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Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability
2016
PLoS Computational Biology
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The advancement of high-throughput sequencing (HTS) technologies and the rapid development of numerous analysis algorithms and pipelines in this field has resulted in an unprecedentedly high demand for ...
To achieve this, we have developed a strategy for materials' curation and dissemination. ...
Acknowledgments The authors wish to thank Matt Drew, from The Genome Analysis Centre (TGAC), and Cathy Hemmings, from the Department of Genetics of the University of Cambridge, for the support with the ...
doi:10.1371/journal.pcbi.1004937
pmid:27309738
pmcid:PMC4910983
fatcat:tqu3o5qzizddxgezlvq7glbksu
Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR
2021
F1000Research
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to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures ...
needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. ...
Acknowledgements The authors would like to acknowledge the important contribution made by Dr Corinne Martin, ELIXIR, who provided critical independent expert review of the manuscript during its preparation ...
doi:10.12688/f1000research.73825.1
fatcat:wphybjxe4bd3dgdewjqobb2hfe
Towards an open grapevine information system
2016
Horticulture Research
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research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. ...
Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine ...
ACKNOWLEDGEMENTS The foundations and the first draft of this paper were set up during a workshop organized in Bordeaux, France in February 2015 with the financial support of the Gallo Wine Company, INRA ...
doi:10.1038/hortres.2016.56
pmid:27917288
pmcid:PMC5120350
fatcat:3ef2aqrrmvbvxgiccdipsx2r6u
Developing data interoperability using standards: A wheat community use case
2017
F1000Research
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Interoperability is a growing concern to the wheat scientific community, and agriculture in general, as the need to interpret the deluge of data obtained through high-throughput technologies grows. ...
Agreeing on common data formats, metadata, and vocabulary standards is an important step to obtain the required data interoperability level in order to add value by encouraging data sharing, and subsequently ...
for handling DNA and RNA sequencing, high throughput genotyping and phenotyping, high throughput imaging, and satellite monitoring. ...
doi:10.12688/f1000research.12234.1
pmid:29333241
pmcid:PMC5747345
fatcat:qp52ypamubbcdp4xrqotjw6msm
Making open data work for plant scientists
2013
Journal of Experimental Botany
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The difficulties involved in sharing sequencing, transcriptomics, proteomics, and metabolomics data are reviewed. ...
In this commentary, some of the challenges encountered by plant researchers at the bench when generating, interpreting, and attempting to disseminate their data have been highlighted. ...
Acknowledgements This paper has benefited from discussions held at a workshop on data dissemination in plant science at the University of Exeter in June 2012 and generously sponsored by the ESRC, GARNet ...
doi:10.1093/jxb/ert273
pmid:24043847
pmcid:PMC3808334
fatcat:wpu4uix4tvdxredwp6vil3gxqi
Report On The Elixir Workshop Organized With The Rare-Disease Communities
2018
Zenodo
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For the both parts the aims were (1) to identify key training contacts/subjects in the RD community, (2) to identify specific training needs in the RD community and (3) to spread specific knowledge needed ...
Training workshops and courses were delivered in partnership with WP11'EXCELERATE Training Programme'. ...
According to the results, there is an urgent need to provide more courses in computational science, high-throughput sequencing and system biology. ...
doi:10.5281/zenodo.1321600
fatcat:6a7flivn4bhmxc7dzdoqqthy5a
An intrinsically disordered proteins community for ELIXIR
2019
F1000Research
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The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. ...
The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders. ...
A strategic meeting to identify the key priority areas for the roadmap was funded by ELIXIR, the research infrastructure for ...
doi:10.12688/f1000research.20136.1
pmid:31824649
pmcid:PMC6880265
fatcat:2rw2z5q3obgrllxjcthcqgoiyu
Developing data interoperability using standards: A wheat community use case
2017
F1000Research
Preserved Fulltext
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Interoperability is a growing concern to the wheat scientific community, and agriculture in general, as the need to interpret the deluge of data obtained through high-throughput technologies grows. ...
