Coordinated Research Infrastructures Building Enduring Life-science services

Livrables

D9.3.2 Pilot courses and staff exchange provided

Pilot courses and staff exchange provided: final report of activities achieved.

D4.1 Strategy for enabling user access within pilot use cases

D4.1 Strategy for enabling user access within pilot use cases (MDC/FVB/EMBL/SZN)

D3.2.2 Assessment of animal model phenotypes against outcome measures

Assessment of animal model phenotypes against outcome measures

D5.1 Report on existing user access models and regulatory access policies identifying common elements

D5.1 Report on existing user access models and regulatory access policies identifying common elements (UOXF/ INFRAFRONTIER)

D2.3 Report on user engagement activities
D3.1.1.2 Medical infrastructure user forum reporting (M22)
D6.1 Review of identifier schemes, standards and interoperability maps and proposed harmonization strategy
D3.3.2 Report on implementation, including economic model and solutions for sustainability

Report on implementation, including economic model and solutions for sustainability for the innovation office.

D2.4 Final stakeholder meeting
D7.1 Report on ELSI support needs for BMS RIs and ethics check procedure
D8.1 Concept paper on intellectual property issues in pre-competitive research
D9.3.1 Pilot courses and staff exchange provided

D9.3.1 Pilot courses and staff exchange provided (M24)

D3.1.1.4 Medical infrastructure user forum reporting (M46)

Report summarising the outcomes of the MIUF meeting in October 2019.

D3.1.1.3 Medical infrastructure user forum reporting (M37)
D8.4 Sustainability plan for extended BMS RI Innovation Office

Sustainability plan for extended BMS RI Innovation Office

D4.2 Sustainable plan for user access to common RI services for 4 use case cross-ESFRI BMS research infrastructure pipelines

D4.2 Sustainable plan for user access to common RI services for 4 use case cross-ESFRI BMS research infrastructure pipelines. (MDC/FVB/EMBL/SZN)

D3.2.1 Core set of outcome measures for clinical trials for each disease condition
D1.1 Project handbook
D9.1 Refined organisational competency framework needed by distributed RIs at 3 development stages
D3.5.2 Report on integrated biomedical data and project proposals for biomarker validation in clinical trial monitoring
D1.3 Implementation of an equal opportunities programme
D3.4.2 Report on final assessment and generalization of integration platform

Report on final assessment and generalization of integration platform (Lygature)

D5.2 Report on common access framework concept
D3.1.1.1 Medical infrastructure user forum reporting (M10)
D8.3 Industry collaboration best practice guide
D6.2 Access to Sustainable cross infrastructure identifier service(s) through ELIXIR service registry
D5.3 Strategy for expanding application of common access model based on feedback from WP3 and WP4 pilots
D1.2 Project-wide data management plan adopted
D4.3 Report on impact of integrated access standards tested for open user access

D4.3 Report on impact of integrated access standards tested for open user access (MDC/FVB/EMBL/SZN/ECRIN): 1st and 2nd Open Call; for the 2nd Open Call this will include the experiences of the users from the medical community in addition (see WP3, Task 3.6).

D3.3.1 Report on conclusions from multi-stakeholder taskforce
D3.5.1 Report describing informational lacunes and data enrichment strategy
D6.4 Report on models and pilot designs for sustainable scalable cloud-based provision of data access and compute across infrastructures
D2.1 Communication strategy based on stakeholder analysis
D1.4 Final report common infrastructures and services

This report will summarise the outcomes of the project from a users perspective. D1.4 “Final report common infrastructures and services” will be due in month 48 and will give an overview about all the services the different BMS Research Infrastructures are offering the scientific community under the umbrella of CORBEL.

D6.6 Ocean Sampling Day a demonstrator of a cross-domain distributed data set
D8.2 Concept paper on new business models related to open innovation
D7.3 Sustainability Plan for extended BMS RI ELSI common services

Sustainability Plan for extended BMS RI ELSI common services

D4.4 Framework in place for launching transnational open user access via the common BMS cluster web-portal and RI specific user community communication channels

D4.4 Framework in place for launching transnational open user access via the common BMS cluster web-portal and RI specific user community communication channels (EMBL / MDC)

D6.5 Prototype implementation of distributed automated data access request, review and authorization and delivery systems
D9.2 New course syllabi for a modular curriculum for piloting in RIs
D7.2 ELSI guidance for new scientific, technological and cross-border developments using a “help-desk format”
D6.3 Delivery of Toolkit supporting community ontology mapping and development
D3.4.1 Robust data upload procedures for biosample data and molecular profiling data

D3.4.1 Robust data upload procedures for biosample data and molecular profiling data (EATRIS-CTMM)

Publications

Four simple recommendations to encourage best practices in research software

Auteurs: Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutierrez, Neil Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla Garcia, Josep Ll. Gelpí, Simon Gladman, Carole Goble, Montserrat González Ferreiro, Alejandra Gonzalez-Beltran, Philippa C. Griffin, Björn Grüning, Jonas Hagberg, Petr Holub, Rob Hooft, Jon Ison, D
Publié dans: F1000Research, Numéro 6, 2017, Page(s) 876, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
DOI: 10.12688/f1000research.11407.1

Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions

Auteurs: Dmitry Shungin, Wei Q. Deng, Tibor V. Varga, Jian'an Luan, Evelin Mihailov, Andres Metspalu, Andrew P. Morris, Nita G. Forouhi, Cecilia Lindgren, Patrik K. E. Magnusson, Nancy L. Pedersen, Göran Hallmans, Audrey Y. Chu, Anne E. Justice, Mariaelisa Graff, Thomas W. Winkler, Lynda M. Rose, Claudia Langenberg, L. Adrienne Cupples, Paul M. Ridker, Nicholas J. Wareham, Ken K. Ong, Ruth J. F. Loos, Dan
Publié dans: PLOS Genetics, Numéro 13/6, 2017, Page(s) e1006812, ISSN 1553-7404
Éditeur: PLOS
DOI: 10.1371/journal.pgen.1006812

Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel

Auteurs: Mario Mitt, Mart Kals, Kalle Pärn, Stacey B Gabriel, Eric S Lander, Aarno Palotie, Samuli Ripatti, Andrew P Morris, Andres Metspalu, Tõnu Esko, Reedik Mägi, Priit Palta
Publié dans: European Journal of Human Genetics, Numéro 25/7, 2017, Page(s) 869-876, ISSN 1018-4813
Éditeur: Natue Publishing Group
DOI: 10.1038/ejhg.2017.51

A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect

Auteurs: Chiara Damiani, Riccardo Colombo, Daniela Gaglio, Fabrizia Mastroianni, Dario Pescini, Hans Victor Westerhoff, Giancarlo Mauri, Marco Vanoni, Lilia Alberghina
Publié dans: PLOS Computational Biology, Numéro 13/9, 2017, Page(s) e1005758, ISSN 1553-7358
Éditeur: PLOS
DOI: 10.1371/journal.pcbi.1005758

Sharing and reuse of individual participant data from clinical trials: principles and recommendations

Auteurs: Christian Ohmann, Rita Banzi, Steve Canham, Serena Battaglia, Mihaela Matei, Christopher Ariyo, Lauren Becnel, Barbara Bierer, Sarion Bowers, Luca Clivio, Monica Dias, Christiane Druml, Hélène Faure, Martin Fenner, Jose Galvez, Davina Ghersi, Christian Gluud, Trish Groves, Paul Houston, Ghassan Karam, Dipak Kalra, Rachel L Knowles, Karmela Krleža-Jerić, Christine Kubiak, Wolfgang Kuchinke, Reb
Publié dans: BMJ Open, Numéro 7/12, 2017, Page(s) e018647, ISSN 2044-6055
Éditeur: BMJ Publishing Group
DOI: 10.1136/bmjopen-2017-018647

SCORE-IT (Selecting Core Outcomes for Randomised Effectiveness trials In Type 2 diabetes): a systematic review of registered trials

Auteurs: Nicola L. Harman, Rebecca James, John Wilding, Paula R. Williamson
Publié dans: Trials, Numéro 18/1, 2017, ISSN 1745-6215
Éditeur: BioMed Central
DOI: 10.1186/s13063-017-2317-5

Trans-ethnic meta-regression of genome-wide association studies accounting for ancestry increases power for discovery and improves fine-mapping resolution

Auteurs: Reedik Mägi, Momoko Horikoshi, Tamar Sofer, Anubha Mahajan, Hidetoshi Kitajima, Nora Franceschini, Mark I. McCarthy, Andrew P. Morris
Publié dans: Human Molecular Genetics, Numéro 26/18, 2017, Page(s) 3639-3650, ISSN 0964-6906
Éditeur: Oxford University Press
DOI: 10.1093/hmg/ddx280

BiobankUniverse: automatic matchmaking between datasets for biobank data discovery and integration

Auteurs: Chao Pang, Fleur Kelpin, David van Enckevort, Niina Eklund, Kaisa Silander, Dennis Hendriksen, Mark de Haan, Jonathan Jetten, Tommy de Boer, Bart Charbon, Petr Holub, Hans Hillege, Morris A Swertz
Publié dans: Bioinformatics, Numéro 33/22, 2017, Page(s) 3627-3634, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btx478

Classification of processes involved in sharing individual participant data from clinical trials

Auteurs: Christian Ohmann, Steve Canham, Rita Banzi, Wolfgang Kuchinke, Serena Battaglia
Publié dans: F1000Research, Numéro 7, 2018, Page(s) 138, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
DOI: 10.12688/f1000research.13789.1

Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms

Auteurs: Michael H. Guo, Satish K. Nandakumar, Jacob C. Ulirsch, Seyedeh M. Zekavat, Jason D. Buenrostro, Pradeep Natarajan, Rany M. Salem, Roberto Chiarle, Mario Mitt, Mart Kals, Kalle Pärn, Krista Fischer, Lili Milani, Reedik Mägi, Priit Palta, Stacey B. Gabriel, Andres Metspalu, Eric S. Lander, Sekar Kathiresan, Joel N. Hirschhorn, Tõnu Esko, Vijay G. Sankaran
Publié dans: Proceedings of the National Academy of Sciences, Numéro 114/3, 2017, Page(s) E327-E336, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.1619052114

3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures

Auteurs: Joan Segura, Ruben Sanchez-Garcia, Marta Martinez, Jesus Cuenca-Alba, Daniel Tabas-Madrid, C O S Sorzano, J M Carazo
Publié dans: Bioinformatics, Numéro 33/22, 2017, Page(s) 3655-3657, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btx483

Selecting Core Outcomes for Randomised Effectiveness trials In Type 2 Diabetes (SCORE-IT): study protocol for the development of a core outcome set

Auteurs: Nicola L. Harman, John Wilding, Dave Curry, James Harris, Jennifer Logue, R. John Pemberton, Leigh Perreault, Gareth Thompson, Sean Tunis, Paula R. Williamson
Publié dans: Trials, Numéro 19/1, 2018, ISSN 1745-6215
Éditeur: BioMed Central
DOI: 10.1186/s13063-018-2805-2

Significant Locus and Metabolic Genetic Correlations Revealed in Genome-Wide Association Study of Anorexia Nervosa

