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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  ...  However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources.  ...  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

Deliverable 10.1 - Data Management Plan [article]

Pedro Campilho, Stephane Pesant, Kate Larkin, Ward Appeltans
2021 Zenodo  
It addresses the European Commission's open access to research data requirements (ORD pilot), as well as Article 29 of the Project's Grant Agreement on the dissemination and exploitation of results.  ...  Deliverable D10.1 constitutes the Data Management Plan (DMP) of project AtlantECO.  ...  The assembly pipeline includes a decontamination filter and tools for the assembly and read mapping (metaSPAdes and MEGAHIT), binning (MetaWrap) and quality assessment (CheckM).  ... 
doi:10.5281/zenodo.5503580 fatcat:pc7i75erhvfvtpznbpfhrwp7bi

Rapport d'activités IFB 2019-2020 [article]

Claudine Médigue, Suzanne Lauriou, Angela Saenz, Jacques Van Helden, IFB Teams
2021 Zenodo  
This funding will lay down the basis of IFB infrastructure for our 2021-2025 roadmap, and strengthen several priority activities, e.g., FAIR data, integration of imaging, multi-omics and phenomics data  ...  ), that gathers 37 teams (IFB platforms, data centers, mesocenters and data-producing infrastructures) from 16 research organizations and 160 persons, totaling 40 FTE of involvement in the 4 work packages  ...  >> Detailed report of the survey  ... 
doi:10.5281/zenodo.5324333 fatcat:py5xp6q7ungkdevdqx25zxfwmq

Referee report. For: Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR [version 1; peer review: 1 approved]

Donald Hobern
2022
However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources.  ...  As a research infrastructure developing services and technical solutions that help integrate and coordinate life science  ...  Page 18 -"It is clear that from barcodes to reference genomes, sequencing hundreds of thousands of species in the near future will generate the foundational data for most biodiversity molecular studies  ... 
doi:10.5256/f1000research.77505.r115285 fatcat:pymueawd6bg57epkaeugcjov7e

Referee report. For: Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR [version 1; peer review: 1 approved, 1 approved with reservations]

Anders Andersson
2022
However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources.  ...  As a research infrastructure developing services and technical solutions that help integrate and coordinate life science  ...  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:10.5256/f1000research.77505.r119683 fatcat:5z53mmvb2rcvtjgmzrwddevmo4

LARGE SCALE ANNOTATION OF BIOMOLECULAR DATA USING INTEGRATED DATABASE MANAGEMENT TOOLS List of Publications

Dissertation, Roberto Vera Alvarez, Sándor Pongor
unpublished
The framework is comprised of a Java API for external use, a desktop client and a webservices application. This system has been supplying integrative data for many bioinformatics projects.  ...  This workflow is applied either to create a marker database for taxonomy binning or just to obtain unique DNA segments among a group of targets sequences.  ...  Acknowledgements This work is the result of an exceptionally fruitful collaboration between institutions from Cuba,  ... 
fatcat:mxt7m3cjdzbezpcjwotpkjz4zm

NOAA 'Omics White Paper: Informing the NOAA 'Omics Strategy and Implementation Plan

Kelly Goodwin
2020
such as assembly of genomes and the transcriptomes (the genes expressed in given tissues and individuals); that older system proved the utility of a locally managed resource for bioinformatics across  ...  The beneficial range and volume of information generated through 'omics tools will allow NOAA to comprehensively address a complex suite of questions across multiple missions.  ...  The OTF membership represented a variety of line offices and programs. OTF members from April 2018-July 2020 are detailed below. Derek Parks  ... 
doi:10.25923/bd7z-zb37 fatcat:2gl6mmvr75chva6qxfdxtenlwm