Agreeing on common data formats, metadata, and vocabulary standards is an important step to obtain the required data interoperability level in order to add value by encouraging data sharing, and subsequently ...
for handling DNA and RNA sequencing, high throughput genotyping and phenotyping, high throughput imaging, and satellite monitoring. ...
doi:10.12688/f1000research.12234.2
pmid:29333241
pmcid:PMC5747345
fatcat:46lgnysdmncf7bbq64de6pw6ie
The International Rare Diseases Research Consortium: Policies and Guidelines to maximize impact
2017
European Journal of Human Genetics
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high-throughput and cost-effective testing to the rare diseases patient community as a whole, e.g., guidelines for diagnostic next-generation sequencing developed by EuroGentest and the European Society ...
The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in a credit line to the material. ...
doi:10.1038/s41431-017-0008-z
pmid:29158551
pmcid:PMC5865169
fatcat:nyuvmitp4zcbrf5a7txjukjfeu
An overview of biomedical platforms for managing research data
2021
Journal of Data, Information and Management
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AbstractBiomedical platforms provide the hardware and software to securely ingest, process, validate, curate, store, and share data. ...
Adoption of Common Data Models, Common Data Elements, and Ontologies can increase the likelihood of data reuse. ...
The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. ...
doi:10.1007/s42488-020-00040-0
fatcat:itiji5ifu5hjhhcjvtzwz6jq6e
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research
2020
F1000Research
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While "High-Throughput" sequencing technologies are increasingly becoming the primary choice for genomic screening analysis, their ability to efficiently detect CNVs is still heterogeneous and remains ...
The meeting led to the definition of priority objectives and tasks, to address a wide range of CNV-related challenges ranging from detection and interpretation to sharing and training. ...
Objective #7: dissemination The global adoption of tools and guidelines is strongly linked to the ability to communicate, produce training materials, and train actors as well as patients and the general ...
doi:10.12688/f1000research.24887.1
fatcat:qncqg4ykijgznjw5grbzzszmeq
ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR
2017
F1000Research
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.: Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability. PLoS Comput Biol. 2016; 12(6): e1004937. ...
Since its foundation in 2014, ELIXIR-UK has played a leading role in training both within the UK and in the ELIXIR Training Platform, which coordinates and delivers training across all ELIXIR members. ...
In particular, GOBLET and ELIXIR-UK have been collaborating on developing best practices and guidelines to enable training material sharing, dissemination and reuse. ...
doi:10.12688/f1000research.11837.1
pmid:28781748
pmcid:PMC5521157
fatcat:ilajvsaxsvcgtaqrkhjvslxsim
Propelling the paradigm shift from reductionism to systems nutrition
2017
Genes & Nutrition
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Journal policies are meant to guide potential authors to adopt the most updated standardization guidelines and shared best practices. ...
As primary actors of dissemination to the scientific community, journals can impose rigid criteria for publishing only sound, reliable, and reproducible data. ...
Microbiome The use of high-throughput sequence technologies spurred the study of the microbiomes that live in and on humans and other organisms. ...
doi:10.1186/s12263-016-0549-8
pmid:28138347
pmcid:PMC5264346
fatcat:n53rwvwuxbh4jbh45qpmazr7le
A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups
2020
Journal of Biomolecular Techniques
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Shared research resource facilities, also known as core laboratories (Cores), are responsible for generating a significant and growing portion of the research data in academic biomedical research institutions ...
This review provides a summary of the contributions of the ABRF RGs to promote scientific rigor and reproducibility in Cores from the published literature, ABRF meetings, and ABRF RGs communications. ...
Continuation of this study resulted in definition and dissemination of best practices for sequencing high GC templates. 115 The second in The Never Ending Story series assessed the state-of-the-art in ...
doi:10.7171/jbt.20-3101-003
pmid:31969795
pmcid:PMC6959150
fatcat:q5gkeiwsq5cy3fnitsh27hskde
ELIXIR-EXCELERATE D7.3: Implementation of BRAPI (Plant Breeding API) at all participating nodes
2019
Zenodo
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High-throughput "omics" technologies are widely used and increasingly important to support plant biology research and breeding of diverse plant species for production of food, feed, fibre and other biomaterials ...
To help unlock the full potential of a multi-omics approach to plant science, the overarching goal of this work package is to make plant data reusable and interoperable in accordance with the FAIR principles ...
The FAIDARE ELIXIR Plant Data Search service will be sustainable beyond EXCELERATE and is already included in the work plan of several ELIXIR Implementation Study projects, in some EOSC Life demonstrators ...
doi:10.5281/zenodo.3354265
fatcat:4zajlvihszaq3kulzxle7dekaq
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