Livrables
First version of the OpenRiskNet APIs will be released to all partners of the consortium and associated partners for feedback and usage.
Report on deployment of virtual infrastructures with service discovery and container orchestrationKey components of OpenRiskNet e-infrastructure, including the live virtual instance for testing and the service discovery, will be online and documented in the report.
Fully functional support infrastructureSupport infrastructure will be fully functional and in operation.
Reference OpenRiskNet system available onlineThe reference OpenRiskNet instance will be fully operable and accessible to demonstrate the functionalities to new users. Additionally, all components will be available in containerized form for easy deployment.
Final API available for internal and external service providersFinal OpenRiskNet APIs will be released.
Development infrastructure onlineComputational infrastructure for the development and testing of the virtual environments, APIs and data and software integration will be completely set up.
Final report on the dissemination and training activities will be filed.
First report on the management processFirst report summarizing the management process will be filed.
Report of the Service Integration with OpenRiskNet (Final Report)This report will describe the status of the service integration including numbers of active services provided by the consortium, associated partners and other third parties.
Report on requirement analysis and recommendations for WP2-4 including Data Management PlanThe report will describe the results obtained from the interviews and interactions with associated partners and projects as part of the requirement analysis.
Final report on the management processFinal report summarizing the management process will be filed.
Report of the Service Integration with OpenRiskNet (Intermediate Report)This report will describe the status of the service integration including numbers of active services provided by the consortium, associated partners and other third parties.
Data management, maintenance and sustainability planFinal data management plan as well as maintenance and sustainability plan will be filed.
Report of the Service Integration with OpenRiskNet (Initial Deployment)This report will describe the status of the service integration including active services provided by the consortium, associated partners and other third parties.
First documentation of the core e-infrastructureFirst documentation of the core e-infrastructure with examples of prototype implementations will be delivered. This documentation will be updated throughout the project.
Report on Re-Identification Risks and Private by Design Risk ManagementThe report will cover possible risk with respect to security, privacy and re-identification of personal data as well as present the private by design risk management concept.
Report on the results of the Implementation ChallengeThis report will summarize the selected data sources and software tools identified by the implementation challenge to be supported by OpenRiskNet partners and the status of their implementation.
Dissemination & Training Activities (Intermediate Report)Intermediate report on the dissemination and training activities will be filed.
Initial version of the data management plan will been delivered.
Interoperability of data and software tools will be established and applied to the case studies.
Associated partner program is establishedRules for the associated partner program will be defined, formalized, legally approved and accepted by the consortium.
Final definition of case studiesCase studies for testing the usability of the infrastructure in state-of-the-art research will be defined.