Auteurs: Laramie Duncan, Zeynep Yilmaz, Helena Gaspar, Raymond Walters, Jackie Goldstein, Verneri Anttila, Brendan Bulik-Sullivan, Stephan Ripke, Laura Thornton, Anke Hinney, Mark Daly, Patrick F. Sullivan, Eleftheria Zeggini, Gerome Breen, Cynthia M. Bulik, Laramie Duncan, Zeynep Yilmaz, Héléna Gaspar, Raymond Walters, Jackie Goldstein, Verneri Anttila, Brendan Bulik-Sullivan, Stephan Ripke, Roger Adan,
Publié dans: American Journal of Psychiatry, Numéro 174/9, 2017, Page(s) 850-858, ISSN 0002-953X
Éditeur: American Psychiatric Publishing, Inc.
DOI: 10.1176/appi.ajp.2017.16121402

Predictable Irreversible Switching Between Acute and Chronic Inflammation

Auteurs: Abulikemu Abudukelimu, Matteo Barberis, Frank A. Redegeld, Nilgun Sahin, Hans V. Westerhoff
Publié dans: Frontiers in Immunology, Numéro 9, 2018, ISSN 1664-3224
Éditeur: Frontier
DOI: 10.3389/fimmu.2018.01596

Mind the Gap: From Tool to Knowledge Base

Auteurs: Michaela Th. Mayrhofer, Irene Schlünder
Publié dans: Biopreservation and Biobanking, 2018, ISSN 1947-5535
Éditeur: Mary Ann Liebert Inc.
DOI: 10.1089/bio.2018.0018

A metadata schema for data objects in clinical research

Auteurs: Canham, Steve; Ohmann, Christian
Publié dans: Trials, Numéro 1, 2016, ISSN 1745-6215
Éditeur: BioMed Central
DOI: 10.1186/s13063-016-1686-5

Assessment of the genetic and clinical determinants of fracture risk: genome wide association and mendelian randomisation study

Auteurs: Katerina Trajanoska, John A Morris, Ling Oei, Hou-Feng Zheng, David M Evans, Douglas P Kiel, Claes Ohlsson, J Brent Richards, Fernando Rivadeneira
Publié dans: BMJ, 2018, Page(s) k3225, ISSN 0959-8138
Éditeur: British Medical Association
DOI: 10.1136/bmj.k3225

3DBIONOTES: A unified, enriched and interactive view of macromolecular information

Auteurs: D. Tabas-Madrid, J. Segura, R. Sanchez-Garcia, J. Cuenca-Alba, C.O.S. Sorzano, J.M. Carazo
Publié dans: Journal of Structural Biology, Numéro 194/2, 2016, Page(s) 231-234, ISSN 1047-8477
Éditeur: Academic Press
DOI: 10.1016/j.jsb.2016.02.007

3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling

Auteurs: Joan Segura, Ruben Sanchez-Garcia, Daniel Tabas-Madrid, Jesus Cuenca-Alba, Carlos Oscar S. Sorzano, Jose Maria Carazo
Publié dans: Biophysical Journal, Numéro 110/4, 2016, Page(s) 766-775, ISSN 0006-3495
Éditeur: Biophysical Society
DOI: 10.1016/j.bpj.2015.11.3519

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

Auteurs: C. O. S. Sorzano, A. Jiménez, J. Mota, J. L. Vilas, D. Maluenda, M. Martínez, E. Ramírez-Aportela, T. Majtner, J. Segura, R. Sánchez-García, Y. Rancel, L. del Caño, P. Conesa, R. Melero, S. Jonic, J. Vargas, F. Cazals, Z. Freyberg, J. Krieger, I. Bahar, R. Marabini, J. M. Carazo
Publié dans: Acta Crystallographica Section F Structural Biology Communications, Numéro 75/1, 2019, Page(s) 19-32, ISSN 2053-230X
Éditeur: John Wiley and Sons Ltd
DOI: 10.1107/S2053230X18015108

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

Auteurs: Julie A. McMurry, Nick Juty, Niklas Blomberg, Tony Burdett, Tom Conlin, Nathalie Conte, Mélanie Courtot, John Deck, Michel Dumontier, Donal K. Fellows, Alejandra Gonzalez-Beltran, Philipp Gormanns, Jeffrey Grethe, Janna Hastings, Jean-Karim Hériché, Henning Hermjakob, Jon C. Ison, Rafael C. Jimenez, Simon Jupp, John Kunze, Camille Laibe, Nicolas Le Novère, James Malone, Maria Jesus Martin, Joh
Publié dans: PLOS Biology, Numéro 15/6, 2017, Page(s) e2001414, ISSN 1545-7885
Éditeur: PLOS Biology
DOI: 10.1371/journal.pbio.2001414

Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates

Auteurs: Simon Jupp, Tony Burdett, Danielle Welter, Sirarat Sarntivijai, Helen Parkinson, James Malone
Publié dans: Journal of Biomedical Semantics, Numéro 7/1, 2016, ISSN 2041-1480
Éditeur: Springer Nature
DOI: 10.1186/s13326-016-0055-3

Multi-omic profiles of human non-alcoholic fatty liver disease tissue highlight heterogenic phenotypes

Auteurs: Wasco Wruck, Karl Kashofer, Samrina Rehman, Andriani Daskalaki, Daniela Berg, Ewa Gralka, Justyna Jozefczuk, Katharina Drews, Vikash Pandey, Christian Regenbrecht, Christoph Wierling, Paola Turano, Ulrike Korf, Kurt Zatloukal, Hans Lehrach, Hans V. Westerhoff, James Adjaye
Publié dans: Scientific Data, Numéro 2, 2015, Page(s) 150068, ISSN 2052-4463
Éditeur: Nature Publishing Group
DOI: 10.1038/sdata.2015.68

The Peculiar Glycolytic Pathway in Hyperthermophylic Archaea: Understanding Its Whims by Experimentation In Silico

