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The European Bioinformatics Institute in 2018: tools, infrastructure and training

Charles E Cook, Rodrigo Lopez, Oana Stroe, Guy Cochrane, Cath Brooksbank, Ewan Birney, Rolf Apweiler
2018 Nucleic Acids Research  
The European Bioinformatics Institute (https://www.ebi.ac.uk/) archives, curates and analyses life sciences data produced by researchers throughout the world, and makes these data available for re-use  ...  This year we have improved the efficiency of our computational infrastructure and doubled the bandwidth of our connection to the worldwide web.  ...  We were able to continue to scale our infrastructure and meet demand thanks in part to support from the UK's Large Facilities Capital Fund (LFCF).  ... 
doi:10.1093/nar/gky1124 pmid:30445657 pmcid:PMC6323906 fatcat:ww5xqc5aorgone5pt43p43o6tu

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  ...  This is reflected in our deep involvement in Open Targets, stewarding of plant phenotyping standards (MIAPPE) and partnership in the Human Cell Atlas data coordination platform, as well as the 2017 launch  ...  INTRODUCTION EMBL's European Bioinformatics Institute (EMBL-EBI) is a publicly funded scientific organization that provides open data, open-source software tools and 'big data' infrastructure to the global  ... 
doi:10.1093/nar/gkx1154 pmid:29186510 pmcid:PMC5753251 fatcat:ubzlegb2kjcltbtdftwsh6mlja

The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences

2019 Nucleic Acids Research  
Training is a core mission of EMBL-EBI and in 2018 our training team served more users, both in-person and through web-based programmes, than ever before.  ...  Data resources at the European Bioinformatics Institute (EMBL-EBI, https://www.ebi.ac.uk/) archive, organize and provide added-value analysis of research data produced around the world.  ...  ACKNOWLEDGEMENTS We were able to continue to scale our infrastructure and meet demand thanks in part to support from the UK's Large Facilities Capital Fund (LFCF).  ... 
doi:10.1093/nar/gkz1033 pmid:31701143 pmcid:PMC6943058 fatcat:i2gcxbfkprb37etd37stq4t74a

The European Nucleotide Archive in 2018

Peter W Harrison, Blaise Alako, Clara Amid, Ana Cerdeño-Tárraga, Iain Cleland, Sam Holt, Abdulrahman Hussein, Suran Jayathilaka, Simon Kay, Thomas Keane, Rasko Leinonen, Xin Liu (+12 others)
2018 Nucleic Acids Research  
template expansion, early pre-submission validation tools and our move towards a new browser and retrieval infrastructure.  ...  Here, we outline ENA services and content in 2018 and provide an overview of a selection of focus areas of development work: extending data coordination services around ENA, sequence submissions through  ...  INTRODUCTION For over a third of a century, the European Nucleotide Archive (ENA) has served as a cornerstone of the world's bioinformatics infrastructure.  ... 
doi:10.1093/nar/gky1078 pmid:30395270 fatcat:kmr4vyojundfzabhv3dwdciamu

ELIXIR-Training-2018-ELIXIR-CZ-Conference

Celia Van Gelder, Patricia M. Palagi, Gabriella Rustici, Pascal Kahlem
2018 Figshare  
In this way the ELIXIR Training Platform facilitates provision and delivery of high quality training in Europe, which helps to further advance research in the life sciences  ...  Together we have established a high-quality and impactful training programme for researchers (TtR), developers and infrastructure operators (TtD), and trainers (TtT) as well as a training infrastructure  ...  Train-the-Trainer (TtT) -Building a highly-skilled and coherent community of trainers • "There is an alarming shortage of data experts both globally and in the European Union" • "Core data experts need  ... 
doi:10.6084/m9.figshare.7378283.v1 fatcat:mpohwwuozjg27jfgqvjbxulgvy

The European Bioinformatics Institute (EMBL-EBI) in 2021

Gaia Cantelli, Alex Bateman, Cath Brooksbank, Anton I Petrov, Rahuman S Malik-Sheriff, Michele Ide-Smith, Henning Hermjakob, Paul Flicek, Rolf Apweiler, Ewan Birney, Johanna McEntyre
2021
The European Bioinformatics Institute (EMBL-EBI) maintains a comprehensive range of freely available and up-to-date molecular data resources, which includes over 40 resources covering every major data  ...  type in the life sciences.  ...  We would like to thank Ivan Anishchanka at the University of Washington in Seattle for creating the trRosetta and RoseTTAfold structural models.  ... 
doi:10.1093/nar/gkab1127 pmid:34850134 pmcid:PMC8690175 fatcat:pki3geb64vanpmav4ytls5dwx4

Clinical Research Informatics: Contributions from 2018

Christel Daniel, Dipak Kalra, Section Editors for the IMIA Yearbook Section on Clinical Research Informatics
2019 IMIA Yearbook of Medical Informatics  
Objectives: To summarize key contributions to current research in the field of Clinical Research Informatics (CRI) and to select best papers published in 2018.  ...  Results: Among the 1,469 retrieved papers published in 2018 in the various areas of CRI, the full review process selected four best papers.  ...  Acknowledgement We would like to acknowledge the support of Adrien Ugon, Martina Hutter and the reviewers in the selection process of the IMIA Yearbook.  ... 
doi:10.1055/s-0039-1677921 pmid:31419833 pmcid:PMC6697501 fatcat:hi6fxrhijjbzfp7jvmysy2cmke