Finalization of case studies and analysis of remaining weaknessesAll case studies will have been finalized and remaining challenges will be identified. Measures to solve these challenges, especially with respect to the regulatory usage of the workflows developed in the case studies will be outlined.
Publications
Auteurs:
Exner, Thomas; Dokler, Joh; Bachler, Daniel; Farcal, Lucian; Evelo, Chris; Willighagen, Egon; Jacobs, Marc; Doganis, Philip; Sarimveis, Haralambos; Lynch, Iseult; Kramer, Stefan; Notredame, Cedric; Jennen, Danyel; Gkoutos, Georgios; Spjuth, Ola; Jennings, Paul; Dudgeon, Tim; Bois, Frederic; Hardy, Barry
Publié dans:
SOT 2018 (Society of Toxicology 57th Annual Meeting and ToxExpo), Numéro 1, 2018
Éditeur:
Society of Toxicology
DOI:
10.5281/zenodo.1199286
Auteurs:
Exner, Thomas
Publié dans:
OpenTox USA, 2017
Éditeur:
OpenTox
DOI:
10.5281/zenodo.831444
Auteurs:
Thomas Exner
Publié dans:
OpenTox Euro 2017, 2017
Éditeur:
OpenTox
Auteurs:
Tim Dudgeon
Publié dans:
Nextflow workshop, 2017
Éditeur:
Centre for Genomic Regulation
Auteurs:
Thomas Exner
Publié dans:
OpenTox Euro 2017, 2017
Éditeur:
OpenTox
Auteurs:
Chris Evelo
Publié dans:
OpenTox Euro 2017, 2017
Éditeur:
OpenTox
Auteurs:
Iseult Lynch
Publié dans:
OpenTox Euro 2017, 2017
Éditeur:
OpenTox
Auteurs:
Marvin Martens, Chris Evelo, Egon Willighagen
Publié dans:
ByteMAL (Bioinformatics for Young inTernational researchers Expo: Maastricht-Aachen-Liège), 2017
Éditeur:
ByteMAL
Auteurs:
Marvin Martens
Publié dans:
OpenTox Euro 2017, 2017
Éditeur:
OpenTox
Auteurs:
Ola Spjuth
Publié dans:
COST-CHARME 'Big Data Training School for Life Sciences', 2017
Éditeur:
COST-CHARME
Auteurs:
Ola Spjuth
Publié dans:
2nd international de.NBI symposium, 2017
Éditeur:
German Network for Bioinformatics Infrastructure
Auteurs:
Philip Doganis, Georgia Tsiliki, Charalampos Chomenidis, Angelos Valsamis, George Drakakis, Evangelia Anagnostopoulou, Haralambos Sarimveis
Publié dans:
Open Science Fair 2017, 2017
Éditeur:
Open Science Fair
Auteurs:
Imane Boudellioua, Rozaimi B. Mahamad Razali, Maxat Kulmanov, Yasmeen Hashish, Vladimir B. Bajic, Eva Goncalves-Serra, Nadia Schoenmakers, Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf
Publié dans:
PLOS Computational Biology, Numéro 13/4, 2017, Page(s) e1005500, ISSN 1553-7358
Éditeur:
PLOS
DOI:
10.1371/journal.pcbi.1005500
Auteurs:
Maris Lapins, Staffan Arvidsson, Samuel Lampa, Arvid Berg, Wesley Schaal, Jonathan Alvarsson, Ola Spjuth
Publié dans:
Journal of Cheminformatics, Numéro 10/1, 2018, ISSN 1758-2946
Éditeur:
Chemistry Central
DOI:
10.1186/s13321-018-0271-1
Auteurs:
T.E. Exner, J. Dokler, D. Bachler, L.R. Farcal, C.T. Evelo, E. Willighagen, D.G.J. Jennen, M. Jabocs, P. Doganis, H. Sarimveis, I. Lynch, G. Gkoutos, S. Kramer, C. Notredame, O. Spjuth, P. Jennings, T. Dudgeon, F. Bois, B. Hardy
Publié dans:
Toxicology Letters, Numéro 295, 2018, Page(s) S104, ISSN 0378-4274
Éditeur:
Elsevier BV
DOI:
10.1016/j.toxlet.2018.06.617
Auteurs:
J.R. Bayjanov, J.C. Kleinjans, D.G.J. Jennen
Publié dans:
Toxicology Letters, Numéro 295, 2018, Page(s) S100-S101, ISSN 0378-4274
Éditeur:
Elsevier BV
DOI:
10.1016/j.toxlet.2018.06.608
Auteurs:
M. Martens, E. Willighagen, P. Nymark, R. Grafström, L.D. Burgoon, H.T. Aladjov, F. Torres Andón, C.T. Evelo
Publié dans:
Toxicology Letters, Numéro 295, 2018, Page(s) S227-S228, ISSN 0378-4274
Éditeur:
Elsevier BV
DOI:
10.1016/j.toxlet.2018.06.962
Auteurs:
Samuel Lampa, Jonathan Alvarsson, Staffan Arvidsson Mc Shane, Arvid Berg, Ernst Ahlberg, Ola Spjuth
Publié dans:
Frontiers in Pharmacology, Numéro 9, 2018, ISSN 1663-9812
Éditeur:
Frontiers Media S.A.
DOI:
10.3389/fphar.2018.01256
Auteurs:
Imane Boudellioua, Maxat Kulmanov, Paul N. Schofield, Georgios V. Gkoutos, Robert Hoehndorf
