Providing an open collaborative space for digital biology in Europe

Rezultaty

FAIRassist software
Cloud implementation of exemplary workflows selected by the RIs/communities

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

Implementation of a mechanism for publishing and sharing workflows across instances of the environment

Implementation of a comprehensive workflow registry solution for publishing and sharing workflows across instances of the Tools Collaboratory

A common environment that can run cross-RIs workflows

A common environment (Tools Collaboratory) that can run cross-RIs workflows following the hackathons/workshops/WP3 use cases

Report on reproducibility
Guidance and policy on standards and tools to facilitate sharing and reuse of multimodal data (including imaging), cohort integration, and biosamples

Guidance and policy on standards and tools to facilitate sharing and reuse of multimodal data including imaging cohort integration and biosamples

Summary of EOSC-Life Main Achievements, Impacts, and Sustainability and Exploitation Plans

Summary of EOSCLife Main Achievements Impacts and Sustainability and Exploitation Plans

Access and User Management System for Life Science (LS AAI) - final implementation and usage report

Access and User Management System for Life Science LS AAI final implementation and usage report

Project plan for optional services and future cooperation with IDDO

Results of exploration for cooperation with IDDO regarding possible optional services including services for the conversion of datasets to a common standard CDISC as well as data integration supporting patientlevel metaanalyses

Access and User Management System for Life Science - the blueprint: 2nd update

Access and User Management System for Life Science the blueprint 2nd update of the initial document

Review of EOSC-Life training activities, their impact and potential adaptations

Review of EOSCLife training activities their impact and potential adaptations

Report on a methodology framework to assess reproducibility
Common Framework for Quality, Data and Service Management

Common Framework for Quality Data and Service Management

Report about use and user satisfaction of COVID-19 repository including a maintenance and sustainability plan

Report about use and user satisfaction of COVID19 repository including a maintenance and sustainability plan

EOSC FAIR services deployment for open call
Report on requirements for regulatory compliance of sensitive health data and biological and medical research data management
Report on data standards for observational and interventional studies, and on interoperability between healthcare and research data

Report on data standards for observational and interventional studies and on interoperability between healthcare and research data

Enhanced COVID-19 Portal and data mobilisation reporting

COVID19 Portal operating systematic data harvesting systems and tools to provide statistics from comprehensive EMBLEBI data resources and tracking of growing data sets offering tools and programmatic access having undergone User Experience testing

Requirements for hosting/distributing and access control for sensitive data

Requirements for hostingdistributing and access control for sensitive data

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.

Review of effectiveness and impact of outreach and stakeholder engagement
EOSC Cloud feasibility assessment for demonstrators
Common provenance model for processing biological material, data generation and computational workflows

Common provenance model for processing biological material data generation and computational workflows

Final report on EOSC-Life training activities and their impact

Final report on EOSCLife training activities and their impact

Summary Report Stakeholder Forum Meetings
Report on identification and application of registries for FAIR data infrastructures
Access and User Management System for Life Science (LS AAI) – the blueprint
Data mobilisation summary

Summary of mobilised data to date highlighting data platforms formats levels of assembly and national contributions

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

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

Access and User Management System for Life Science - the blueprint: 1st update

Access and User Management System for Life Science the blueprint 1st update of the initial document

Provenance proposed model

Provenance proposed model available

Access and User Management System for Life Science (LS AAI) - the implementation and usage report

Access and User Management System for Life Science LS AAI the implementation and usage report

Life Science in EOSC: Summary of EOSC-Life impact and key results

Life Science in EOSC Summary of EOSCLife impact and key results

Report about technical implementation and validation of the COVID-19 portal

Report about technical implementation and validation of the COVID19 portal

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 Sustainability best practice
Final 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

Report on the work of the Open Call Projects
Strategic Marketing and Stakeholder mapping report
Report on the work of the initial Demonstrators
EOSC repository deployment for project demonstrators
Final report of analysis of the training needs of different EOSC-Life users

Public database inventorying the national health databases and registries and describing their access procedures for reuse for research purposes

FAIRsharing webpage

Launch of FAIRsharing webpage

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.

Publikacje

Removing Barriers to Reproducible Research in Archaeology

Autorzy: Karoune, Emma; Plomp, Esther
Opublikowane w: 2022
Wydawca: Zenodo
DOI: 10.5281/zenodo.6618672

EOSC-Life Report on data standards for observational and interventional studies, and interoperability between healthcare and research data

Autorzy: Canham, Steve; Ohmann, Christian; Boiten, Jan-Willem; Panagiotopoulou, Maria; Hughes, Nigel; David, Romain; Sanchez Pla, Alex; Maxwell, Lauren; Aerts, Jozef; Facile, Rhonda; Griffon, Nicolas; Saunders, Gary; van Bochove, Kees; Ewbank, Jonathan
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.5810611

Introduction to Semantic Interoperability Challenges for RIs

Autorzy: David, Romain; Madon, Bénédicte; Torralba, Antonio
Opublikowane w: 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.8059821

Non-repudiable provenance for clinical decision support systems

Autorzy: Fairweather, Elliot; Wittner, Rudolf; Chapman, Martin; Holub, Petr; Curcin, Vasa
Opublikowane w: 2021
Wydawca: ArXiv
DOI: 10.48550/arxiv.2006.11233

EOSC-Life WP14: COVID-19 Repository Data Sharing Policy

Autorzy: Ohmann, Christian; Matei, Mihaela; Canham, Steve; Panagiotopoulou, Maria; Demotes, Jacques; Thomassen, Gard; Blomberg, Niklas
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.5519122

EOSC-Life WP4 Toolbox: Update of the categorisation system (version 3)

Autorzy: Ohmann, Christian; Cano Abadía, Mónica; Bietrix, Florence; Boiten, Jan-Willem; Canham, Steve; Chiusano, Marie Luisa; Dastru, Walter; David, Romain; Laroquette, Arnaud; Longo, Dario; Mayrhofer, Michaela Theresia; Panagiotopoulou, Maria; Richard, Audrey
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.5507324

