Coordinated Research Infrastructures Building Enduring Life-science services

Deliverables

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

Author(s): 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
Published in: F1000Research, Issue 6, 2017, Page(s) 876, ISSN 2046-1402
Publisher: 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

Author(s): 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
Published in: PLOS Genetics, Issue 13/6, 2017, Page(s) e1006812, ISSN 1553-7404
Publisher: 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

Author(s): 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
Published in: European Journal of Human Genetics, Issue 25/7, 2017, Page(s) 869-876, ISSN 1018-4813
Publisher: 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

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

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

Author(s): 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
Published in: BMJ Open, Issue 7/12, 2017, Page(s) e018647, ISSN 2044-6055
Publisher: 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

Author(s): Nicola L. Harman, Rebecca James, John Wilding, Paula R. Williamson
Published in: Trials, Issue 18/1, 2017, ISSN 1745-6215
Publisher: 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

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

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

Author(s): 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
Published in: Bioinformatics, Issue 33/22, 2017, Page(s) 3627-3634, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btx478

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

Author(s): Christian Ohmann, Steve Canham, Rita Banzi, Wolfgang Kuchinke, Serena Battaglia
Published in: F1000Research, Issue 7, 2018, Page(s) 138, ISSN 2046-1402
Publisher: F1000 Research Ltd.
DOI: 10.12688/f1000research.13789.1

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

Author(s): 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
Published in: Proceedings of the National Academy of Sciences, Issue 114/3, 2017, Page(s) E327-E336, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1619052114

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

Author(s): Joan Segura, Ruben Sanchez-Garcia, Marta Martinez, Jesus Cuenca-Alba, Daniel Tabas-Madrid, C O S Sorzano, J M Carazo
Published in: Bioinformatics, Issue 33/22, 2017, Page(s) 3655-3657, ISSN 1367-4803
Publisher: 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

Author(s): Nicola L. Harman, John Wilding, Dave Curry, James Harris, Jennifer Logue, R. John Pemberton, Leigh Perreault, Gareth Thompson, Sean Tunis, Paula R. Williamson
Published in: Trials, Issue 19/1, 2018, ISSN 1745-6215
Publisher: BioMed Central
DOI: 10.1186/s13063-018-2805-2

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

Author(s): 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,
Published in: American Journal of Psychiatry, Issue 174/9, 2017, Page(s) 850-858, ISSN 0002-953X
Publisher: American Psychiatric Publishing, Inc.
DOI: 10.1176/appi.ajp.2017.16121402

Predictable Irreversible Switching Between Acute and Chronic Inflammation

Author(s): Abulikemu Abudukelimu, Matteo Barberis, Frank A. Redegeld, Nilgun Sahin, Hans V. Westerhoff
Published in: Frontiers in Immunology, Issue 9, 2018, ISSN 1664-3224
Publisher: Frontier
DOI: 10.3389/fimmu.2018.01596

Mind the Gap: From Tool to Knowledge Base

Author(s): Michaela Th. Mayrhofer, Irene Schlünder
Published in: Biopreservation and Biobanking, 2018, ISSN 1947-5535
Publisher: Mary Ann Liebert Inc.
DOI: 10.1089/bio.2018.0018

A metadata schema for data objects in clinical research

Author(s): Canham, Steve; Ohmann, Christian
Published in: Trials, Issue 1, 2016, ISSN 1745-6215
Publisher: 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

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

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

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

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

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

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

Author(s): 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
Published in: Acta Crystallographica Section F Structural Biology Communications, Issue 75/1, 2019, Page(s) 19-32, ISSN 2053-230X
Publisher: 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

Author(s): 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
Published in: PLOS Biology, Issue 15/6, 2017, Page(s) e2001414, ISSN 1545-7885
Publisher: 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

Author(s): Simon Jupp, Tony Burdett, Danielle Welter, Sirarat Sarntivijai, Helen Parkinson, James Malone
Published in: Journal of Biomedical Semantics, Issue 7/1, 2016, ISSN 2041-1480
Publisher: Springer Nature
DOI: 10.1186/s13326-016-0055-3

