comparative studies, method ...
citations in more than 8,000 patents from 2014, demonstrating substantial use and an important role for data resources in defining biological concepts in granted patents to both academic and industrial innovators ...
Supplementary Material The methodology is well described. Authors note that "citation analysis is a cornerstone of research impact and evaluation". ...
doi:10.12688/f1000research.7911.1
pmid:27092246
pmcid:PMC4821287
fatcat:dk732skdhbfyzkvzoo2o47o5yi
Lessons learnt on the analysis of large sequence data in animal genomics
2018
Animal Genetics
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DRYAD (http://datadryad.org/), Zenodo (https://zenodo.org/), the Short Read
Archive (NCBI, http://www.ncbi.nlm.nih.gov/sra), the European Nucleotide Archive (EBI,
http://www.ebi.ac.uk/ena). ...
over 60 petabytes (60 x 10 15 bytes) of data, of which over 2 petabytes are genomic data (Marx, 2013) ; the Sequence Read Archive (SRA) at the National Centre for Biotechnology Information (NCBI) contains ...
doi:10.1111/age.12655
pmid:29624711
fatcat:vrdnm3ir5vc55m6pfukkvep2ha
D2.1 Blue data infrastructures - Services Description Report
2020
Zenodo
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The pilot Blue-Cloud project aims at federating initially in total 10blue data infrastructures. ...
This analysis, technical specification and workplan for the implementation and deployment of the Blue Cloud data discovery and access service will be documented in Deliverable D2.2 at M8. ...
: http://www.opensealab.eu/data2019 > R Tutorials > EMODnet > EMODnet Biology
The European Nucleotide Archive (ENA) provides a comprehensive open record of the world's nucleotide sequencing information ...
doi:10.5281/zenodo.6338527
fatcat:qcn6qvb4vjdz3borr6kqhcydgu
Deliverable 4.1 Integration of Mature PID Types
2018
Zenodo
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This first report for Work Package 4 presents considerations and implementations stemming from the first year of work carried out by the pilot applications and sets the scene for the future integration ...
types into the different disciplinary systems. ...
In June 2017, CERN's data center reached the 200 petabyte milestone of data permanently archived in the tape library 3 . ...
doi:10.5281/zenodo.2414839
fatcat:wlcjwt75xnaxhfnkhscalcia6q
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