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Providing an open collaborative space for digital biology in Europe

Deliverables

Cloud implementation of exemplary workflows selected by the RIs/communities

Cloud implementation of exemplary workflows selected by the RIs/communities including demonstrators

Report on requirements for regulatory compliance of sensitive health data and biological and medical research data management

Report on requirements for regulatory compliance of sensitive health data and biological and medical research data management

FAIR Requirements document

Requirements document available

Strategic plan for the development of a COVID-19 repository including specification of technical requirements, policies and procedures

Strategic plan for the development of a COVID-19 repository including specification of technical requirements, policies and procedures.

EOSC Cloud feasibility assessment for demonstrators

EOSC Cloud feasibility assessment for demonstrators

Access and User Management System for Life Science (LS AAI) – the blueprint

Access and User Management System for Life Science (LS AAI) – the blueprint

Publication of generic guidelines for the organization of topic-specific Open Calls

Publication of generic guidelines for the organisation of topic-specific Open Calls

Initial EOSC-LS Cloud Observatory Report

The report will detail the support mechanisms available to the BMS RIs and how the allocated cloud resources have been used so far by the BMS RIs. It will analyse the activities to date and provide recommendations on how the service can be evolved during the rest of the project.

EOSC repository deployment for project demonstrators

EOSC repository deployment for project demonstrators

Final report of analysis of the training needs of different EOSC-Life users

Final report of analysis of the training needs of different EOSC-Life users

EOSC-Life Data Management Plan

EOSC-Life Data Management Plan: WP11 will deliver a data management plan in collaboration with WP4 (ethics and legal) to provide further evidence of appropriate ethics committees and competent authorities. EOSC-life’s SEAB will consist of an ethics expert who will be consulted on this specific deliverable.

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Publications

Measuring local-directional resolution and local anisotropy in cryo-EM maps

Author(s): Jose Luis Vilas, Hemant D. Tagare, Javier Vargas, Jose Maria Carazo, Carlos Oscar S. Sorzano
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
DOI: 10.1038/s41467-019-13742-w

DrugComb: an integrative cancer drug combination data portal.

Author(s): Zagidullin, Bulat; Aldahdooh, Jehad; Zheng, Shuyu; Wang, Wenyu; Wang, Yinyin; Saad, Joseph; Malyutina, Alina; Jafari, Mohieddin; Tanoli, Ziaurrehman; Pessia, Alberto; Tang, Jing
Published in: Nucleic Acids Research, 2019, Page(s) W43-W51, ISSN 1362-4962
DOI: 10.1101/560227

FAIRness Literacy: The Achilles’ Heel of Applying FAIR Principles

Author(s): Romain David, Laurence Mabile, Alison Specht, Sarah Stryeck, Mogens Thomsen, Mohamed Yahia, Clement Jonquet, Laurent Dollé, Daniel Jacob, Daniele Bailo, Elena Bravo, Sophie Gachet, Hannah Gunderman, Jean-Eudes Hollebecq, Vassilios Ioannidis, Yvan Le Bras, Emilie Lerigoleur, Anne Cambon-Thomsen
Published in: Data Science Journal, Issue 19, 2020, ISSN 1683-1470
DOI: 10.5334/dsj-2020-032

Accessible and reproducible mass spectrometry imaging data analysis in Galaxy

Author(s): Melanie Christine Föll, Lennart Moritz, Thomas Wollmann, Maren Nicole Stillger, Niklas Vockert, Martin Werner, Peter Bronsert, Karl Rohr, Björn Andreas Grüning, Oliver Schilling
Published in: GigaScience, Issue 8/12, 2019, ISSN 2047-217X
DOI: 10.1093/gigascience/giz143

39 Hints to Facilitate the Use of Semantics for Data on Agriculture and Nutrition

Author(s): Caracciolo, Caterina; Aubin, Sophie; Jonquet, Clement; Amdouni, Emna; David, Romain; Garcia, Leyla; Whitehead, Brandon; Roussey, Catherine; Stellato, Armando; Villa, Ferdinando
Published in: "CODATA Data Science Journal, Committee on Data for Science and Technology (CODATA), 2020, 19 (1), ⟨10.5334/dsj-2020-047⟩", Issue 3, 2020, ISSN 1683-1470
DOI: 10.5334/dsj-2020-047

Evaluating FAIR maturity through a scalable, automated, community-governed framework

Author(s): Mark D. Wilkinson, Michel Dumontier, Susanna-Assunta Sansone, Luiz Olavo Bonino da Silva Santos, Mario Prieto, Dominique Batista, Peter McQuilton, Tobias Kuhn, Philippe Rocca-Serra, Mercѐ Crosas, Erik Schultes
Published in: Scientific Data, Issue 6/1, 2019, ISSN 2052-4463
DOI: 10.1038/s41597-019-0184-5