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

Author(s): 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
Published in: Scientific Data, Issue 2, 2015, Page(s) 150068, ISSN 2052-4463
Publisher: Nature Publishing Group
DOI: 10.1038/sdata.2015.68

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

Author(s): Yanfei Zhang, Theresa Kouril, Jacky Snoep, Bettina Siebers, Matteo Barberis, Hans Westerhoff
Published in: International Journal of Molecular Sciences, Issue 18/4, 2017, Page(s) 876, ISSN 1422-0067
Publisher: 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

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

Targeting pathogen metabolism without collateral damage to the host

Author(s): 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
Published in: Scientific Reports, Issue 7, 2017, Page(s) 40406, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/srep40406

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

Author(s): Birol Tilki, Thomas Schulenberg, Steve Canham, Rita Banzi, Wolfgang Kuchinke, Christian Ohmann
Published in: F1000Research, Issue 9, 2020, Page(s) 311, ISSN 2046-1402
Publisher: 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

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
Publisher: 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”

Author(s): Nicolas Bosc, Francis Atkinson, Eloy Félix, Anna Gaulton, Anne Hersey, Andrew R. Leach
Published in: Journal of Cheminformatics, Issue 11/1, 2019, ISSN 1758-2946
Publisher: Chemistry Central
DOI: 10.1186/s13321-019-0388-x

Parents of early‐maturing girls die younger

Author(s): Peeter Hõrak, Markus Valge, Krista Fischer, Reedik Mägi, Tanel Kaart
Published in: Evolutionary Applications, Issue 12/5, 2019, Page(s) 1050-1061, ISSN 1752-4571
Publisher: John Wiley & Sons
DOI: 10.1111/eva.12780

Using Scipion for stream image processing at Cryo-EM facilities

Author(s): 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
Published in: Journal of Structural Biology, Issue 204/3, 2018, Page(s) 457-463, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2018.10.001

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

Author(s): Ruben Sanchez-Garcia, Carlos Sorzano, Jose Carazo, Joan Segura
Published in: Molecules, Issue 22/12, 2017, Page(s) 2230, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules22122230

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

Author(s): Nicolas Bosc, Francis Atkinson, Eloy Felix, Anna Gaulton, Anne Hersey, Andrew R. Leach
Published in: Journal of Cheminformatics, Issue 11/1, 2019, ISSN 1758-2946
Publisher: 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

Author(s): 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
Published in: Nucleic Acids Research, Issue 48/D1, 2019, Page(s) D704-D715, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz997

PiGx: reproducible genomics analysis pipelines with GNU Guix

Author(s): Ricardo Wurmus, Bora Uyar, Brendan Osberg, Vedran Franke, Alexander Gosdschan, Katarzyna Wreczycka, Jonathan Ronen, Altuna Akalin
Published in: GigaScience, Issue 7/12, 2018, ISSN 2047-217X
Publisher: 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

Author(s): Cinzia Colombo, Anna Roberto, Karmela Krleza-Jeric, Elena Parmelli, Rita Banzi
Published in: BMJ Open, Issue 9/2, 2019, Page(s) e024863, ISSN 2044-6055
Publisher: BMJ Publishing Group
DOI: 10.1136/bmjopen-2018-024863

Ten quick tips for biocuration

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

Neural plasticity and adult neurogenesis: the deep biology perspective

Author(s): AnnaMaria Colangelo, HansV Westerhoff, Giovanni Cirillo, Lilia Alberghina, Michele Papa
Published in: Neural Regeneration Research, Issue 14/2, 2019, Page(s) 201, ISSN 1673-5374
Publisher: Neural Regeneration Research
DOI: 10.4103/1673-5374.244775

Light sheet microscopy with acoustic sample confinement

Author(s): 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
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-08514-5

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

Author(s): Ruben Sanchez-Garcia, C O S Sorzano, J M Carazo, Joan Segura
Published in: Bioinformatics, Issue 35/3, 2018, Page(s) 470-477, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty647

