Deliverables
Integrated multiomics tranSMART repository with available datasets within the iReceptor Plus platform
D1.7 Protocol Capstone workshopA handson workshop where potential users can test and interact with iReceptor Plus giving feedback and exploring how they might incorporate the platform into their workflow
D3.1 Holistic Security and Privacy Concept D2.6 iReceptor Plus Turnkey repository available for AIRR CommunityWorking documented and production iReceptor Plus Turnkey repository available for AIRR Community
D8.3 Project-specific innovation approach D4.3 Analysis tool mgt and vis UI impl, in Scientific Gateway D1.5 ImmuneDB releaseAdapt and incorporate the developments made through work packages WP2 through WP7 to enhance the capabilities of the ImmuneDB web interface
D4.5 Basic toolkit of advanced AIRR-seq analysis tools integratedBasic toolkit of advanced AIRRseq analysis tools integrated into the iReceptor Plus Platform
D3.3 Monitoring and GDPR AspectsMonitoring the changes in security and privacy developments and will carefully monitor latest research and industry developments
D3.4 Recommendations and proposals for new regulatory regimesecommendations will be made regarding improved legal regimes as to facilitate flexibility to a large audience and to facilitate wide adoption of project results while allowing rewarding those that invested Focus will be on a realistic regulatory solution
D9.1 Communication plan finalised D1.4 VDJServer releaseRelease of VDJServer a cloudbased analysis portal for AIRRseq data that provides access to a suite of tools for a complete analysis workflow
D10.1 Establishing governance structure D2.1 iReceptor Plus IPA repository interactively exploreiReceptor IPA repository that can interactively explore 100s of millions or billions of annotated sequences M36
D9.5 A final dissemination reportAt the end of the project M48 a dissemination report will be delivered
D1.1 Protocol Kick-off meeting D2.5 iReceptor Plus REST API available for platform integrationProduction version of iReceptor Plus REST API available for platform integration
D7.1 An updated MiAIRR standardAn updated MiAIRR standard containing a proper representation of singlecell AIRRseq data and a corresponding API supporting singlecell queries
D1.3 iReceptor Plus Gateway implementing use case scenariosImplementation of the iReceptor Scientific Gateway based on user feedback and the needs of the other work packages
D4.2 Tool integration methodology and implementation completed D5.1 A list of features that can be used for potential biomarkers D2.3 Data repositories from partner institutions (6) integratedData repositories from partner institutions 6 integrated into the AIRR Data Commons
D6.1 A multi-omic data model D2.2 iReceptor repositories able to link data related to single cell D7.3 Tool for automated import and annotation into iReceptor PlusA tool for automated import and annotation for flow cytometry data into iReceptor Plus
D9.6 Protocol Concluding ConferenceA concluding conference will be organised at the end of the project in Brussels to present the final results to key target audiences opinion leadersregulators researchers healthcare providers industry owners providers of data repositories the media and the general public A webinar will be recorded and made publicly available
D7.2 A generic single-cell data import toolkit for iReceptor Plus D5.2 S/W to apply ML approaches for classifying individualsSoftware to apply machine learning approaches for classifying individuals from different clinical cohorts
D1.2 Use cases identified and documented for developmentUse cases identified and documented for development and further iteration
D4.4 User interface release candidates for deploymentUser interface release candidates for deployment in Scientific Gateway
D8.2 Legal, ethics, privacy & security frameworkTo maximize the project impact partners will take all opportunities to disseminate and raise awareness of the project and encourage joining the AIRR Community
Creating communication tools required to support the successful implementation of the communication plan
D1.6 Intermediate beta release of platform wide system D5.3 Implementation of networks and AI-functionality iReceptorImplementation of networks and AI-functionality iReceptor for querying the AIRR space for biomarker signatures
D3.2 Layered Security FrameworkImplementation of a software framework that ensures that the FAIR principles of scientific data management and stewardship are attained, while the security of personal data is not compromised.