Auteurs: Yanfei Zhang, Theresa Kouril, Jacky Snoep, Bettina Siebers, Matteo Barberis, Hans Westerhoff
Publié dans: International Journal of Molecular Sciences, Numéro 18/4, 2017, Page(s) 876, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms18040876

Identification of Three Early Phases of Cell-Fate Determination during Osteogenic and Adipogenic Differentiation by Transcription Factor Dynamics

Auteurs: Jeroen van de Peppel, Tanja Strini, Julia Tilburg, Hans Westerhoff, Andre J. van Wijnen, Johannes P. van Leeuwen
Publié dans: Stem Cell Reports, Numéro 8/4, 2017, Page(s) 947-960, ISSN 2213-6711
Éditeur: Cell Press
DOI: 10.1016/j.stemcr.2017.02.018

Targeting pathogen metabolism without collateral damage to the host

Auteurs: Jurgen R. Haanstra, Albert Gerding, Amalia M. Dolga, Freek J. H. Sorgdrager, Manon Buist-Homan, François du Toit, Klaas Nico Faber, Hermann-Georg Holzhütter, Balázs Szöör, Keith R. Matthews, Jacky L. Snoep, Hans V. Westerhoff, Barbara M. Bakker
Publié dans: Scientific Reports, Numéro 7, 2017, Page(s) 40406, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/srep40406

Assessment of a demonstrator repository for individual clinical trial data built upon DSpace

Auteurs: Birol Tilki, Thomas Schulenberg, Steve Canham, Rita Banzi, Wolfgang Kuchinke, Christian Ohmann
Publié dans: F1000Research, Numéro 9, 2020, Page(s) 311, ISSN 2046-1402
Éditeur: F1000 Research Ltd.
DOI: 10.12688/f1000research.23468.2

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

Auteurs: Abulikemu Abudukelimu, Matteo Barberis, Frank Redegeld, Nilgun Sahin, Raju P. Sharma, Hans V. Westerhoff
Publié dans: Frontiers in Immunology, Numéro 10, 2020, ISSN 1664-3224
Éditeur: Frontiers Media SA
DOI: 10.3389/fimmu.2019.03091

Reply to “Missed opportunities in large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery”

Auteurs: Nicolas Bosc, Francis Atkinson, Eloy Félix, Anna Gaulton, Anne Hersey, Andrew R. Leach
Publié dans: Journal of Cheminformatics, Numéro 11/1, 2019, ISSN 1758-2946
Éditeur: Chemistry Central
DOI: 10.1186/s13321-019-0388-x

Parents of early‐maturing girls die younger

Auteurs: Peeter Hõrak, Markus Valge, Krista Fischer, Reedik Mägi, Tanel Kaart
Publié dans: Evolutionary Applications, Numéro 12/5, 2019, Page(s) 1050-1061, ISSN 1752-4571
Éditeur: John Wiley & Sons
DOI: 10.1111/eva.12780

Using Scipion for stream image processing at Cryo-EM facilities

Auteurs: J. Gómez-Blanco, J.M. de la Rosa-Trevín, R. Marabini, L. del Cano, A. Jiménez, M. Martínez, R. Melero, T. Majtner, D. Maluenda, J. Mota, Y. Rancel, E Ramírez-Aportela, J.L. Vilas, M. Carroni, S. Fleischmann, E. Lindahl, A.W. Ashton, M. Basham, D.K. Clare, K. Savage, C.A. Siebert, G.G. Sharov, C.O.S. Sorzano, P. Conesa, J.M. Carazo
Publié dans: Journal of Structural Biology, Numéro 204/3, 2018, Page(s) 457-463, ISSN 1047-8477
Éditeur: Academic Press
DOI: 10.1016/j.jsb.2018.10.001

3DCONS-DB: A Database of Position-Specific Scoring Matrices in Protein Structures

Auteurs: Ruben Sanchez-Garcia, Carlos Sorzano, Jose Carazo, Joan Segura
Publié dans: Molecules, Numéro 22/12, 2017, Page(s) 2230, ISSN 1420-3049
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules22122230

Large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery

Auteurs: Nicolas Bosc, Francis Atkinson, Eloy Felix, Anna Gaulton, Anne Hersey, Andrew R. Leach
Publié dans: Journal of Cheminformatics, Numéro 11/1, 2019, ISSN 1758-2946
Éditeur: Chemistry Central
DOI: 10.1186/s13321-018-0325-4

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

Auteurs: Kent A Shefchek, Nomi L Harris, Michael Gargano, Nicolas Matentzoglu, Deepak Unni, Matthew Brush, Daniel Keith, Tom Conlin, Nicole Vasilevsky, Xingmin Aaron Zhang, James P Balhoff, Larry Babb, Susan M Bello, Hannah Blau, Yvonne Bradford, Seth Carbon, Leigh Carmody, Lauren E Chan, Valentina Cipriani, Alayne Cuzick, Maria Della Rocca, Nathan Dunn, Shahim Essaid, Petra Fey, Chris Grove, Jean-Phillip
Publié dans: Nucleic Acids Research, Numéro 48/D1, 2019, Page(s) D704-D715, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkz997

PiGx: reproducible genomics analysis pipelines with GNU Guix

Auteurs: Ricardo Wurmus, Bora Uyar, Brendan Osberg, Vedran Franke, Alexander Gosdschan, Katarzyna Wreczycka, Jonathan Ronen, Altuna Akalin
Publié dans: GigaScience, Numéro 7/12, 2018, ISSN 2047-217X
Éditeur: Oxford University Press
DOI: 10.1093/gigascience/giy123

Sharing individual participant data from clinical studies: a cross-sectional online survey among Italian patient and citizen groups