Ensembl Genomes 2020—enabling non-vertebrate genomic research

Author(s): 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,
Published in: Nucleic Acids Research, Issue 48/D1, 2019, Page(s) D689-D695, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz890

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

Author(s): 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
Published in: Endocrinology, Issue 160/7, 2019, Page(s) 1731-1742, ISSN 1945-7170
Publisher: Endocrine Society
DOI: 10.1210/en.2019-00165

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

Author(s): Zahid Hassan, Munawar Sultana, Sirajul I. Khan, Martin Braster, Wilfred F.M. Röling, Hans V. Westerhoff
Published in: Microorganisms, Issue 7/8, 2019, Page(s) 246, ISSN 2076-2607
Publisher: MDPI
DOI: 10.3390/microorganisms7080246

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

Author(s): 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
Published in: Acta Crystallographica Section D Structural Biology, Issue 75/10, 2019, Page(s) 882-894, ISSN 2059-7983
Publisher: International Union of Crystallography
DOI: 10.1107/s2059798319011860

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

Author(s): Jacopo Sforzi, Giuseppe Ferrauto, Silvio Aime, Simonetta Geninatti Crich
Published in: ACS Omega, Issue 5/4, 2020, Page(s) 1764-1772, ISSN 2470-1343
Publisher: ACS Publications
DOI: 10.1021/acsomega.9b01457

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

Author(s): Rita Banzi, Steve Canham, Wolfgang Kuchinke, Karmela Krleza-Jeric, Jacques Demotes-Mainard, Christian Ohmann
Published in: Trials, Issue 20/1, 2019, ISSN 1745-6215
Publisher: BioMed Central
DOI: 10.1186/s13063-019-3253-3

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

Author(s): Denise Carvalho-Silva, Leyla Garcia, Sarah L. Morgan, Cath Brooksbank, Ian Dunham
Published in: PLOS Computational Biology, Issue 14/11, 2018, Page(s) e1006419, ISSN 1553-7358
Publisher: 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

Author(s): 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
Published in: BMJ Open Diabetes Research & Care, Issue 7/1, 2019, Page(s) e000700, ISSN 2052-4897
Publisher: 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

Author(s): Kazuhiro Maeda, Hans V. Westerhoff, Hiroyuki Kurata, Fred C. Boogerd
Published in: npj Systems Biology and Applications, Issue 5/1, 2019, ISSN 2056-7189
Publisher: Springer Nature
DOI: 10.1038/s41540-019-0091-6

CORBEL Pilot courses and staff exchange provided

Author(s): Matser, Vera; Battaglia, Serena; Amaral, Ana Margarida
Published in: 2017
Publisher: zenodo
DOI: 10.5281/zenodo.1044176

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

Author(s): Segura, Joan; Sanchez-Garcia, Ruben; Martinez, Marta; Cuenca-Alba, Jesus; Tabas-Madrid, Daniel; Sorzano, C.O.S; Carazo, JM
Published in: 2017
Publisher: Zenodo

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

Author(s): Carazo, J M
Published in: 2017
Publisher: Zenodo
DOI: 10.5281/zenodo.1026294

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

Author(s): Zacherl, Nikolaus; Zatloukal, Kurt
Published in: 2017
Publisher: Zenodo
DOI: 10.5281/zenodo.1109265

CORBEL Concept paper on new business models related to Open Innovation

Author(s): Abuja, Peter M., Zatloukal, Kurt
Published in: 2018
Publisher: Zenodo
DOI: 10.5281/zenodo.1408808

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

Author(s): Mayrhofer, Michaela Th., Schlünder, Irene
Published in: 2018
Publisher: Zenodo
DOI: 10.5281/zenodo.1408804

CORBEL Report on conclusions from multi-stakeholder taskforce

Author(s): Serena Battaglia
Published in: 2017
Publisher: 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

Author(s): Rita Banzi, Steve Canham, Christian Ohmann, Wolfgang Kuchinke, Karmela Krleza-Jeric, Birol Tilki, Serena Battaglia, Jacques Demotes-Mainard
Published in: 2018
Publisher: Zenodo
DOI: 10.5281/zenodo.1438261