EOSC-Life Summary of EOSC-Life Main Achievements and Impacts with Sustainability and Exploitation Plans

Autorzy: Blomberg, Niklas; Schmidt-Tremmel, Friederike; Crockett, Sara
Opublikowane w: 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.8304575

Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language

Autorzy: Crusoe, Michael R.; Abeln, Sanne; Iosup, Alexandru; Amstutz, Peter; Chilton, John; Tijanić, Nebojša; Ménager, Hervé; Soiland-Reyes, Stian; Gavrilovic, Bogdan; Goble, Carole
Opublikowane w: 2021
Wydawca: arXiv.org
DOI: 10.48550/arxiv.2105.07028

EOSC-Life FAIRsharing webpage

Autorzy: Sansone, Susanna-Assunta; Lister, Allyson; Thurston, Milo; Mirian, Hossein; Rocca-Serra, Philippe; Batista, Dominique; Granell, Ramon; Gailani, Prakhyat
Opublikowane w: 2022
Wydawca: Zenodo
DOI: 10.5281/zenodo.7019783

Life Science in EOSC: Summary of EOSC-Life impact and key results

Autorzy: Blomberg, Niklas; Schmidt-Tremmel, Friederike; Ahern, Caitlin
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.5179992

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

Autorzy: Canham, Steve; Ohmann, Christian; Thomassen, Gard; Matei, Mihaela; Demotes, Jacques; Panagiotopoulou, Maria
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.4141619

EOSC-Life Guidance and policy on standards and tools to facilitate sharing and reuse of multimodal data (including imaging), cohort integration, and biosamples

Autorzy: Boiten, Jan-Willem; Ohmann, Christian; Adeniran, Ayodeji; Canham, Steve; Cano Abadia, Monica; Chassang, Gauthier; Chiusano, Maria Luisa; David, Romain; Fratelli, Maddalena; Gribbon, Phil; Holub, Petr; Ludwig, Rebecca; Th. Mayrhofer, Michaela; Matei, Mihaela; Merchant, Arshiya; Panagiotopoulou, Maria; Pireddu, Luca; Richard, Audrey; Sanchez Pla, Alex; Schlünder, Irene; Tsamis, George; Wagener, Har
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.4591011

EOSC-Life Access and User Management System for Life Science – the implementation and usage report

Autorzy: Licehammer, Slavek; Linden, Mikael; Smith, Callum
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.4559400

"Introduction to the ""Open Science and COVID-19"" webinar series"

Autorzy: De Leo, Francesca
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.5534897

EOSC-Life Access and User Management System for Life Science – the blueprint update

Autorzy: 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
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.4633190

Open Phytoliths Community Launch Event Presentations

Autorzy: Karoune, Emma; García-Granero, Juan José; Lancelotti, Carla; Ruiz-Pérez, Javier; Kerfant, Celine; Dunseth, Zachary C; Musaubach, Maria Gabriela; Bates, Jennifer
Opublikowane w: 2022
Wydawca: Zenodo
DOI: 10.5281/zenodo.7090455

EOSC-Life Methodology framework to enhance reproducibility within EOSC-Life

Autorzy: Bietrix, Florence; Carazo, José Maria; Capella-Gutierrez, Salvador; Coppens, Frederik; Chiusano, Maria Luisa; David, Romain; Fernandez, Jose Maria; Fratelli, Maddalena; Heriche, Jean-Karim; Goble, Carole; Gribbon, Philip; Holub, Petr; P. Joosten, Robbie; Leo, Simone; Owen, Stuart; Parkinson, Helen; Pieruschka, Roland; Pireddu, Luca; Porcu, Luca; Raess, Michael; Rodriguez- Navas, Laura; Scherer, A
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.4705078

ECRIN Clinical Research Metadata Schema Version 3.0 (November 2019)

Autorzy: Canham, Steve
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.1312538

EOSC-Life Report about use and user satisfaction of the COVID-19 repository, including a maintenance and sustainability plan

Autorzy: Contrino, Sergio; Felder, Gerd; Ohmann, Christian; Panagiotopoulou, Maria; Kichenassamy, Swarnalathaa; Gorianin, Sergei; Demotes, Jacques; Kouylekov, Milen; Thomassen, Gard
Opublikowane w: 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.7836812

EOSC-LIFE WP4 TOOLBOX: Toolbox for sharing of sensitive data - a concept description

Autorzy: Boiten, Jan Willem; Ohmann, Christian; Adeniran, Ayodeji; Canham, Steve; Cano Abadia, Monica; Chassang, Gauthier; Chiusano, Maria Luisa; David, Romain; Fratelli, Maddalena; Gribbon, Phil; Holub, Petr; Ludwig, Rebecca; Mayrhofer, Michaela Th.; Matei, Mihaela; Merchant, Arshiya; Panagiotopoulou, Maria; Pireddu, Luca; Sanchez Pla, Alex; Schlünder, Irene; Tsamis, George; Wagener, Harald
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.4483694

EOSC-Life Project plan for optional services and future cooperation with IDDO

Autorzy: Panagiotopoulou, Maria; Rujano, Maria; Felder, Gerd; Contrino, Sergio; Ohmann, Christian; Kichenassamy, Swarnalathaa; Gorianin, Sergei; Demotes, Jacques; Kouylekov, Milen; Thomassen, Gard; Guerin, Philippe; Brack, Mathew
Opublikowane w: 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.8272763

EOSC-Life Data Management Plan

Autorzy: Blomberg, Niklas; Sarntivijai, Sirarat; Mayrhofer, Michaela Th.
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.4010442

EOSC-Life Report on identification and application of registries for FAIR data infrastructures

Autorzy: Roos, Marco; da Salva Santos, Luiz Olavo Bonino
Opublikowane w: 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.8306174

EOSC-Life EOSC Cloud feasibility assessment for Demonstrators

Autorzy: Gribbon, Philip; Parkinson, Helen; Witt, Gesa
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.4010372