Auteurs: Cinzia Colombo, Anna Roberto, Karmela Krleza-Jeric, Elena Parmelli, Rita Banzi
Publié dans: BMJ Open, Numéro 9/2, 2019, Page(s) e024863, ISSN 2044-6055
Éditeur: BMJ Publishing Group
DOI: 10.1136/bmjopen-2018-024863

Ten quick tips for biocuration

Auteurs: Y. Amy Tang, Klemens Pichler, Anja Füllgrabe, Jane Lomax, James Malone, Monica C. Munoz-Torres, Drashtti V. Vasant, Eleanor Williams, Melissa Haendel
Publié dans: PLOS Computational Biology, Numéro 15/5, 2019, Page(s) e1006906, ISSN 1553-7358
Éditeur: PLOS
DOI: 10.1371/journal.pcbi.1006906

Neural plasticity and adult neurogenesis: the deep biology perspective

Auteurs: AnnaMaria Colangelo, HansV Westerhoff, Giovanni Cirillo, Lilia Alberghina, Michele Papa
Publié dans: Neural Regeneration Research, Numéro 14/2, 2019, Page(s) 201, ISSN 1673-5374
Éditeur: Neural Regeneration Research
DOI: 10.4103/1673-5374.244775

Light sheet microscopy with acoustic sample confinement

Auteurs: Zhengyi Yang, Katy L. H. Cole, Yongqiang Qiu, Ildikó M. L. Somorjai, Philip Wijesinghe, Jonathan Nylk, Sandy Cochran, Gabriel C. Spalding, David A. Lyons, Kishan Dholakia
Publié dans: Nature Communications, Numéro 10/1, 2019, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-019-08514-5

BIPSPI: a method for the prediction of partner-specific protein–protein interfaces

Auteurs: Ruben Sanchez-Garcia, C O S Sorzano, J M Carazo, Joan Segura
Publié dans: Bioinformatics, Numéro 35/3, 2018, Page(s) 470-477, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/bty647

Ensembl Genomes 2020—enabling non-vertebrate genomic research

Auteurs: Kevin L Howe, Bruno Contreras-Moreira, Nishadi De Silva, Gareth Maslen, Wasiu Akanni, James Allen, Jorge Alvarez-Jarreta, Matthieu Barba, Dan M Bolser, Lahcen Cambell, Manuel Carbajo, Marc Chakiachvili, Mikkel Christensen, Carla Cummins, Alayne Cuzick, Paul Davis, Silvie Fexova, Astrid Gall, Nancy George, Laurent Gil, Parul Gupta, Kim E Hammond-Kosack, Erin Haskell, Sarah E Hunt, Pankaj Jaiswal,
Publié dans: Nucleic Acids Research, Numéro 48/D1, 2019, Page(s) D689-D695, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkz890

Search for Early Pancreatic Cancer Blood Biomarkers in Five European Prospective Population Biobanks Using Metabolomics

Auteurs: Jesse Fest, Lisanne S Vijfhuizen, Jelle J Goeman, Olga Veth, Anni Joensuu, Markus Perola, Satu Männistö, Eivind Ness-Jensen, Kristian Hveem, Toomas Haller, Neeme Tonisson, Kairit Mikkel, Andres Metspalu, Cornelia M van Duijn, Arfan Ikram, Bruno H Stricker, Rikje Ruiter, Casper H J van Eijck, Gert-Jan B van Ommen, Peter A C ʼt Hoen
Publié dans: Endocrinology, Numéro 160/7, 2019, Page(s) 1731-1742, ISSN 1945-7170
Éditeur: Endocrine Society
DOI: 10.1210/en.2019-00165

Ample Arsenite Bio-Oxidation Activity in Bangladesh Drinking Water Wells: A Bonanza for Bioremediation?

Auteurs: Zahid Hassan, Munawar Sultana, Sirajul I. Khan, Martin Braster, Wilfred F.M. Röling, Hans V. Westerhoff
Publié dans: Microorganisms, Numéro 7/8, 2019, Page(s) 246, ISSN 2076-2607
Éditeur: MDPI
DOI: 10.3390/microorganisms7080246

Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion

Auteurs: D. Maluenda, T. Majtner, P. Horvath, J. L. Vilas, A. Jiménez-Moreno, J. Mota, E. Ramírez-Aportela, R. Sánchez-García, P. Conesa, L. del Caño, Y. Rancel, Y. Fonseca, M. Martínez, G. Sharov, C.A. García, D. Strelak, R. Melero, R. Marabini, J. M. Carazo, C. O. S. Sorzano
Publié dans: Acta Crystallographica Section D Structural Biology, Numéro 75/10, 2019, Page(s) 882-894, ISSN 2059-7983
Éditeur: International Union of Crystallography
DOI: 10.1107/s2059798319011860

A Simple and Fast Assay Based on Carboxyfluorescein-Loaded Liposome for Quantitative DNA Detection

Auteurs: Jacopo Sforzi, Giuseppe Ferrauto, Silvio Aime, Simonetta Geninatti Crich
Publié dans: ACS Omega, Numéro 5/4, 2020, Page(s) 1764-1772, ISSN 2470-1343
Éditeur: ACS Publications
DOI: 10.1021/acsomega.9b01457

Evaluation of repositories for sharing individual-participant data from clinical studies

Auteurs: Rita Banzi, Steve Canham, Wolfgang Kuchinke, Karmela Krleza-Jeric, Jacques Demotes-Mainard, Christian Ohmann
Publié dans: Trials, Numéro 20/1, 2019, ISSN 1745-6215
Éditeur: BioMed Central
DOI: 10.1186/s13063-019-3253-3

Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars

Auteurs: Denise Carvalho-Silva, Leyla Garcia, Sarah L. Morgan, Cath Brooksbank, Ian Dunham
Publié dans: PLOS Computational Biology, Numéro 14/11, 2018, Page(s) e1006419, ISSN 1553-7358
Éditeur: PLOS
DOI: 10.1371/journal.pcbi.1006419