Gramene 2018: unifying comparative genomics and pathway resources for plant research

Marcela K Tello-Ruiz, Sushma Naithani, Joshua C Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J Geniza, Yinping Jiao, Young Koung Lee, Bo Wang (+27 others)
2017 Nucleic Acids Research  
, and user-defined omics data in the context of these pathways.  ...  As a community portal, Gramene integrates best-of-class software and infrastructure components including the Ensembl genome browser, Reactome pathway browser, and Expression Atlas widgets, and undergoes  ...  We also thank the Cold Spring Harbor Laboratory (CSHL) and the Dolan DNA Learning Center, the Center for Genome Research and Biocomputing (CGRB) at Oregon State University, and the Ontario Institute for  ... 
doi:10.1093/nar/gkx1111 pmid:29165610 pmcid:PMC5753211 fatcat:bxgarlrs6rab5lwpixua6gotgq

IMISC 2018 - Book of Abstracts

Imisc Admin
2020 figshare.com  
If we have seen further it is by standing on the shoulders of giants.In The Book of Abstracts of the IMISC 2018, reader can find the abstracts of papers submitted, reviewed, and presented in the conference  ...  ://2018.imisc.net) and figshare portal (http://imisc.figshare.com).Best regards,On behalf of the Organizing CommitteeH.  ...  Some of her latest journal publications include 'Technology Management and the Change in the European Geodata market' and 'How to manage government?  ... 
doi:10.6084/m9.figshare.7217858.v4 fatcat:26z6hgr3zbedhhbtvsb46xbyca

IMISC 2018 - Book of Abstracts

Imisc Admin
2020 figshare.com  
If we have seen further it is by standing on the shoulders of giants.In The Book of Abstracts of the IMISC 2018, reader can find the abstracts of papers submitted, reviewed, and presented in the conference  ...  ://2018.imisc.net) and figshare portal (http://imisc.figshare.com).Best regards,On behalf of the Organizing CommitteeH.  ...  Some of her latest journal publications include 'Technology Management and the Change in the European Geodata market' and 'How to manage government?  ... 
doi:10.6084/m9.figshare.7217858.v5 fatcat:7tqbtruzcbhc7mzgc752b2spdq

EMPHASIS-PREP Deliverable 3.2: Mapping of training activities

Silvana Moscatelli, Michela Janni, Francesco Loreto
2018 Zenodo  
Some of the best infrastructures for plant phenotyping are based on laboratories and platforms leaded by European institutions.  ...  Rationale: A number of education and training activities on phenotyping are currently already performed at European and International level.  ...  Some of the best infrastructures for plant phenotyping are based on laboratories and platforms leaded by European institutions.  ... 
doi:10.5281/zenodo.3766747 fatcat:judot7j5o5hm5lejojhokjle4i

IMISC 2018 - Book of Abstracts

Imisc Admin
2020 figshare.com  
If we have seen further it is by standing on the shoulders of giants.In The Book of Abstracts of the IMISC 2018, reader can find the abstracts of papers submitted, reviewed, and presented in the conference  ...  ://2018.imisc.net) and figshare portal (http://imisc.figshare.com).Best regards,On behalf of the Organizing CommitteeH.  ...  Some of her latest journal publications include 'Technology Management and the Change in the European Geodata market' and 'How to manage government?  ... 
doi:10.6084/m9.figshare.7217858.v3 fatcat:quztkju7nbfn3pgf5y75a6n5wa

D14.2 Popd - Requirement No. 4

Pascal Khalem, Jerry Lanfear, Regina Becker
2018 Zenodo  
The strategy describes the essential procedures and practices within ELIXIR concerning GDPR compliance, performing risk assessment and mitigation.  ...  This deliverable describes the ELIXIR risk management strategy with respect to the General Data Protection Regulation (GDPR)1, which came into force on 25 May 2018.  ...  ELIXIR will provide open access to bioinformatics resources by providing a data, compute, tools, standards and training infrastructure.  ... 
doi:10.5281/zenodo.1452482 fatcat:vr2fz5yl5fg77pdsc3n575axjm

Türkiye'de 2008-2018 Döneminde Yapılan Biyomedikal Mühendisliğindeki Araştırmaların Derlemesi

Mehlika Karamanlioglu
2019 International Journal of Advances in Engineering and Pure Sciences  
research papers conducted by Turkish Institutes published during the period 2008-2018 that contribute and/or have a potential to contribute to research and development (R&D) in biomedical engineering  ...  The aim of this review is to summarize the problems regarding biomedical engineering in Turkey; to present the main subjects that are conducted in biomedical field in Turkey; and to summarize the prominent  ...  Bioinformatics is the analysis of biological data especially used in molecular biology and likewise, bioinformatics has not been taught or studied effectively in Turkey [13] .  ... 
doi:10.7240/jeps.578024 fatcat:loqong2yofe4xhz2ox5jff2wnq

Lessons Learned as President of the Institute for Systems Biology (2000–2018)

Leroy E. Hood
2018 Genomics, Proteomics & Bioinformatics  
out at the end of 2018.  ...  We transformed K-12 science education in Seattle schools and more recently have engaged almost half the school districts in the state in STEM education through professional teach training.  ... 
doi:10.1016/j.gpb.2018.02.002 pmid:29496591 pmcid:PMC6000253 fatcat:5lx6nv4ncbd65bg35zc2dsulru
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