Publié dans:
Scientific Reports, Numéro 8/1, 2018, ISSN 2045-2322
Éditeur:
Nature Publishing Group
DOI:
10.1038/s41598-018-32876-3
Auteurs:
Boudellioua, Imane; Kulmanov, Maxat; Schofield, Paul N.; Gkoutos, Georgios V.; Hoehndorf, Robert
Publié dans:
BMC Bioinformatics, Vol 20, Iss 1, Pp 1-8 (2019), Numéro 4, 2019, ISSN 1471-2105
Éditeur:
BioMed Central
DOI:
10.17863/CAM.36763
Auteurs:
Dudgeon, Tim; Spjuth, Ola; Bois, Frederic; Bachler, Daniel
Publié dans:
Numéro 1, 2018
Éditeur:
OpenRiskNet
DOI:
10.5281/zenodo.1479138
Auteurs:
Jennings, Paul; Exner, Thomas; Farcal, Lucian; Oki, Noffisat; Sarimveis, Harry; Doganis, Philip; Jennen, Danyel; Geerke, Daan; Willighagen, Egon; Bois, Frederic; Rautenberg, Micha; Dudgeon, Tim; Hardy, Barry
Publié dans:
Numéro 1, 2018
Éditeur:
OpenRiskNet
DOI:
10.5281/zenodo.1479127
Auteurs:
Spjuth, Ola; Dudgeon, Tim; Bachler, Daniel; Gebele, Denis; Rautenberg, Micha; Alvarsson, Jonathan; Karatzas, Pantelis; Willighagen, Egon; Evelo, Chris; Martens, Marvin; Exner, Thomas
Publié dans:
Numéro 1, 2018
Éditeur:
OpenRiskNet
DOI:
10.5281/zenodo.1479475
Auteurs:
Doganis, Philip; Karatzas, Pantelis; Sarimveis, Harry; Dudgeon, Tim; Spjuth, Ola; Farcal, Lucian; Exner, Thomas; Lynch, Iseult; Hardy, Barry
Publié dans:
Numéro 2, 2018
Éditeur:
OpenRiskNet
DOI:
10.5281/zenodo.1479648
Auteurs:
Rautenberg, Micha; Karwath, Andreas; Kramer, Stefan; Dudgeon, Tim; Spjuth, Ola; Bachler, Daniel; Exner, Thomas; Dokler, Joh; Sarimveis, Haralambos; Valsamis, Angelos; Doganis, Philip; Willighagen, Egon; Bois, Frederic
Publié dans:
Numéro 3, 2018
Éditeur:
OpenRiskNet
DOI:
10.5281/zenodo.1479444
Auteurs:
Bachler, Daniel; Dokler, Joh; Dudgeon, Tim; Willighagen, Egon; Karatzas, Pantelis; Lynch, Iseult; Hardy, Barry; Exner, Thomas
Publié dans:
Numéro 2, 2019
Éditeur:
OpenRiskNet
DOI:
10.5281/zenodo.2597061
Auteurs:
Spjuth, Ola; Farcal, Lucian; Lynch, Iseult; Dudgeon, Tim; Exner, Thomas
Publié dans:
Numéro 2, 2018
Éditeur:
OpenRiskNet
DOI:
10.5281/zenodo.2558121
Auteurs:
Danyel, Jennen; Bayjanov, Jumamurat; Farcal, Lucian; Oki, Noffisat; Geerke, Daan; Doganis, Philip; Martens, Marvin; Willighagen, Egon; Gebele, Denis; Jacobs, Marc; Dudgeon, Tim; Lynch, Iseult; Exner, Thomas
Publié dans:
Numéro 5, 2018
Éditeur:
OpenRiskNet
DOI:
10.5281/zenodo.2596998
Auteurs:
Dudgeon, Tim; Christie, Alan; Bachler, Daniel; Farcal, Lucian; Sarimveis, Harry; Doganis, Philip; Karatzas, Pantelis; Spjuth, Ola; Lynch, Iseult; Hardy, Barry
Publié dans:
Numéro 1, 2018
Éditeur:
OpenRiskNet
DOI:
10.5281/zenodo.1483397
Auteurs:
Floden, Evan; Lloret-Villas, Audald; Di Tommaso, Paolo; Spjuth, Ola; Farcal, Lucian; Dudgeon, Tim; Jennen, Danyel
Publié dans:
Numéro 2, 2019
Éditeur:
OpenRiskNet
DOI:
10.5281/zenodo.3256306
Auteurs:
Farcal, Lucian; Florean, Oana; Doganis, Philip; Jennen, Danyel; Willighagen, Egon; Martens, Marvin; Bachler, Daniel; Oki, Noffisat; Exner, Thomas
Publié dans:
Numéro 1, 2018
Éditeur:
OpenRiskNet
DOI:
10.5281/zenodo.2558116
Auteurs:
Farcal, Lucian; Lynch, Iseult; Exner, Thomas
Publié dans:
Numéro 5, 2018
Éditeur:
OpenRiskNet
DOI:
10.5281/zenodo.2557741
Auteurs:
Jennen, Danyel; Dudgeon, Tim; Sarimveis, Haralambos; Doganis, Philip; Karatzas, Pantelis; Rautenberg, Micha; Willighagen, Egon; Exner, Thomas
Publié dans:
Numéro 2, 2018
Éditeur:
OpenRiskNet
DOI:
10.5281/zenodo.1484309
Auteurs:
Farcal , Lucian; Exner, Thomas; Hardy, Barry
Publié dans:
Numéro 5, 2018
Éditeur:
OpenRiskNet
DOI:
10.5281/zenodo.1484358
Auteurs:
Farcal, Lucian; Exner, Thomas
Publié dans:
Numéro 5, 2018
Éditeur:
OpenRiskNet
DOI:
10.5281/zenodo.1484319
Auteurs:
Farcal, Lucian; Bachler, Daniel; Dokler, Joh; Exner, Thomas
Publié dans:
Numéro 4, 2018
Éditeur:
OpenRiskNet
DOI:
10.5281/zenodo.2557731
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