Selecting Core Outcomes for Randomised Effectiveness trials In Type 2 diabetes (SCORE-IT): a patient and healthcare professional consensus on a core outcome set for type 2 diabetes

Auteurs: Nicola L Harman, John P H Wilding, Dave Curry, James Harris, Jennifer Logue, R John Pemberton, Leigh Perreault, Gareth Thompson, Sean Tunis, Paula R Williamson
Publié dans: BMJ Open Diabetes Research & Care, Numéro 7/1, 2019, Page(s) e000700, ISSN 2052-4897
Éditeur: BMJ Publishing Group Ltd.
DOI: 10.1136/bmjdrc-2019-000700

Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network

Auteurs: Kazuhiro Maeda, Hans V. Westerhoff, Hiroyuki Kurata, Fred C. Boogerd
Publié dans: npj Systems Biology and Applications, Numéro 5/1, 2019, ISSN 2056-7189
Éditeur: Springer Nature
DOI: 10.1038/s41540-019-0091-6

CORBEL Pilot courses and staff exchange provided

Auteurs: Matser, Vera; Battaglia, Serena; Amaral, Ana Margarida
Publié dans: 2017
Éditeur: zenodo
DOI: 10.5281/zenodo.1044176

3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures

Auteurs: Segura, Joan; Sanchez-Garcia, Ruben; Martinez, Marta; Cuenca-Alba, Jesus; Tabas-Madrid, Daniel; Sorzano, C.O.S; Carazo, JM
Publié dans: 2017
Éditeur: Zenodo

CORBEL Briefing document: Evidence of shared services provided through Instruct structural biology infrastructure to other Biomedical Sciences Research Infrastructures in the CORBEL partnership

Auteurs: Carazo, J M
Publié dans: 2017
Éditeur: Zenodo
DOI: 10.5281/zenodo.1026294

Intellectual Property Issues in Open Science, pre-competitive Research and Open Innovation

Auteurs: Zacherl, Nikolaus; Zatloukal, Kurt
Publié dans: 2017
Éditeur: Zenodo
DOI: 10.5281/zenodo.1109265

CORBEL Concept paper on new business models related to Open Innovation

Auteurs: Abuja, Peter M., Zatloukal, Kurt
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1408808

"CORBEL ELSI guidance for new scientific, technological and cross-border developments using a ""help-desk format"""

Auteurs: Mayrhofer, Michaela Th., Schlünder, Irene
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1408804

CORBEL Report on conclusions from multi-stakeholder taskforce

Auteurs: Serena Battaglia
Publié dans: 2017
Éditeur: Zenodo
DOI: 10.5281/zenodo.1409571

Report about a workshop on sensitive data: Repositories for sharing individual participant data from clinical trials and existing tools/services for storing clinical trial data

Auteurs: Rita Banzi, Steve Canham, Christian Ohmann, Wolfgang Kuchinke, Karmela Krleza-Jeric, Birol Tilki, Serena Battaglia, Jacques Demotes-Mainard
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1438261

CORBEL Equal Opportunities Survey and Recommendations

Auteurs: Asrar Ali Khan, Michael Raess
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1441066

CORBEL Access to Sustainable cross infrastructure identifier service(s) through ELIXIR service registry

Auteurs: Nick Juty, Carole Goble, Helen Parkinson, Simon Jupp
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1441303

Federated Identity Management for Research Collaborations

Auteurs: Christopher John Atherton, Thomas Barton, Jim Basney, Daan Broeder, Alessandro Costa, Mirjam van Daalen, Stephanie Dyke, Willem Elbers, Carl-Fredrik Enell, Enrico Maria Vincenzo Fasanelli, João Fernandes, Licia Florio, Peter Gietz, David L. Groep, Matthias Bernhard Junker, Christos Kanellopoulos, David Kelsey, Philip Kershaw, Cristina Knapic, Thorsten Kollegger, Scott Koranda, Mikael Linden, Fili
Publié dans: 2018
Éditeur: Zenodo
DOI: 10.5281/zenodo.1307551

CORBEL Sustainable plan for user access to common RI services for 4 use case cross-ESFRI BMS research infrastructure pipelines

Auteurs: Leitner, Frauke; Popp, Christian; Vidal, Marie
Publié dans: 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.2222358

CORBEL Delivery of Toolkit supporting community ontology mapping and development

Auteurs: Jupp, Simon; Parkinson, Helen; Goble, Carol; Juty, Nick; Boiten, Jan-Willem; Swertz, Morris
Publié dans: 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.2559160

CORBEL 3rd Medical Infrastructure user forum reporting

Auteurs: Battaglia, Serena
Publié dans: 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.2025791

CORBEL Strategy for enabling user access within pilot use cases

Auteurs: Leither, Frauke; Vanmaele, Sofie; Stechmann, Bahne; Vidal, Marie
Publié dans: 2016
Éditeur: zenodo
DOI: 10.5281/zenodo.154081

CORBEL Refined organisational competency framework needed by distributed RIs at 3 development stages

Auteurs: Brooksbank, Cath; Pasterk, Markus
Publié dans: 2016
Éditeur: zenodo
DOI: 10.5281/zenodo.154085

CORBEL Report describing informational lacunes and data enrichment strategy: Expanding the consortium and selecting samples for CORBEL Use case

Auteurs: Toernwall, Outi; van Ommen, Gertjan
Publié dans: 2016
Éditeur: zenodo
DOI: 10.5281/zenodo.154076

CORBEL Communication Strategy based on stakeholder analysis

Auteurs: Schuengel, Manuela
Publié dans: 2016
Éditeur: zenodo
DOI: 10.5281/zenodo.154033