CORBEL Equal Opportunities Survey and Recommendations

Author(s): Asrar Ali Khan, Michael Raess
Published in: 2018
Publisher: Zenodo
DOI: 10.5281/zenodo.1441066

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

Author(s): Nick Juty, Carole Goble, Helen Parkinson, Simon Jupp
Published in: 2018
Publisher: Zenodo
DOI: 10.5281/zenodo.1441303

Federated Identity Management for Research Collaborations

Author(s): 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
Published in: 2018
Publisher: 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

Author(s): Leitner, Frauke; Popp, Christian; Vidal, Marie
Published in: 2019
Publisher: Zenodo
DOI: 10.5281/zenodo.2222358

CORBEL Delivery of Toolkit supporting community ontology mapping and development

Author(s): Jupp, Simon; Parkinson, Helen; Goble, Carol; Juty, Nick; Boiten, Jan-Willem; Swertz, Morris
Published in: 2019
Publisher: Zenodo
DOI: 10.5281/zenodo.2559160

CORBEL 3rd Medical Infrastructure user forum reporting

Author(s): Battaglia, Serena
Published in: 2019
Publisher: Zenodo
DOI: 10.5281/zenodo.2025791

CORBEL Strategy for enabling user access within pilot use cases

Author(s): Leither, Frauke; Vanmaele, Sofie; Stechmann, Bahne; Vidal, Marie
Published in: 2016
Publisher: zenodo
DOI: 10.5281/zenodo.154081

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

Author(s): Brooksbank, Cath; Pasterk, Markus
Published in: 2016
Publisher: 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

Author(s): Toernwall, Outi; van Ommen, Gertjan
Published in: 2016
Publisher: zenodo
DOI: 10.5281/zenodo.154076

CORBEL Communication Strategy based on stakeholder analysis

Author(s): Schuengel, Manuela
Published in: 2016
Publisher: zenodo
DOI: 10.5281/zenodo.154033

CORBEL Project-wide data management plan adopted

Author(s): Jenkinson, Andrew M.
Published in: 2016
Publisher: zenodo
DOI: 10.5281/zenodo.154022

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

Author(s): Battaglia, Serena
Published in: 2016
Publisher: zenodo
DOI: 10.5281/zenodo.154035

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

Author(s): Schluender, Irene; Cambon-Thomsen, Anne; Suhr, Stephanie (editor); Chassang, Gauthier; Mayrhofer, Michaela Th.
Published in: 2016
Publisher: zenodo
DOI: 10.5281/zenodo.154084

CORBEL Report on Common Access Framework Concept

Author(s): Haley, Natalie
Published in: 2019
Publisher: Zenodo
DOI: 10.5281/zenodo.2662134

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

Author(s): 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
Published in: 2019
Publisher: Zenodo
DOI: 10.5281/zenodo.3238496

CORBEL Industry Collaboration Best Practice Guide

Author(s): Abuja, Peter M.; Carapina, Tamara; de Kort, Martin; Raess, Michael; Tieken, Chris; Wagstaff, Nigel
Published in: 2019
Publisher: Zenodo
DOI: 10.5281/zenodo.2615364

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

Author(s): van Ommen, Gertjan
Published in: 2019
Publisher: 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

Author(s): Morris Swertz, Fleur Kelpin, David van Enckevort, Ilkka Lappalainen, Mikael Linden, Tommi Nyrönen, Petr Holub, Jan-Willem Boiten, Anna Leida Molder, Helen Parkinson
Published in: 2017
Publisher: Zenodo
DOI: 10.5281/zenodo.376279

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

Author(s): 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
Published in: 2017
Publisher: Zenodo
DOI: 10.5281/zenodo.376236

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

Author(s): Susan Daenke, Narayanan Krishnan
Published in: 2017
Publisher: Zenodo
DOI: 10.5281/zenodo.376187

CORBEL Report on final assessment and generalization of integration platform

Author(s): 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
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3628369