EOSC-Life Review of EOSC-Life training activities, their impact and potential adaptations

Autorzy: Ludwig, Rebecca; Matser, Vera; Milano, Annalisa; Morgan, Sarah; López, Daniel Thomas; Deprez, Tim
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.4562143

Umbrella Data Management Plans to integrate FAIR data : lessons from the ISIDORe and BY-COVID consortia for pandemic preparedness

Autorzy: David, Romain; S. Richard, Audrey; Connellan, Claire; Lauer, Katharina B; Chiusano, Maria Luisa; Goble, Carole; Houde, Martin; Kemmer, Isabel; Keppler, Antje; Lieutaud, Philippe; Ohmann, Christian; Panagiotopoulou, Maria; Raza Khan, Sara; Rybina, Arina; Soiland-Reyes, Stian; Wit, Charlotte; Wittner, Rudolf; Andrade Buono, Rafael; Marsh, Sarah Arnaud; Audergon, Pauline; Bonfils, Dylan; Carazo, Jose
Opublikowane w: Data Science Journal, 2023, ISSN 1683-1470
Wydawca: Ubiquity Press
DOI: 10.5281/zenodo.7516084

EOSC-Life Strategic Marketing and Stakeholder Mapping Report

Autorzy: Ahern, Caitlin; Beatrix, Florence; Panagiotopoulou, Maria; Biziou, Laura
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.4560453

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

Autorzy: Canham, Steve
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.4028900

A dataset for assessing phytolith data for implementation of the FAIR data principles

Autorzy: Kerfant, Celine; Ruiz-Pérez, Javier; García-Granero, Juan José; Lancelotti, Carla; Madella, Marco; Karoune, Emma
Opublikowane w: 2022
Wydawca: Zenodo
DOI: 10.5281/zenodo.7215804

EOSC-Life Common Provenance Model

Autorzy: Wittner, Rudolf; Mascia, Cecilia; Frexia, Francesca; Müller, Heimo; Geiger, Jörg; Exter, Katrina; Holub, Petr
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.4705074

EOSC-Life Requirements for hosting/ distributing and access control for sensitive data

Autorzy: Álvarez, Eva García; Ohmann, Christian; Saunders, Gary; Wagener, Harald; Colussi, Ilaria; Boiten, Jan-Willem; Panagiotopoulou, Maria; Cano Abadía, Mónica; David, Romain; Schluender, Irene; Holub, Petr; Mayrhofer, Michaela Th.
Opublikowane w: 2022
Wydawca: Zenodo
DOI: 10.5281/zenodo.7037444

Towards FAIR phytolith data: first steps down a long and winding road

Autorzy: Karoune, Emma; Lancelotti, Carla; Ruiz-P��rez, Javier; Garc��a-Granero, Juanjo; Madella, Marco
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.5336872

Non-repudiable provenance for clinical decision support systems

Autorzy: Fairweather, Elliot; Wittner, Rudolf; Chapman, Martin; Holub, Petr; Curcin, Vasa
Opublikowane w: 2020
Wydawca: Cornell University

Packaging research artefacts with RO-Crate

Autorzy: Stian Soiland-Reyes; Peter Sefton; Mercè Crosas; Leyla Jael Castro; Frederik Coppens; José M. Fernández; Daniel Garijo; Björn Grüning; Marco La Rosa; Simone Leo; Eoghan Ó Carragáin; Marc Portier; Ana Trisovic; RO-Crate Community; Paul Groth; Carole Goble
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.5146228

EOSC-Life WP4 Toolbox: Pilot study protocol for the evaluation of the categorisation system

Autorzy: Ohmann, Christian; Canham, Steve; Boiten, Jan-Willem; Cano Abadía, Mónica; Chassang, Gautier; Chiusano, Maria Luisa; David, Romain; Mayrhofer, Michaela Theresia; Pireddu, Luca
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.4311114

EOSC-Life Access and User Management System for Life Science – the implementation and usage report

Autorzy: Matyska, Ludek; Povey, Marcus; Frantisek Bucik, Dominik; Broncova, Jana; Licehammer, Slavek; Farrell, Gavin; Tedds, Jonathan; Romano, Paolo; Kankaanpää, Pasi; Linden, Mikael; Haley, Natalie; Gormanns, Philipp
Opublikowane w: 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.8144215

EOSC-Life EOSC FAIR services deployment for open calls

Autorzy: Parkinson, Helen; Gribbon, Philip; Sarkans, Ugis; Witt, Gesa; Zaliani, Andrea; Kohler, Manfred; Swedlow, Jason; Burel, Jean-Marie; Swertz, Morris; van Enckevort, Esther; Holub, Petr; Massimi, Marzia; Matteoni, Rafaele; Maier, Holger; Hinttala, Reetta; Heikkinen, Anne; Gormanns, Philipp; Vasseur, Laurent; Leblanc, Sophie; Herault, Yann; Kontoyiannis, Dimitris; Chandras, Christina; Panou, Dimitra; L
Opublikowane w: 2022
Wydawca: Zenodo
DOI: 10.5281/zenodo.6208249

EOSC-Life Public database inventorying the national health databases and registries and describing their access procedures for reuse for research purposes

Autorzy: Panagiotopoulou, Maria; Yaïche, Sarhan; Michon, Amélie; Ohmann, Christian; Demotes, Jacques; Matei, Mihaela; Canham, Steve; Hjelle, Sigrun Margrethe; Klusek, Patrycja; Batuca, Joana; Schmid, Caecilia; Buoncervello, Maria; Toschi, Elena; Minghetti, Luisa; Chiusano, Maria Luisa; Vives Vilatersana, Adriana; Calvo I Orteu, María; Szabó, Zsolt; Součková, Lenka; Noskova, Kristyna; Kappala, Sharon;
Opublikowane w: 2022
Wydawca: Zenodo
DOI: 10.5281/zenodo.7148860

