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Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability

Bastian Schiffthaler, Myrto Kostadima, Nicolas Delhomme, Gabriella Rustici, Francis Ouellette
2016 PLoS Computational Biology  
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

Robert M. Waterhouse, Anne-Françoise Adam-Blondon, Donat Agosti, Petr Baldrian, Bachir Balech, Erwan Corre, Robert P. Davey, Henrik Lantz, Graziano Pesole, Christian Quast, Frank Oliver Glöckner, Niels Raes (+7 others)
2021 F1000Research  
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

A-F Adam-Blondon, M Alaux, C Pommier, D Cantu, Z-M Cheng, GR Cramer, C Davies, S Delrot, L Deluc, G Di Gaspero, J Grimplet, A Fennell (+12 others)
2016 Horticulture Research  
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

Esther Dzale Yeumo, Michael Alaux, Elizabeth Arnaud, Sophie Aubin, Ute Baumann, Patrice Buche, Laurel Cooper, Hanna Ćwiek-Kupczyńska, Robert P. Davey, Richard Allan Fulss, Clement Jonquet, Marie-Angélique Laporte (+9 others)
2017 F1000Research  
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

Sabina Leonelli, Nicholas Smirnoff, Jonathan Moore, Charis Cook, Ruth Bastow
2013 Journal of Experimental Botany  
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

Brane Leskosek, Leslie Matalonga, Andrej Kastrin, Jure Dimec, Femke Francissen, Sergi Beltran, Eivind Coward, Hedi Peterson, Ivo Gut, Marco Roos, Susheel Varma
2018 Zenodo  
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

Norman E. Davey, M. Madan Babu, Martin Blackledge, Alan Bridge, Salvador Capella-Gutierrez, Zsuzsanna Dosztanyi, Rachel Drysdale, Richard J. Edwards, Arne Elofsson, Isabella C. Felli, Toby J. Gibson, Aleksandras Gutmanas (+32 others)
2019 F1000Research  
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

Esther Dzale Yeumo, Michael Alaux, Elizabeth Arnaud, Sophie Aubin, Ute Baumann, Patrice Buche, Laurel Cooper, Hanna Ćwiek-Kupczyńska, Robert P. Davey, Richard Allan Fulss, Clement Jonquet, Marie-Angélique Laporte (+9 others)
2017 F1000Research  
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

Hanns Lochmüller, Josep Torrent i Farnell, Yann Le Cam, Anneliene H Jonker, Lilian PL Lau, Gareth Baynam, Petra Kaufmann, Hugh JS Dawkins, Paul Lasko, Christopher P Austin, Kym M Boycott
2017 European Journal of Human Genetics  
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

Vivek Navale, Denis von Kaeppler, Matthew McAuliffe
2021 Journal of Data, Information and Management  
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

David Salgado, Irina M. Armean, Michael Baudis, Sergi Beltran, Salvador Capella-Gutierrez, Denise Carvalho-Silva, Victoria Dominguez Del Angel, Joaquin Dopazo, Laura I. Furlong, Bo Gao, Leyla Garcia, Dietlind Gerloff (+30 others)
2020 F1000Research  
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

L. Larcombe, R. Hendricusdottir, T.K. Attwood, F. Bacall, N. Beard, L.J. Bellis, W.B. Dunn, J.M. Hancock, A. Nenadic, C. Orengo, B. Overduin, S-A Sansone (+6 others)
2017 F1000Research  
.: 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

Jim Kaput, Giuditta Perozzi, Marijana Radonjic, Fabio Virgili
2017 Genes & Nutrition  
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

Sheenah M. Mische, Nancy C. Fisher, Susan M. Meyn, Katia Sol Church, Rebecca L. Hegstad-Davies, Frances Weis-Garcia, Marie Adams, John M. Ashton, Kym M. Delventhal, Julie A. Dragon, Laura Holmes, Pratik Jagtap (+5 others)
2020 Journal of Biomolecular Techniques  
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

Célia Miguel, Cyril Pommier, Richard Finkers, Frederik Coppens, Dan Bolser, Manuel Ruiz, Anne-Françoise Adam-Blondon, Kristina Gruden, Živa Ramšak, Evangelia Papoutsoglou, Daniel Faria, Bruno Costa (+1 others)
2019 Zenodo  
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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