CORBEL Assessment of animal model phenotypes against outcome measures

Author(s): Nicola Harman; Adrian Sanz-Moreno; Patricia da Silva-Buttkus; Serena Battaglia
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3685932

CORBEL Report on user engagement activities

Author(s): 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
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3678774

CORBEL Sustainability plan for extended BMS RI Innovation Office

Author(s): Abuja, Peter M.; Carapina, Tamara; de Kort, Martin; Fauvel, Anne-Charlotte; Tieken, Chris; Ussi, Anton; Wagstaff, Nigel
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3663759

CORBEL Pilot courses and staff exchange provided (Summary)

Author(s): 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.
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3738191

CORBEL 4th Medical Infrastructure user forum reporting

Author(s): Battaglia, Serena
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3726777

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

Author(s): Glöckner, Frank Oliver; Kostadinov, Ivaylo; Cochrane, Guy
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3839957

BBMRI-ERIC ELSI Glossary

Author(s): Grewal, Jasjote; Mayrhofer, Michaela Th.
Published in: 2019
Publisher: Zenodo
DOI: 10.5281/zenodo.3754254

CORBEL Final Stakeholder Meeting

Author(s): Gaber, Sabrina; Battaglia, Serena; Schmidt-Tremmel, Friederike; Blomberg, Niklas
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3744802

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

Author(s): Haley, Natalie; Räß, Michael
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3859788

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

Author(s): Hansen, Sonja; Leitner, Frauke
Published in: 2020
Publisher: 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

Author(s): Hansen, Sonja; Leitner, Frauke
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3856040

CORBEL Sustainability Plan for extended BMS RI ELSI Services

Author(s): Mayrhofer, Michaela Th.; Grewal, Jasjote; Schlünder, Irene; Goisauf, Melanie; Akyüz, Kaya; Adeniran, Ayodeji
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3859796

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

Author(s): Lydall, Ben
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3862715

CORBEL Final report common infrastructures and services

Author(s): Schmidt-Tremmel, Friederike; Blomberg, Niklas
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3865548

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

Author(s): 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
Published in: 2017
Publisher: zenodo
DOI: 10.5281/zenodo.886494

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

Author(s): Boiten, Jan-Willem; Bierkens, Mariska; Hansson, Matthias; Klein, Stefan; Peelen, Sjaak
Published in: 2017
Publisher: zenodo
DOI: 10.5281/zenodo.886508

CORBEL 2nd Medical Infrastructure user forum reporting

Author(s): Battaglia, Serena
Published in: 2017
Publisher: zenodo
DOI: 10.5281/zenodo.825054

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

Author(s): Matser, Vera; Schuengel, Manuela
Published in: 2017
Publisher: zenodo
DOI: 10.5281/zenodo.841702

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

Author(s): Zatloukal, Kurt; Zacherl, Nikolaus; Schreiner, Christoph
Published in: 2017
Publisher: zenodo
DOI: 10.5281/zenodo.580056

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

Author(s): BBMRI-ERIC; EATRIS; ECRIN; ELIXIR; EMBRC; EMPHASIS; ERINHA; EU-OPENSCREEN; Euro-BioImaging; INFRAFRONTIER; Instruct; ISBE; MIRRI
Published in: 2017
Publisher: zenodo
DOI: 10.5281/zenodo.834332

Informed Consent Matrix for Clinical Trials

Author(s): 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
Published in: 2019
Publisher: Zenodo
DOI: 10.5281/zenodo.3928317

Non-repudiable provenance for clinical decision support systems

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

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

Author(s): Pieruschka, Roland
Published in: CORBEL User Meeting, Heidelberg, Germany, 2019-10-01 - 2019-10-02, 2019
Publisher: N/A

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: 2020
Publisher: 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

Author(s): Sarah L. Gorst, Bridget Young, Paula R. Williamson, John PH Wilding, Nicola Harman
Published in: SSRN Electronic Journal, 2019, ISSN 1556-5068
Publisher: ELSEVIER
DOI: 10.2139/ssrn.3234869

Searching for OpenAIRE data...

Deliverables

Publications

Share this page

Download