EOSC-Life Cloud implementation of exemplary workflows

Autorzy: Rosato, Antonio; Hériché, Jean-Karim; Serrano-Solano, Beatriz; Grüning, Björn; Pireddu, Luca; Goble, Carole
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.4010401

Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory

Autorzy: Goble, Carole; Soiland-Reyes, Stian; Bacall, Finn; Owen, Stuart; Williams, Alan; Eguinoa, Ignacio; Droesbeke, Bert; Leo, Simone; Pireddu, Luca; Rodríguez-Navas, Laura; Fernández, José Mª; Capella-Gutierrez, Salvador; Ménager, Hervé; Grüning, Björn; Serrano-Solano, Beatriz; Ewels, Philip; Coppens, Frederik
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.4605654

EOSC-Life Data mobilisation summary

Autorzy: Rahman, Nadim; Ventouratou, Marianna
Opublikowane w: 2022
Wydawca: Zenodo
DOI: 10.5281/zenodo.7097237

XNAT-PIC: Extending XNAT to Preclinical Imaging Centers

Autorzy: Zullino, Sara; Paglialonga, Alessandro; Dastrù, Walter; Longo, Dario Livio; Aime, Silvio
Opublikowane w: 2021
Wydawca: Cornell University

EOSC - a tool for enabling Open Science in Europe

Autorzy: 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
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.4044010

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

Autorzy: De Leo, Francesca; Lazzeri, Emma; Le Pera, Loredana; Pavone, Gina; Via, Allegra
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.4147034

Final release: COVID-19 guidelines

Autorzy: Research Data Alliance
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.15497/rda00052

EOSC-Life Initial EOSC-LS Cloud Observatory Report

Autorzy: Newhouse, Steven; Wagener, Harald; González Ferrero, Montserrat; Fano-Bilbao, Oihane; Wildish, Tony; Dieckmann, Marius; Niewielska, Ania; Kapoor, Shubham; Nyrönen, Tommi
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.4010420

RO-Crate Metadata Specification 1.1.1

Autorzy: Peter Sefton; Eoghan Ó Carragáin; Stian Soiland-Reyes; Oscar Corcho; Daniel Garijo; Raul Palma; Frederik Coppens; Carole Goble; José María Fernández; Kyle Chard; Jose Manuel Gomez-Perez; Michael R Crusoe; Ignacio Eguinoa; Nick Juty; Kristi Holmes; Jason A. Clark; Salvador Capella-Gutierrez; Alasdair J. G. Gray; Stuart Owen; Alan R. Williams; Giacomo Tartari; Finn Bacall; Thomas Thelen; Hervé
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.3406497

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

Autorzy: 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
Opublikowane w: https://hal.inrae.fr/hal-02570809, 2019
Wydawca: INRA
DOI: 10.15454/1.5572412770331912E12

EOSC-Life Strategic plan for the development of a COVID-19 repository including specification of technical requirements, policies and procedures - v2

Autorzy: Canham, Steve; Ohmann, Christian; Thomassen, Gard; Matei, Mihaela; Demotes, Jacques; Panagiotopoulou, Maria
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.4341385

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

Autorzy: Canham, Steve
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.4133889

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

Autorzy: Haley, Natalie; Leitner, Frauke; Bischof, Johanna; Audergon, Pauline
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.4048442

Open Science Strength and its cooperation method in the current pandemic context

Autorzy: Lazzeri, Emma
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.3955640

Open Source Secure Data Infrastructure and Processes for Data Visiting

Autorzy: Weise, Martin; Rauber, Andreas
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.4632903

Making Canonical Workflow Building Blocks interoperable across workflow languages

Autorzy: Soiland-Reyes, Stian; Genís Bayarri; Andrio, Pau; Long, Robin; Lowe, Douglas; Niewielska, Ania; Hospital, Adam; Groth, Paul
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.5727730

Sensitive Data IG RDA17 Session Report

Autorzy: Akmon, Dharma; Burton, Nichola; David, Romain; Davidson, Sarah; McEachern, Steven; Michalewicz, Aleksandra; Pillai, Priyanka; Rb-Silva, Rita; Spreadborough, Kristal; Stevens, Frankie
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.5002793

EOSC-Life Implementation of a mechanism for publishing and sharing workflows across instances of the environment

Autorzy: Goble, Carole; Soiland-Reyes, Stian; Bacall, Finn; Owen, Stuart; Pireddu, Luca; Leo, Simone
Opublikowane w: 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.7886545

EOSC-Life Review of Effectiveness and Impact of Outreach and Stakeholder Engagement

Autorzy: Crockett, Sara; Panagiotopoulou, Maria; Esdaile, Martina; Ludwig, Rebecca; Gurwitz, Kim; Saunders, Gary
Opublikowane w: 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.8276753

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

Autorzy: Ramirez-Aportela, Erney; Maluenda, David; Fonseca, Yunior C.; Conesa, Pablo; Marabini, Roberto; Heymann, J. Bernard; Carazo, Jose Maria; Sorzano, Carlos Oscar S.
Opublikowane w: BioRxiv, 2020
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/2020.05.12.069831

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

EOSC-Life FAIR Requirements Document

Autorzy: Perseil, Isabelle; Sansone, Susanna-Assunta; McQuilton, Peter; Dumontier, Michel; Roos, Marco; Bonino, Luiz; Wittner, Rudolf; Holub, Petr; Geiger, Jörg
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.3693883

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

Autorzy: Gotz, Andy; Petzold, Andreas; Asmi, Ari; Blomberg, Niklas; Lamanna, Giovanni; Dekker, Ron
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.3675081

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

Autorzy: 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
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.3692068

Towards a reconstructive methodology for building a provenance metamodel that fits the complex bioinformatics pipelines

Autorzy: Isabelle Perseil; Petr Holub
Opublikowane w: 2019
Wydawca: Zenodo
DOI: 10.5281/zenodo.3362412

usegalaxy.be

Autorzy: Coppens, Frederik
Opublikowane w: 2022
Wydawca: Zenodo
DOI: 10.5281/zenodo.6607021