Exploration of databases and methods supporting drug repurposing: a comprehensive survey

Author(s): Ziaurrehman Tanoli, Umair Seemab, Andreas Scherer, Krister Wennerberg, Jing Tang, Markus Vähä-Koskela
Published in: Briefings in Bioinformatics, 2020, ISSN 1477-4054
DOI: 10.1093/bib/bbaa003

A Marine Biodiversity Observation Network for Genetic Monitoring of Hard-Bottom Communities (ARMS-MBON)

Author(s): Matthias Obst, Katrina Exter, A. Louise Allcock, Christos Arvanitidis, Alizz Axberg, Maria Bustamante, Ibon Cancio, Diego Carreira-Flores, Eva Chatzinikolaou, Giorgos Chatzigeorgiou, Nathan Chrismas, Melody S. Clark, Thierry Comtet, Thanos Dailianis, Neil Davies, Klaas Deneudt, Oihane Diaz de Cerio, Ana Fortič, Vasilis Gerovasileiou, Pascal I. Hablützel, Kleoniki Keklikoglou, Georgios Kotoulas,
Published in: Frontiers in Marine Science, Issue 7, 2020, ISSN 2296-7745
DOI: 10.3389/fmars.2020.572680

Experiment design driven FAIRification of omics data matrices, an exemplar

Author(s): Philippe Rocca-Serra, Susanna-Assunta Sansone
Published in: Scientific Data, Issue 6/1, 2019, ISSN 2052-4463
DOI: 10.1038/s41597-019-0286-0

Improvements on marker-free images alignment for electron tomography

Author(s): C.O.S. Sorzano, F. de Isidro-Gómez, E. Fernández-Giménez, D. Herreros, S. Marco, J.M. Carazo, C. Messaoudi
Published in: Journal of Structural Biology: X, Issue 4, 2020, Page(s) 100037, ISSN 2590-1524
DOI: 10.1016/j.yjsbx.2020.100037

FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy

Author(s): David Střelák, Jiří Filipovič, Amaya Jiménez-Moreno, Jose Carazo, Carlos Sánchez Sorzano
Published in: Electronics, Issue 9/6, 2020, Page(s) 1040, ISSN 2079-9292
DOI: 10.3390/electronics9061040

Making experimental data tables in the life sciences more FAIR: a pragmatic approach

Author(s): Daniel Jacob, Romain David, Sophie Aubin, Yves Gibon
Published in: GigaScience, Issue 9/12, 2020, ISSN 2047-217X
DOI: 10.1093/gigascience/giaa144

Complex Stability and an Irrevertible Transition Reverted by Peptide and Fibroblasts in a Dynamic Model of Innate Immunity

Author(s): Abulikemu Abudukelimu, Matteo Barberis, Frank Redegeld, Nilgun Sahin, Raju P. Sharma, Hans V. Westerhoff
Published in: Frontiers in Immunology, Issue 10, 2020, ISSN 1664-3224
DOI: 10.3389/fimmu.2019.03091

FAIRsharing as a community approach to standards, repositories and policies

Author(s): Susanna-Assunta Sansone, Peter McQuilton, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran, Massimiliano Izzo, Allyson L. Lister, Milo Thurston
Published in: Nature Biotechnology, Issue 37/4, 2019, Page(s) 358-367, ISSN 1087-0156
DOI: 10.1038/s41587-019-0080-8

3DBionotes COVID-19 edition

Author(s): Jose Ramon Macias, Ruben Sanchez-Garcia, Pablo Conesa, Erney Ramirez-Aportela, Marta Martinez Gonzalez, Carlos Wert-Carvajal, Alberto M Parra-Perez, Joan Segura Mora, Sam Horrell, Andrea Thorn, Carlos O S Sorzano, Jose Maria Carazo
Published in: Bioinformatics, 2021, ISSN 1367-4803
DOI: 10.1093/bioinformatics/btab397

FAIR Computational Workflows

Author(s): Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober
Published in: Data Intelligence, Issue 2/1-2, 2020, Page(s) 108-121, ISSN 2641-435X
DOI: 10.1162/dint_a_00033

Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures

Author(s): Roberto Melero, Carlos Oscar S. Sorzano, Brent Foster, José-Luis Vilas, Marta Martínez, Roberto Marabini, Erney Ramírez-Aportela, Ruben Sanchez-Garcia, David Herreros, Laura del Caño, Patricia Losana, Yunior C. Fonseca-Reyna, Pablo Conesa, Daniel Wrapp, Pablo Chacon, Jason S. McLellan, Hemant D. Tagare, Jose-Maria Carazo
Published in: IUCrJ, Issue 7/6, 2020, Page(s) 1059-1069, ISSN 2052-2525
DOI: 10.1107/s2052252520012725

Measurement of local resolution in electron tomography

Author(s): J.L. Vilas, J. Oton, C. Messaoudi, R. Melero, P. Conesa, E. Ramirez-Aportela, J. Mota, M. Martinez, A. Jimenez, R. Marabini, J.M. Carazo, J. Vargas, C.O.S. Sorzano
Published in: Journal of Structural Biology: X, Issue 4, 2020, Page(s) 100016, ISSN 2590-1524
DOI: 10.1016/j.yjsbx.2019.100016

EOSC-Life Strategic plan for the development of a COVID-19 repository including specification of technical requirements, policies and procedures

Author(s): Canham, Steve; Ohmann, Christian; Thomassen, Gard; Matei, Mihaela; Demotes, Jacques; Panagiotopoulou, Maria
Published in: 2020
DOI: 10.5281/zenodo.4141619

ECRIN Clinical Research Metadata Schema Version 3.0 (November 2019)

Author(s): Canham, Steve
Published in: 2020
DOI: 10.5281/zenodo.1312538

EOSC-Life Data Management Plan

Author(s): Blomberg, Niklas; Sarntivijai, Sirarat; Mayrhofer, Michaela Th.
Published in: 2020
DOI: 10.5281/zenodo.4010442

EOSC-Life EOSC Cloud feasibility assessment for Demonstrators

Author(s): Gribbon, Philip; Parkinson, Helen; Witt, Gesa
Published in: 2020
DOI: 10.5281/zenodo.4010372

ECRIN Clinical Research Metadata Schema Version 4.0 (September 2020) Appendices

Author(s): Canham, Steve
Published in: 2020
DOI: 10.5281/zenodo.4028900

Non-repudiable provenance for clinical decision support systems

Author(s): Fairweather, Elliot; Wittner, Rudolf; Chapman, Martin; Holub, Petr; Curcin, Vasa
Published in: 2020

EOSC-Life Cloud implementation of exemplary workflows

Author(s): Rosato, Antonio; Hériché, Jean-Karim; Serrano-Solano, Beatriz; Grüning, Björn; Pireddu, Luca; Goble, Carole
Published in: 2020
DOI: 10.5281/zenodo.4010401

XNAT-PIC: Extending XNAT to Preclinical Imaging Centers

Author(s): Zullino, Sara; Paglialonga, Alessandro; Dastrù, Walter; Longo, Dario Livio; Aime, Silvio
Published in: 2021

EOSC - a tool for enabling Open Science in Europe

Author(s): Owen Appleton; Ari Asmi; Ian Bird; Ron Dekker; Niklas Blomberg; Rudolf Dimper; Tiziana Ferrari; Annabel Grant; Sarah Jones; Natalia Manola; Andreas Petzold; Najla Rettberg; Dale Robertson; Ville Tenhunen; Debora Testi; Mark van de Sanden
Published in: 2020
DOI: 10.5281/zenodo.4044010

Event series: Open Science and Covid-19. Working together to fight the pandemic

Author(s): De Leo, Francesca; Lazzeri, Emma; Le Pera, Loredana; Pavone, Gina; Via, Allegra
Published in: 2020
DOI: 10.5281/zenodo.4147034

EOSC-Life Initial EOSC-LS Cloud Observatory Report

Author(s): Newhouse, Steven; Wagener, Harald; González Ferrero, Montserrat; Fano-Bilbao, Oihane; Wildish, Tony; Dieckmann, Marius; Niewielska, Ania; Kapoor, Shubham; Nyrönen, Tommi
Published in: 2020
DOI: 10.5281/zenodo.4010420

Towards FAIRification of experimental data tables in life sciences: a pragmatic approach

Author(s): Bernillon, Stéphane; Cabasson, Cecile; CASSAN, Cédric; Da Costa, Grégory; Deborde, Catherine; Flandin, Amélie; Fouillen, Laetitia; Gibon, Yves; Jacob, Daniel; Moing, Annick; Mongrand, Sebastien; Pedrot, Eric; Petriacq, Pierre; Prigent, Sylvain; Renouf, Elodie; Richard, Tristan; Rolin, Dominique; Rouger, Caroline; Valls, Josep; Van Delft, Pierre
Published in: https://hal.inrae.fr/hal-02570809, 2019
DOI: 10.15454/1.5572412770331912E12