CORBEL Project-wide data management plan adopted

Auteurs: Jenkinson, Andrew M.
Publié dans: 2016
Éditeur: zenodo
DOI: 10.5281/zenodo.154022

CORBEL 1st Medical Infrastructure/Users Forum (MIUF) Report

Auteurs: Battaglia, Serena
Publié dans: 2016
Éditeur: zenodo
DOI: 10.5281/zenodo.154035

CORBEL Report on ELSI support needs for BMS RIs and towards a joint Ethical Governance Framework

Auteurs: Schluender, Irene; Cambon-Thomsen, Anne; Suhr, Stephanie (editor); Chassang, Gauthier; Mayrhofer, Michaela Th.
Publié dans: 2016
Éditeur: zenodo
DOI: 10.5281/zenodo.154084

CORBEL Report on Common Access Framework Concept

Auteurs: Haley, Natalie
Publié dans: 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.2662134

CORBEL Prototype implementation of distributed automated data access request, review and authorization and delivery systems

Auteurs: Linden, Mikael; Boiten, Jan-Willem; Courtot, Melanie; Holub, Petr; van de Geijn, Gert-Jan; van Enckevort, David; Lappalainen, Ilkka; Nyrönen, Tommi; Parkinson, Helen; Reihs, Robert; Senf, Alexander; Spalding, Dylan; Swedlow, Jason; Swertz, Morris; Törnroos, Juha; Kankaanpää, Pasi; van Iperen, Erik
Publié dans: 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.3238496

CORBEL Industry Collaboration Best Practice Guide

Auteurs: Abuja, Peter M.; Carapina, Tamara; de Kort, Martin; Raess, Michael; Tieken, Chris; Wagstaff, Nigel
Publié dans: 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.2615364

CORBEL Report on integrated biomedical data and project proposals for biomarker validation in clinical trial monitoring

Auteurs: van Ommen, Gertjan
Publié dans: 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.3238313

CORBEL Report on models and pilot designs for sustainable scalable cloud-based provision of data access and compute across infrastructures

Auteurs: Morris Swertz, Fleur Kelpin, David van Enckevort, Ilkka Lappalainen, Mikael Linden, Tommi Nyrönen, Petr Holub, Jan-Willem Boiten, Anna Leida Molder, Helen Parkinson
Publié dans: 2017
Éditeur: Zenodo
DOI: 10.5281/zenodo.376279

CORBEL Review of identifier schemes, standards and interoperability maps and proposed harmonization strategy

Auteurs: Carole Goble, Helen Parkinson, Simon Jupp, Renzo Kottmann, Jan-Willem Boiten, Frank Oliver Glöckner, Eleanor Williams, Jason Swedlow, Morris Swertz, David van Enckevort, Nick Juty, Anna Gaulton
Publié dans: 2017
Éditeur: Zenodo
DOI: 10.5281/zenodo.376236

CORBEL Report on existing user access models and regulatory access policies identifying common elements

Auteurs: Susan Daenke, Narayanan Krishnan
Publié dans: 2017
Éditeur: Zenodo
DOI: 10.5281/zenodo.376187

CORBEL Report on final assessment and generalization of integration platform

Auteurs: Boiten, Jan-Willem; Aime, Silvio; Bierkens, Mariska; Dastrù, Walter; Hansson, Mattias; Klein, Stefan; Longo, Dario; Peelen, Sjaak; Zullino, Sara; Sangiorgi, Luca; Mordenti, Marina; Boarini, Manila; Welsing, Paco
Publié dans: 2020
Éditeur: Zenodo
DOI: 10.5281/zenodo.3628369

CORBEL Assessment of animal model phenotypes against outcome measures

Auteurs: Nicola Harman; Adrian Sanz-Moreno; Patricia da Silva-Buttkus; Serena Battaglia
Publié dans: 2020
Éditeur: Zenodo
DOI: 10.5281/zenodo.3685932

CORBEL Report on user engagement activities

Auteurs: Hauk, Christiane; Schmidt-Tremmel, Friederike; Battaglia, Serena; Leitner, Frauke; Hansen, Sonja; Haley, Natalie; Raess, Michael; Parkinson, Helen; Jupp, Simon; Mayrhofer, Michaela Th.; Wagstaff, Nigel; Matser, Vera
Publié dans: 2020
Éditeur: Zenodo
DOI: 10.5281/zenodo.3678774

CORBEL Sustainability plan for extended BMS RI Innovation Office

Auteurs: Abuja, Peter M.; Carapina, Tamara; de Kort, Martin; Fauvel, Anne-Charlotte; Tieken, Chris; Ussi, Anton; Wagstaff, Nigel
Publié dans: 2020
Éditeur: Zenodo
DOI: 10.5281/zenodo.3663759

CORBEL Pilot courses and staff exchange provided (Summary)

Auteurs: Lloret Llinares, Marta; Matser, Vera; Raess, Michael; Herzog, Katja; Haley, Natalie; Alen Amaro, Claudia; Battaglia, Serena; Brooksbank, Cath; Vidal, Marie; Ludwig, Rebecca; Hauk, Christiane; Leitner, Frauke; Popp, Christian; Hansen, Sonja; Kalinowska, Gosia; Mayrhofer, Michaela Th.
Publié dans: 2020
Éditeur: Zenodo
DOI: 10.5281/zenodo.3738191

CORBEL 4th Medical Infrastructure user forum reporting

Auteurs: Battaglia, Serena
Publié dans: 2020
Éditeur: Zenodo
DOI: 10.5281/zenodo.3726777

CORBEL Ocean Sampling Day: a demonstrator of a cross-domain distributed data set

Auteurs: Glöckner, Frank Oliver; Kostadinov, Ivaylo; Cochrane, Guy
Publié dans: 2020
Éditeur: Zenodo
DOI: 10.5281/zenodo.3839957