FAIR Computational Workflows

Autorzy: Goble, Carole; Cohen-Boulakia, Sarah; Schober, Daniel; Peters, Kristian; Soiland-Reyes, Stian; Garijo, Daniel; Gil, Yolanda; Crusoe, Michael R.
Opublikowane w: 2019
Wydawca: Zenodo
DOI: 10.5281/zenodo.3528076

Open Science in Archaeobotany - The FAIR Phytoliths Project

Autorzy: Kerfant, Celine; Karoune, Emma; Lancelotti, Carla; Ruiz-P��rez, Javier; Garc��a-Granero, Juan Jos��; Madella, Marco
Opublikowane w: 2022
Wydawca: Zenodo
DOI: 10.5281/zenodo.6335633

Machine actionable metadata models

Autorzy: Batista, Dominique; Gonzalez-Beltran, Alejandra; Sansone, Susanna-Assunta; Rocca-Serra, Philippe
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.5596465

ECRIN Metadata Schemas for Clinical Research, Version 8 (September 2023)

Autorzy: Steve Canham
Opublikowane w: 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.8368709

EOSC-Life Access and User Management System for Life Science – the blueprint update

Autorzy: 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; Shigaval, Athresh; Povey, Marcus; Tedds, Jonathan
Opublikowane w: 2022
Wydawca: Zenodo
DOI: 10.5281/zenodo.6782892

EOSC-Life WP4 Toolbox: Update of the categorisation system

Multitarget Virtual Screening for Drug Repurposing in COVID19

Autorzy: Sorzano, carlos oscar; Crisman, Enrique; Carazo, Jose Maria; leon, rafael
Opublikowane w: 2020
Wydawca: ChemXriv
DOI: 10.26434/chemrxiv.12652997.v2

EOSC-Life Report on the work of the initial demonstrators

Autorzy: Leitner, Frauke; Carazo, Jose Maria; Bischof, Johanna; Haley, Natalie; Audergon, Pauline; Sorzano, Carlos Oscar; del Cano, Laura; Conesa, Pablo; Cox, Cymon J.; De Moro, Gianluca; Erwan, Corre; Exter, Katrina; Le Corguillé, Gildas; Dallet, Romain; Gueguen, Lorraine; Heriche, Jean-Karim; Serrano, Beatriz; Sun, Yi; Burel, Jean-Marie; Zullino, Sara; Longo, Dario Livio; Pommier, Cyril; Hallab, Asis; E
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.4817723

EOSC-Life FAIR assistance

Autorzy: Sansone, Susanna-Assunta; Lister, Allyson; Thurston, Milo; Rocca-Serra, Philippe; Batista, Dominique; Granell, Ramon; Gailani, Prakhyat; Dumontier, Michel
Opublikowane w: 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.8264604

EOSC-Life Final EOSC-LS Cloud Observatory Report

Autorzy: Newhouse, Steven; Wagener, Harald; Dieckmann, Marius; Niewielska, Ania; Clark-Casey, Justin; Insua, Santiago
Opublikowane w: 2022
Wydawca: Zenodo
DOI: 10.5281/zenodo.6555209

Building a FAIR image data ecosystem for microscopy communities

Autorzy: Kemmer, Isabel; Keppler, Antje; Serrano-Solano, Beatriz; Rybina, Arina; Özdemir, Bugra; Bischof, Johanna; El Ghadraoui, Ayoub; Eriksson, John E.; Mathur, Aastha
Opublikowane w: 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.7788898

EOSC-Life Report on the work of the Open Call Projects

Autorzy: Rybina, Arina; Audergon, Pauline; Pfander, Claudia
Opublikowane w: 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.8263074

EOSC-Life Common provenance model for processing biological material, data generation and computational workflows

Autorzy: Wittner, Rudolf; Geiger, Jörg; Müller, Heimo; Frexia, Francesca; Mascia, Cecilia; Exter, Katrina; Cancio, Ibon; Holub, Petr
Opublikowane w: 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.8279525

ESFRI Science Clusters Position Statement on Expectations and Long-Term Commitment in Open Science

Autorzy: Giovanni Lamanna; Ian Bird; Andreas Petzold; Ari Asmi; Magdalena Brus; Niklas Blomberg; Michael Räß; Rudolf Dimper; Andrew Gotz; Ron Dekker
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.4892245

EOSC FAIR services deployment for open calls

Autorzy: Parkinson H. et al.
Opublikowane w: 2022, Numer 20, 2022
Wydawca: CNR

EOSC-Life Final report on EOSC-Life training activities and their impact

Autorzy: Ludwig, Rebecca; Duquenne, Lauranne; Gurwitz, Kim; Swan, Anna; Thomas Lopez, Daniel; Lloret Llinares, Marta; Delgado, Claudia
Opublikowane w: 2023
Wydawca: Zenodo
DOI: 10.5281/zenodo.8083413

EOSC-Life EOSC repository deployment for project demonstrators

Autorzy: Parkinson, Helen; Gribbon, Philip; Sarkans, Ugis; Witt, Gesa; Zaliani, Andrea; Kohler, Manfred; Swedlow, Jason; Burel, Jean-Marie; Swertz, Morris; van Enckevort, Esther; Holub, Petr; Massimi, Marzia; Matteonie, Rafaele; Maier, Holger; Hinttala, Reetta; Heikkinen, Anne; Gormanns, Philipp; del Cano, Laura; Vasseur, Laurent; Leblanc, Sophie; Herault, Yann; Kontoyiannis, Dimitris; Chandras, Christina;
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.4432029

EOSC-Life Enhanced COVID-19 Portal and data mobilisation reporting

Autorzy: Cochrane, Guy; Ventouratou, Marianna
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.5642935

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

Autorzy: Battaglia, Serena; Mayrhofer, Michaela T.; Matei, Mihaela; Boiten, Jan-Willem; Ohmann, Christian; Schlünder, Irene; Adeniran, Ayodeji
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.3820389