D6.2 Data curation and integration pipeline within tranSMARTData curation and integration pipeline within a tranSMART repository
D2.4 Integration testing completed across all repositoriesIntegration testing completed across all repositories in the AIRR Data Commons, Capstone Demonstration completed
D9.2 A project identity and specific project website D7.4 A version of iReceptor Plus that can be queried using (Kd)A version of iReceptor Plus that can be queried using target affinity (Kd) as search parameter
Publications
Author(s):
Pierre Barennes, Valentin Quiniou, Mikhail Shugay, Evgeniy S. Egorov, Alexey N. Davydov, Dmitriy M. Chudakov, Imran Uddin, Mazlina Ismail, Theres Oakes, Benny Chain, Anne Eugster, Karl Kashofer, Peter P. Rainer, Samuel Darko, Amy Ransier, Daniel C. Douek, David Klatzmann, Encarnita Mariotti-Ferrandiz
Published in:
Nature Biotechnology, 2020, ISSN 1087-0156
Publisher:
Nature Publishing Group
DOI:
10.1038/s41587-020-0656-3
Author(s):
Ivana Mikocziova, Moriah Gidoni, Ida Lindeman, Ayelet Peres, Omri Snir, Gur Yaari, Ludvig M Sollid
Published in:
Nucleic Acids Research, Issue 48/10, 2020, Page(s) 5499-5510, ISSN 0305-1048
Publisher:
Oxford University Press
DOI:
10.1093/nar/gkaa310
Author(s):
Kerui Peng, Yana Safonova, Mikhail Shugay, Alice B. Popejoy, Oscar L. Rodriguez, Felix Breden, Petter Brodin, Amanda M. Burkhardt, Carlos Bustamante, Van-Mai Cao-Lormeau, Martin M. Corcoran, Darragh Duffy, Macarena Fuentes-Guajardo, Ricardo Fujita, Victor Greiff, Vanessa D. Jönsson, Xiao Liu, Lluis Quintana-Murci, Maura Rossetti, Jianming Xie, Gur Yaari, Wei Zhang, Malak S. Abedalthagafi, Khalid
Published in:
Nature Methods, Issue 18/6, 2021, Page(s) 588-591, ISSN 1548-7091
Publisher:
Nature Publishing Group
DOI:
10.1038/s41592-021-01169-5
Author(s):
Or Shemesh, Pazit Polak, Knut E. A. Lundin, Ludvig M. Sollid, Gur Yaari
Published in:
Frontiers in Immunology, Issue 12, 2021, ISSN 1664-3224
Publisher:
Cold Spring Harbor Laboratory
DOI:
10.3389/fimmu.2021.627813
Author(s):
Andreas H. Laustsen, Victor Greiff, Aneesh Karatt-Vellatt, Serge Muyldermans, Timothy P. Jenkins
Published in:
Trends in Biotechnology, 2021, ISSN 0167-7799
Publisher:
Elsevier BV
DOI:
10.1016/j.tibtech.2021.03.003
Author(s):
Victor Greiff, Gur Yaari, Lindsay Cowell
Published in:
Current Opinion in Systems Biology, 2020, ISSN 2452-3100
Publisher:
Elsevier
DOI:
10.1016/j.coisb.2020.10.010
Author(s):
Simone Mester, Mitchell Evers, Saskia Meyer, Jeannette Nilsen, Victor Greiff, Inger Sandlie, Jeanette Leusen, Jan Terje Andersen
Published in:
mAbs, Issue 13/1, 2021, Page(s) 1893888, ISSN 1942-0870
Publisher:
Landes Bioscience
DOI:
10.1080/19420862.2021.1893888
Author(s):
Ayelet Peres, Moriah Gidoni, Pazit Polak, Gur Yaari
Published in:
Bioinformatics, Issue 35/22, 2019, Page(s) 4840-4842, ISSN 1367-4803
Publisher:
Oxford University Press
DOI:
10.1093/bioinformatics/btz481
Author(s):
Gur Yaari; William Lees; Adrian Shepherd
Published in:
Nucleic Acids Research, Issue 48, 2020, ISSN 0305-1048
Publisher:
Oxford University Press
DOI:
10.1093/nar/gkz872
Author(s):
Uri Alon, Osnat Mokryn, Uri Hershberg
Published in:
Frontiers in Immunology, Issue 12, 2021, ISSN 1664-3224
Publisher:
Frontiers in Immunology
DOI:
10.3389/fimmu.2021.642673
Author(s):
Rahmad Akbar, Philippe A. Robert, Milena Pavlović, Jeliazko R. Jeliazkov, Igor Snapkov, Andrei Slabodkin, Cédric R. Weber, Lonneke Scheffer, Enkelejda Miho, Ingrid Hobæk Haff, Dag Trygve Tryslew Haug, Fridtjof Lund-Johansen, Yana Safonova, Geir K. Sandve, Victor Greiff
Published in:
Cell Reports, Issue 34/11, 2021, Page(s) 108856, ISSN 2211-1247
Publisher:
Cell Press
DOI:
10.1016/j.celrep.2021.108856
Author(s):
Philippe A. Robert, Heike Kunze-Schumacher, Victor Greiff, Andreas Krueger
Published in:
Entropy, Issue 23/4, 2021, Page(s) 437, ISSN 1099-4300
Publisher:
Multidisciplinary Digital Publishing Institute (MDPI)
DOI:
10.3390/e23040437
Author(s):
Michael Widrich; Bernhard Schäfl; Hubert Ramsauer; Milena Pavlović; Lukas Gruber; Markus Holzleitner; Johannes Brandstetter; Geir Kjetil Sandve; Victor Greiff; Sepp Hochreiter; Günter Klambauer
Published in:
NeurIPS, Issue 8, 2020, ISBN 9780262561457
Publisher:
Neural Information Processing Systems
DOI:
10.1101/2020.04.12.038158
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