ECRIN Metadata Schemas for Clinical Research Data Objects Version 5.0 (October 2020)

Author(s): Canham, Steve
Published in: 2020
DOI: 10.5281/zenodo.4133889

EOSC-Life Publication of generic guidelines for the organization of topic-specific Open Calls

Author(s): Haley, Natalie; Leitner, Frauke; Bischof, Johanna; Audergon, Pauline
Published in: 2020
DOI: 10.5281/zenodo.4048442

FSC-Q: A CryoEM map-to-atomic model quality validation based on the local Fourier Shell Correlation

Author(s): Ramirez-Aportela, Erney; Maluenda, David; Fonseca, Yunior C.; Conesa, Pablo; Marabini, Roberto; Heymann, J. Bernard; Carazo, Jose Maria; Sorzano, Carlos Oscar S.
Published in: BioRxiv, 2020
DOI: 10.1101/2020.05.12.069831

EOSC-Life Access and user management system for life science – the blueprint

Author(s): Linden, Mikael; Bucik, Dominik Frantisek; Gormanns, Philipp; Haley, Natalie; Heikkinen, Jani; Holub, Petr; Kankaanpää, Pasi; Kouril, Daniel; Kuba, Martin; Licehammer, Slavek; Matyska, Ludek; Nyrönen, Tommi; Prochazka, Michal; Reihs, Robert; Romano, Paolo; Sanderson, Fiona; Shigaval, Athresh; Smith, Callum; Tedds, Jonathan
Published in: 2019
DOI: 10.5281/zenodo.3386306

EOSC-Life FAIR Requirements Document

Author(s): Perseil, Isabelle; Sansone, Susanna-Assunta; McQuilton, Peter; Dumontier, Michel; Roos, Marco; Bonino, Luiz; Wittner, Rudolf; Holub, Petr; Geiger, Jörg
Published in: 2020
DOI: 10.5281/zenodo.3693883

ESFRI cluster projects - Position papers on expectations and planned contributions to the EOSC

Author(s): Gotz, Andy; Petzold, Andreas; Asmi, Ari; Blomberg, Niklas; Lamanna, Giovanni; Dekker, Ron
Published in: 2020
DOI: 10.5281/zenodo.3675081

EOSC-Life Final report of analysis of the training needs of different EOSC-Life users

Author(s): Matser, Vera; Ludwig, Rebecca; Kolodkin, Alexey; Milano, Annalisa; Keppler, Antje; Brooksbank, Cath; Von Gelder, Celia; Amaro, Claudia Alen; Leitner, Frauke; Rustici, Gabriella; Westerhoff, Hans; Heriche, Jean-Karim; EXTER, Katrina; Haley, Natalie; Kankaanpää, Pasi; Scholtens, Salome; Morgan, Sarah
Published in: 2020
DOI: 10.5281/zenodo.3692068

Multitarget Virtual Screening for Drug Repurposing in COVID19

Author(s): Sorzano, carlos oscar; Crisman, Enrique; Carazo, Jose Maria; leon, rafael
Published in: 2020
DOI: 10.26434/chemrxiv.12652997.v2

EOSC-Life Report on requirements for regulatory compliance of sensitive health data and biological and medical research data

Author(s): Battaglia, Serena; Mayrhofer, Michaela T.; Matei, Mihaela; Boiten, Jan-Willem; Ohmann, Christian; Schlünder, Irene; Adeniran, Ayodeji
Published in: 2020
DOI: 10.5281/zenodo.3820389

Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial

Author(s): Bray, Simon A.; Senapathi, Tharindu; Barnett, Christopher B.; Grüning, Björn A.
Published in: BioRxiv, 2020
DOI: 10.1101/2020.05.08.084780

Packaging workflows with RO-Crate

Author(s): Stian Soiland-Reyes; Ignacio Eguinoa
Published in: 2020
DOI: 10.5281/zenodo.4011999

Provenance Week 2020 Poster: ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data

Author(s): Wittner, Rudolf; Holub, Petr; Geiger, Jörg; Müller, Heimo; Goble, Carole; Soiland-Reyes, Stian; Fairweather, Elliot; Pirredu, Luca; Frexia, Francesca; Mascia, Cecilia; Zanetti, Gianluigi; Nakae, Hiroki; Strambio, Caterina; Moore, Josh; Grunwald, David; Swedlow, Jason
Published in: 4th Provenance Week 2020, 2020
DOI: 10.5281/zenodo.3901011

The WorkflowHub - a registry for workflows. The Bioschemas workflow profile.

Author(s): Carole Goble
Published in: 2020
DOI: 10.5281/zenodo.4012124