Open Phytolith Publishing Guidelines

Autorzy: Karoune, Emma; Barboni, Doris; Bates, Jennifer; Dabengwa, Abraham; Dunseth, Zachary C; García-Granero, Juan José; Kerfant, Celine; Lancelotti, Carla; Madella, Marco; Musaubach, Maria Gabriela; Ruiz-Pérez, Javier
Opublikowane w: 2022
Wydawca: Zenodo
DOI: 10.5281/zenodo.6803489

EOSC-Life A common environment that can run cross-RIs workflows

Autorzy: Rosato, Antonio; Hériché, Jean-Karim
Opublikowane w: 2022
Wydawca: Zenodo
DOI: 10.5281/zenodo.7217293

EOSC-Life WP4 Toolbox: Categorisation system for resources to be referenced in the toolbox for sharing of sensitive data

Autorzy: Ohmann, Christian; Canham, Steve; Boiten, Jan-Willem; Cano Abadía, Mónica; Chassang, Gautier; Chiusano, Marie Luisa; David, Romain; Mayrhofer, Michaela Theresia; Pireddu, Luca
Opublikowane w: 2020
Wydawca: Zenodo
DOI: 10.5281/zenodo.4311094

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

Autorzy: Bray, Simon A.; Senapathi, Tharindu; Barnett, Christopher B.; Grüning, Björn A.
Opublikowane w: BioRxiv, 2020
Wydawca: Cold Spring Harbor Laboratory
DOI: 10.1101/2020.05.08.084780

10 Simple Rules for making a software tool workflow-ready

Autorzy: Brack, Paul; Crowther, Peter; Soiland-Reyes, Stian; Owen, Stuart; Lowe, Douglas; Williams, Alan R; Groom, Quentin; Dillen, Mathias; Coppens, Frederik; Grüning, Björn; Eguinoa, Ignacio; Ewels, Philip; Goble, Carole
Opublikowane w: 2021
Wydawca: Zenodo
DOI: 10.5281/zenodo.5636487

EOSC-Life Methodology framework to enhance reproducibility within EOSC-Life – revised version

Autorzy: Bietrix, Florence; Carazo, José Maria; Capella-Gutierrez, Salvador; Coppens, Frederik; Chiusano, Maria Luisa; David, Romain; Fernandez, Jose Maria; Fratelli, Maddalena; Heriche, Jean-Karim; Goble, Carole; Gribbon, Philip; Holub, Petr; P. Joosten, Robbie; Leo, Simone; Owen, Stuart; Parkinson, Helen; Pieruschka, Roland; Pireddu, Luca; Porcu, Luca; Raess, Michael; Rodriguez-Navas, Laura; Scherer, An
Opublikowane w: 2022
Wydawca: Zenodo
DOI: 10.5281/zenodo.7137743

EOSC-Life Report about technical implementation and validation of the COVID-19 portal

Autorzy: Canham, Steve; Gorianin, Sergey; Kouylekov, Milen; Panagiotopoulou, Maria; Ohmann, Christian; Kichenassamy, Swarnalathaa; Thomassen, Gard; Fugelli, Pål; Demotes, Jacques
Opublikowane w: 2022
Wydawca: Zenodo
DOI: 10.5281/zenodo.6555207

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

Autorzy: Jose Luis Vilas, Hemant D. Tagare, Javier Vargas, Jose Maria Carazo, Carlos Oscar S. Sorzano
Opublikowane w: Nature Communications, Numer 11/1, 2020, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-019-13742-w

Automated Determination of Nuclear Magnetic Resonance Chemical Shift Perturbations in Ligand Screening Experiments: The PICASSO Web Server.

Autorzy: Vincenzo Laveglia; Andrea Giachetti; Linda Cerofolini; Kevin Haubrich; Marco Fragai; Alessio Ciulli; Antonio Rosato
Opublikowane w: Journal of Chemical Information and Modeling, 2021, Strona(/y) 5726–5733, ISSN 1549-9596
Wydawca: American Chemical Society
DOI: 10.1021/acs.jcim.1c00871

DrugComb: an integrative cancer drug combination data portal.

Autorzy: Zagidullin, Bulat; Aldahdooh, Jehad; Zheng, Shuyu; Wang, Wenyu; Wang, Yinyin; Saad, Joseph; Malyutina, Alina; Jafari, Mohieddin; Tanoli, Ziaurrehman; Pessia, Alberto; Tang, Jing
Opublikowane w: Nucleic Acids Research, 2019, Strona(/y) W43-W51, ISSN 1362-4962
Wydawca: Oxford University Press
DOI: 10.1101/560227

Privacy Risks of Whole-Slide Image Sharing in Digital Pathology

Autorzy: Petr Holub; Heimo Müller; Tomáš Bíl; Luca Pireddu; Markus Plass; Fabian Prasser; Irene Schlünder; Kurt Zatloukal; Rudolf Nenutil; Tomáš Brázdil
Opublikowane w: Nature Communications, 2023, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.21203/rs.3.rs-1593472/v1

Importing genetically altered animals: ensuring quality.

