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Petabyte-scale innovations at the European Nucleotide Archive

G. Cochrane, R. Akhtar, J. Bonfield, L. Bower, F. Demiralp, N. Faruque, R. Gibson, G. Hoad, T. Hubbard, C. Hunter, M. Jang, S. Juhos (+15 others)
2009 Nucleic Acids Research  
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

Charles E Cook, Mary T Bergman, Guy Cochrane, Rolf Apweiler, Ewan Birney
2017 Nucleic Acids Research  
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

Louis Papageorgiou, Picasi Eleni, Sofia Raftopoulou, Meropi Mantaiou, Vasileios Megalooikonomou, Dimitrios Vlachakis
2018 EMBnet journal  
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

Louis Papageorgiou, Picasi Eleni, Sofia Raftopoulou, Meropi Mantaiou, Vasileios Megalooikonomou, Dimitrios Vlachakis
2018 EMBnet journal  
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

Nick Goldman, Paul Bertone, Siyuan Chen, Christophe Dessimoz, Emily M. LeProust, Botond Sipos, Ewan Birney
2013 Nature  
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

Xueqin Guo, Fengzhen Chen, Fei Gao, Ling Li, Ke Liu, Lijin You, Cong Hua, Fan Yang, Wanliang Liu, Chunhua Peng, Lina Wang, Xiaoxia Yang (+14 others)
2020 Database: The Journal of Biological Databases and Curation  
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

Siddhant Shrivastava, Rohan Badlani
2014 International Journal of Electrical Energy  
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

Steven Munevar
2017 Nature Biotechnology  
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

Rachel Finn, Anna Donovan, Kush Wadhwa, Lorenzo Bigagli, José María García
2014 Zenodo  
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)

Lyubomir Penev, Dimitrios Koureas, Quentin Groom, Jerry Lanfear, Donat Agosti, Ana Casino, Joe Miller, Christos Arvanitidis, Guy Cochrane, Donald Hobern, Olaf Banki, Wouter Addink (+10 others)
2022 Research Ideas and Outcomes  
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

D. S. Gonzalez
2003 Briefings in Bioinformatics  
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

David Bousfield, Johanna McEntyre, Sameer Velankar, George Papadatos, Alex Bateman, Guy Cochrane, Jee-Hyub Kim, Florian Graef, Vid Vartak, Blaise Alako, Niklas Blomberg
2016 F1000Research  
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

F. Biscarini, P. Cozzi, P. Orozco-ter Wengel
2018 Animal Genetics  
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

Dick M.A. Schaap
2020 Zenodo  
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

Artemis Lavasa, Sünje Dallmeier-Tiessen, Stephanie Van De Sandt, Ioannis Tsanaktsidis, Anna Trzcinska, Pamfilos Fokianos, Tina Dohna, Ketil Koop-Jakobsen, Uwe Schindler, Barbara Lemon, Rachael Kotarski, Christine Ferguson (+5 others)
2018 Zenodo  
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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