BBMRI-ERIC ELSI Glossary

Auteurs: Grewal, Jasjote; Mayrhofer, Michaela Th.
Publié dans: 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.3754254

CORBEL Final Stakeholder Meeting

Auteurs: Gaber, Sabrina; Battaglia, Serena; Schmidt-Tremmel, Friederike; Blomberg, Niklas
Publié dans: 2020
Éditeur: Zenodo
DOI: 10.5281/zenodo.3744802

CORBEL Strategy for expanding application of common access model based on feedback from WP3 and WP4 pilots

Auteurs: Haley, Natalie; Räß, Michael
Publié dans: 2020
Éditeur: Zenodo
DOI: 10.5281/zenodo.3859788

CORBEL Report on impact of integrated access standards tested for open user access

Auteurs: Hansen, Sonja; Leitner, Frauke
Publié dans: 2020
Éditeur: Zenodo
DOI: 10.5281/zenodo.3856121

CORBEL Framework in place for launching transnational open user access via the common LS (formerly BMS) cluster web portal and RI specific user community communication channels

Auteurs: Hansen, Sonja; Leitner, Frauke
Publié dans: 2020
Éditeur: Zenodo
DOI: 10.5281/zenodo.3856040

CORBEL Sustainability Plan for extended BMS RI ELSI Services

Auteurs: Mayrhofer, Michaela Th.; Grewal, Jasjote; Schlünder, Irene; Goisauf, Melanie; Akyüz, Kaya; Adeniran, Ayodeji
Publié dans: 2020
Éditeur: Zenodo
DOI: 10.5281/zenodo.3859796

CORBEL Report on implementation, including economic model and solutions for sustainability

Auteurs: Lydall, Ben
Publié dans: 2020
Éditeur: Zenodo
DOI: 10.5281/zenodo.3862715

CORBEL Final report common infrastructures and services

Auteurs: Schmidt-Tremmel, Friederike; Blomberg, Niklas
Publié dans: 2020
Éditeur: Zenodo
DOI: 10.5281/zenodo.3865548

CORBEL Core set of outcome measures for clinical trials for each disease condition

Auteurs: Battaglia, Serena; Da Silva-Buttkus, Patricia; Demotes, Jacques; Fuchs, Helmut; Gailus-Durner, Valérie; Garattini, Silvio; Harman, Nicola; Prinsen, Cecilia; Raess, Michael; Terwee, Caroline; Williamson, Paula
Publié dans: 2017
Éditeur: zenodo
DOI: 10.5281/zenodo.886494

CORBEL Robust data upload procedures for biosample data and molecular profiling data

Auteurs: Boiten, Jan-Willem; Bierkens, Mariska; Hansson, Matthias; Klein, Stefan; Peelen, Sjaak
Publié dans: 2017
Éditeur: zenodo
DOI: 10.5281/zenodo.886508

CORBEL 2nd Medical Infrastructure user forum reporting

Auteurs: Battaglia, Serena
Publié dans: 2017
Éditeur: zenodo
DOI: 10.5281/zenodo.825054

CORBEL New course syllabi for a modular curriculum for piloting in RIs

Auteurs: Matser, Vera; Schuengel, Manuela
Publié dans: 2017
Éditeur: zenodo
DOI: 10.5281/zenodo.841702

CORBEL Concept paper on intellectual property issues in pre-competitive research

Auteurs: Zatloukal, Kurt; Zacherl, Nikolaus; Schreiner, Christoph
Publié dans: 2017
Éditeur: zenodo
DOI: 10.5281/zenodo.580056

A framework for quality management in the biomedical research infrastructures (BMS RIs)

Auteurs: BBMRI-ERIC; EATRIS; ECRIN; ELIXIR; EMBRC; EMPHASIS; ERINHA; EU-OPENSCREEN; Euro-BioImaging; INFRAFRONTIER; Instruct; ISBE; MIRRI
Publié dans: 2017
Éditeur: zenodo
DOI: 10.5281/zenodo.834332

Informed Consent Matrix for Clinical Trials

Auteurs: Colombo, Cinzia; Mosconi, Paola; Mayrhofer, Michaela; Kubiak, Christine; Battaglia, Serena; Matei, Mihaela; Lavitrano, Marialuisa; Casati, Sara; Chico, Victoria; Schlünder, Irene; Boiten, Jan-Willem; Carapina, Lygature Tamara; Uzun, Oskar; Suhr, Stephanie
Publié dans: 2019
Éditeur: Zenodo
DOI: 10.5281/zenodo.3928317

Non-repudiable provenance for clinical decision support systems

Auteurs: Fairweather, Elliot; Wittner, Rudolf; Chapman, Martin; Holub, Petr; Curcin, Vasa
Publié dans: 2020
Éditeur: Arxiv.org

EMPHASIS - European Infrastructure for Multi-scale Plant Phenomics and Simulation for Food Security in a Chancing Climate

Auteurs: Pieruschka, Roland
Publié dans: CORBEL User Meeting, Heidelberg, Germany, 2019-10-01 - 2019-10-02, 2019
Éditeur: N/A

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

Auteurs: 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
Publié dans: 2020
Éditeur: Zenodo
DOI: 10.5281/zenodo.3901011

Incorporating Patients' Perspectives into the Initial Stages of Core Outcome Set Development: A Rapid Review of Qualitative Studies of Type 2 Diabetes

Auteurs: Sarah L. Gorst, Bridget Young, Paula R. Williamson, John PH Wilding, Nicola Harman
Publié dans: SSRN Electronic Journal, 2019, ISSN 1556-5068
Éditeur: ELSEVIER
DOI: 10.2139/ssrn.3234869

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