Autorzy: Marie-Christine Birling; Martin Fray; Petr Kasparek; J. Kopkanova; M. Massimi; R. Matteoni; Lluis Montoliu; Lauryl M J Nutter; Marcello Raspa; Jan Rozman; Edward Ryder; Edward Ryder; Ferdinando Scavizzi; V. Voikar; Sara Wells; Guillaume Pavlovic; Lydia Teboul
Opublikowane w: Mammalian Genome, Numer 09388990, 2022, Strona(/y) 100-107, ISSN 0938-8990
Wydawca: Springer Verlag
DOI: 10.1007/s00335-021-09908-x

FAIRness Literacy: The Achilles’ Heel of Applying FAIR Principles

Autorzy: 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
Opublikowane w: Data Science Journal, Numer 19, 2020, ISSN 1683-1470
Wydawca: Committee on Data for Science and Technology (CODATA) International Council for Science (ICSU)
DOI: 10.5334/dsj-2020-032

Accessible and reproducible mass spectrometry imaging data analysis in Galaxy

Autorzy: Melanie Christine Föll, Lennart Moritz, Thomas Wollmann, Maren Nicole Stillger, Niklas Vockert, Martin Werner, Peter Bronsert, Karl Rohr, Björn Andreas Grüning, Oliver Schilling
Opublikowane w: GigaScience, Numer 8/12, 2019, ISSN 2047-217X
Wydawca: Oxford University Press
DOI: 10.1093/gigascience/giz143

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

Autorzy: Caracciolo, Caterina; Aubin, Sophie; Jonquet, Clement; Amdouni, Emna; David, Romain; Garcia, Leyla; Whitehead, Brandon; Roussey, Catherine; Stellato, Armando; Villa, Ferdinando
Opublikowane w: "CODATA Data Science Journal, Committee on Data for Science and Technology (CODATA), 2020, 19 (1), ⟨10.5334/dsj-2020-047⟩", Numer 3, 2020, ISSN 1683-1470
Wydawca: Committee on Data for Science and Technology (CODATA) International Council for Science (ICSU)
DOI: 10.5334/dsj-2020-047

Evaluation of the Higher Order Structure of Biotherapeutics Embedded in Hydrogels for Bioprinting and Drug Release

Autorzy: Domenico Rizzo; Linda Cerofolini; Anna Pérez-Ràfols; Stefano Giuntini; Fabio Baroni; Enrico Ravera; Claudio Luchinat; Marco Fragai
Opublikowane w: Analytical Chemistry, 2021, ISSN 0003-2700
Wydawca: American Chemical Society
DOI: 10.1021/acs.analchem.1c01850

Learning to Identify Physiological and Adventitious Metal-Binding Sites in the Three-Dimensional Structures of Proteins by Following the Hints of a Deep Neural Network

Autorzy: Vincenzo Laveglia; Andrea Giachetti; Davide Sala; Claudia Andreini; Antonio Rosato
Opublikowane w: Journal of Chemical Information and Modeling, Numer 62, 2022, Strona(/y) 2951, ISSN 1549-9596
Wydawca: American Chemical Society
DOI: 10.1021/acs.jcim.2c00522

Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service.

Autorzy: Marco Antonio Tangaro; Pietro Mandreoli; Pietro Mandreoli; Matteo Chiara; Matteo Chiara; Giacinto Donvito; Marica Antonacci; Antonio Parisi; Angelica Bianco; Angelo Romano; Daniela Bianchi; Davide Cangelosi; Paolo Uva; Ivan Molineris; Vladimir Nosi; Raffaele A. Calogero; Luca Alessandrì; Elena Pedrini; Marina Mordenti; Emanuele Bonetti; Luca Sangiorgi; Graziano Pesole; Graziano Pesole; Federico Z
Opublikowane w: BMC Bioinformatics, Vol 22, Iss S15, Pp 1-21 (2021), Numer 16, 2021, ISSN 1471-2105
Wydawca: BioMed Central
DOI: 10.1186/s12859-021-04401-3

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

Autorzy: 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
Opublikowane w: Scientific Data, Numer 6/1, 2019, ISSN 2052-4463
Wydawca: Springer Nature
DOI: 10.1038/s41597-019-0184-5

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

Autorzy: Ziaurrehman Tanoli, Umair Seemab, Andreas Scherer, Krister Wennerberg, Jing Tang, Markus Vähä-Koskela
Opublikowane w: Briefings in Bioinformatics, 2020, ISSN 1477-4054
Wydawca: Oxford University Press
DOI: 10.1093/bib/bbaa003

GXP: Analyze and Plot Plant Omics Data in Web Browsers

Autorzy: Constantin Eiteneuer; David Velasco; Joseph Atemia; Dan Wang; Rainer Schwacke; Vanessa Wahl; Andrea Schrader; Julia J. Reimer; Sven Fahrner; Roland Pieruschka; Ulrich Schurr; Björn Usadel; Asis Hallab
Opublikowane w: Plants, Numer 11, 2022, Strona(/y) 745, ISSN 2223-7747
Wydawca: MDPI Journals
DOI: 10.3390/plants11060745

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

Autorzy: 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,
Opublikowane w: Frontiers in Marine Science, Numer 7, 2020, ISSN 2296-7745
Wydawca: Frontiers Media
DOI: 10.3389/fmars.2020.572680

An iterative and interdisciplinary categorisation process towards FAIRer digital resources for sensitive life-sciences data

Autorzy: Romain David; Christian Ohmann; Jan-Willem Boiten; Mónica Cano Abadía; Florence Bietrix; Steve Canham; Maria Luisa Chiusano; Walter Dastrù; Arnaud Laroquette; Dario Longo; Michaela Th. Mayrhofer; Maria Panagiotopoulou; Audrey S. Richard; Sergey Goryanin; Pablo Emilio Verde
Opublikowane w: Scientific Reports, Numer 12, 2022, Strona(/y) 20989, ISSN 2045-2322
Wydawca: Nature Publishing Group
DOI: 10.1038/s41598-022-25278-z

Experiment design driven FAIRification of omics data matrices, an exemplar

Autorzy: Philippe Rocca-Serra, Susanna-Assunta Sansone
Opublikowane w: Scientific Data, Numer 6/1, 2019, ISSN 2052-4463
Wydawca: Springer Nature
DOI: 10.1038/s41597-019-0286-0

Radical collaboration during a global health emergency: development of the RDA COVID-19 data sharing recommendations and guidelines

Autorzy: Brian Pickering; Timea Biro; Claire C. Austin; Alexander Bernier; Louise Bezuidenhout; Carlos Casorran; Francis P. Crawley; Romain David; Claudia Engelhardt; Geta Mitrea; Ingvill C. Mochmann; Rajini Nagrani; Mary O'Brien-Uhlmansiek; Simon Parker; Minglu Wang; Leyla Jael Castro; Zoe Cournia; Kheeran Dharmawardena; Gayo Diallo; Ingrid Dillo; Alejandra Gonzalez-Beltran; Anupama Gururaj; Sridhar Gutam
Opublikowane w: Open Research Europe, Numer 15, 2021, ISSN 2732-5121
Wydawca: European Commission
DOI: 10.12688/openreseurope.13369.1

Improvements on marker-free images alignment for electron tomography

Autorzy: C.O.S. Sorzano, F. de Isidro-Gómez, E. Fernández-Giménez, D. Herreros, S. Marco, J.M. Carazo, C. Messaoudi
Opublikowane w: Journal of Structural Biology: X, Numer 4, 2020, Strona(/y) 100037, ISSN 2590-1524
Wydawca: ELSEVIER
DOI: 10.1016/j.yjsbx.2020.100037

Cryo-EM density maps adjustment for subtraction, consensus and sharpening.

Autorzy: E. Fernández-Giménez; María Jesús Martínez; Rubén J. Sánchez-García; Roberto Marabini; Erney Ramírez-Aportela; Pablo Conesa; José María Carazo; Carlos Oscar S. Sorzano
Opublikowane w: Journal of Structural Biology, Numer 15, 2021, ISSN 1047-8477
Wydawca: Academic Press
DOI: 10.1016/j.jsb.2021.107780

XNAT-PIC: Extending XNAT to Preclinical Imaging Centers

Autorzy: Sara Zullino; Alessandro Paglialonga; Walter Dastrù; Dario Livio Longo; Silvio Aime
Opublikowane w: J Digit Imaging, 2022, ISSN 1618-727X
Wydawca: Springer Nature
DOI: 10.1007/s10278-022-00612-z

Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion.

Autorzy: David Strelak; A. Jiménez-Moreno; José Luis Vilas; Erney Ramírez-Aportela; Rubén J. Sánchez-García; David Maluenda; Javier Vargas; David Herreros; E. Fernández-Giménez; Federico P. de Isidro-Gómez; Jan Horáček; David Myška; Martin Horacek; Pablo Conesa; Yunior C. Fonseca-Reyna; Jorge Jiménez; Marta Martínez; Mohamad Harastani; Slavica Jonic; Jiri Filipovic; Roberto Marabini; José Ma
Opublikowane w: Volume 26, Numer 2, 2021, ISSN 1420-3049
Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules26206224

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

Autorzy: David Střelák, Jiří Filipovič, Amaya Jiménez-Moreno, Jose Carazo, Carlos Sánchez Sorzano
Opublikowane w: Electronics, Numer 9/6, 2020, Strona(/y) 1040, ISSN 2079-9292
Wydawca: MDPI
DOI: 10.3390/electronics9061040

Expanding the Galaxy's reference data

Autorzy: Nagampalli Vijaykrishna; Jayadev Joshi; Nate Coraor; Jennifer Hillman-Jackson; Dave Bouvier; Marius van den Beek; Ignacio Eguinoa; Frederik Coppens; Sergey Golitsynskiy; Michał Stolarczyk; Nathan C. Sheffield; Simon Gladman; Gianmauro Cuccuru; Björn Grüning; Nicola Soranzo; Helena Rasche; Bradley W. Langhorst; Matthias Bernt; Daniel Fornika; David Anderson de Lima Morais; Michel Barrette; Peter
Opublikowane w: urn:issn:2635-0041, Numer 4, 2022, ISSN 2635-0041
Wydawca: Oxford University Press
DOI: 10.1101/2020.10.09.327114

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

Autorzy: Daniel Jacob, Romain David, Sophie Aubin, Yves Gibon
Opublikowane w: GigaScience, Numer 9/12, 2020, ISSN 2047-217X
Wydawca: GigaScience, BioMed Central
DOI: 10.1093/gigascience/giaa144

DeepEMhancer: a deep learning solution for cryo-EM volume post-processing

Autorzy: Rubén J. Sánchez-García; Rubén J. Sánchez-García; Josué Gómez-Blanco; Josué Gómez-Blanco; Ana Maria Cuervo; José María Carazo; Carlos Oscar S. Sorzano; Javier Vargas; Javier Vargas
Opublikowane w: Communications Biology, Numer 10, 2021, ISSN 2399-3642
Wydawca: Nature Portfolio
DOI: 10.1101/2020.06.12.148296

Ten simple rules for making a software tool workflow-ready

Autorzy: Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R. Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn Grüning, Ignacio Eguinoa, Philip Ewels, Carole Goble
Opublikowane w: PLOS Computational Biology, 2022, ISSN 1553-7358
Wydawca: PLOS
DOI: 10.1371/journal.pcbi.1009823

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

Autorzy: Abulikemu Abudukelimu, Matteo Barberis, Frank Redegeld, Nilgun Sahin, Raju P. Sharma, Hans V. Westerhoff
Opublikowane w: Frontiers in Immunology, Numer 10, 2020, ISSN 1664-3224
Wydawca: Frontiers
DOI: 10.3389/fimmu.2019.03091

A complete search of combinatorial peptide library greatly benefited from probabilistic incorporation of prior knowledge

Autorzy: Miroslav Hruska; Dusan Holub
Opublikowane w: International Journal of Mass Spectrometry, Numer 3, 2021, ISSN 1387-3806
Wydawca: Elsevier BV
DOI: 10.1016/j.ijms.2021.116723

FAIRsharing as a community approach to standards, repositories and policies

Autorzy: Susanna-Assunta Sansone, Peter McQuilton, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran, Massimiliano Izzo, Allyson L. Lister, Milo Thurston
Opublikowane w: Nature Biotechnology, Numer 37/4, 2019, Strona(/y) 358-367, ISSN 1087-0156
Wydawca: Nature Publishing Group
DOI: 10.1038/s41587-019-0080-8

Perspectives on automated composition of workflows in the life sciences

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