CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.
I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .
Risultati finali
List of identified risks prioritised and with adequate mitigation and contingency plans This Deliverable will also feed on WP5
Risk analysis final reportFinal report on risks related to the PerMedCoE’s activity, including the list of identified risks and any actions implemented during the project
Final tools releaseFinal public release of all code developed, with documentation, use-case tests, and benchmark reports. UNILU will significantly contribute to this report
Data protection impact assessment of use casesBased on D38 D32 and in close exchange with WP51 a data protection impact assessment DPIA will be made The exact timing will depend on input from WP5 as well as the partners In any case they will be done before the processing of the respective data in the use cases will be done
Guidelines for using exascale methods/software on the medical/healthcare use casesThis report will consist of a set of guidelines with a focus on privacy aspects of the softwareworkflows to enable processing of sensitive data in a GDPR compliant way privacy by design and default and provision of the necessary information for external users to entrust the CoE with their data Where the CoE acts only as processor rather than as joint controller the controller using the services can require a lengthy description and justification of the privacypreserving measures in place A template for information provision to enable compliance with Art 28 GDPR will also be developed
Software best practices and optimisation interim reportInterim report on software best practices that have been implemented into the core applications optimisation process including a revised roadmap of software scalability and extension processes It will also report on the iterative process followed in collaboration with POP and preliminary results on efficiencies
Roadmap of software scalability to pre-exascale, extension processes and best practices for software developmentThis deliverable will merge three different milestones 1 The roadmap for each of the core applications with details on the sections to be refactored for preexascale architectures and use cases 2 The roadmap specifying the extensions processes of the core applications and their impact on their functionality interoperability and usability 3 A report on software best practices that will be implemented in our software developments and 4 Annual report on POP forensics results on the core applications prior to optimisation IC will significantly contribute to this report
Final report on trainingFinal deliverable report on user training, including the evaluation and impact assessment of conducted training.
Derivation of general guidelines on data protection and privacy preservation of a use-case independent method/software development that will be exascale readyA document that generalizes the findings identified from the use-case specific guidelines and formulate a set of generic ones aiming to be applied to any software that will run on exascale platforms.
Use case work plansDetailed work plans for the use cases including the collaboration with domain experts organised communities and coordination with other CoEs for the use of some of their developments such as with BioExcel and Use Case 2 It will include the definition of requirements to have use cases run in a preexascale environment The appropriate ethics clearance steps that will be taken towards data usage in the project if needed will also be provided
Use case progress reportsThe detailed work plans from D31 will be updated with information from D11 and D21 and new work plans will be designed if required It will also include a benchmark report of running use cases Any ethics clearance documentation required to use the data will also be reported
Midterm code releaseRelease of the current catalogue of building blocks usecase workflows and infrastructure tooling including the exploration of ML techniques following software best practices and recommendations D11 It will also include the roadmaps and design choices made during year 1 and their implementation
Use case final progress reportFinal report on the work performed on the different use cases of the PerMed CoE. All the ethics clearance documentation required to use the data and steps taken to grant it will also be reported.
First PerMed technology observatory release and benchmark reportWe will gather a first annual report on new software algorithms and standards in the PerMed area that are relevant for the PerMedCoE This release will include preliminary results for the benchmarks of the applications in the PerMed technology observatory against the core applications which are already optimised by month 12 in a dedicated webpage publicly accessible
Catalogue of functionalitiesFinal catalogue of building blocks and use case workflows.
Software best practices and optimisation final reportFinal report on software best practices that have been implemented into the core applications optimisation process, including a roadmap for potential future developments. It will also report on lessons learned from the iterative process followed in collaboration with POP and final results on pre-exascale-optimised core applications efficiencies.
Infrastructure code releaseRelease of the code to the infrastructure and the usability tools (interfaces). Include report about the compliance of the final product with the objectives of the WP. ATOS will significantly contribute to this report.
Report on Pilot workflowReport on progress made enacting the pilot workflow across de infrastructure, exemplifying progress on hybrid pre-exascale architecture deployment, data mobilisation, intelligent orchestration, etc.
Training needs analysis and training planReport outlining the strategy to address the training needs of stakeholders including preliminary planned user training It will include a competency profile user profiles and needs analysis
Pilot workflow to test infrastructureProposal of exemplary workflow incorporating a representative selection of building blocks that can be used to drive the development of the workflow enactment infrastructure
Mid-term tools releaseRelease of all code developed with documentation and usecase tests contributed by UKHD
Second PerMed technology observatory release and benchmark reportWe will gather a second annual report on new software, algorithms and standards in the PerMed area that are relevant for the PerMedCoE. This release will include results for the benchmarks of the applications in the PerMed technology observatory against the core applications optimised by month 24 in a dedicated public webpage
Final PerMed technology observatory release and benchmark reportWe will gather a final report on software, algorithms in the area of interest of the CoE. This release will include final results for the benchmarks of the applications in the PerMed technology observatory in a dedicated webpage publicly accessible.
Report on recommendations based on risk analysis of guidelines on data protection and privacy preservation, addressing a broader scope and further optimised or developed methods andRisk analysis matrix of a broader and open set-up of future applications. A report on recommendations which are based on the risk analysis of guidelines on data protection and privacy preservation, aiming to address a broader scope and further optimized/developed methods/software will be compiled
Final report on Dissemination, communication and industry engagementReport on all outreach and dissemination activities undertaken from M19 to M36, including a final user event attached to an existing conference. ATOS will significantly contribute to this report
First Dissemination, industry engagement and Training ReportReport on all dissemination engagement and training activities undertaken M1 to M18 including updated dissemination industry engagement and training plans for the second half of the project with significant contributions from BSC and ATOS and updated KPIs
Dissemination communication and industry engagement planThis deliverable will detail the activities to be undertaken as part of an overall project communication strategy and will provide guidance to ensure that all communication activities reflect the projects identity events scientific publications etc as well as detail the roadmap for industry engagement for implementation during the project lifetime A stakeholder map including pain points will be included with significant contributions from ATOS
First report on User communities' identification and engagementFirst report on User communities identification and engagement
Project HandbookOverview of the administrative procedures of the project to ensure efficient implementation and highquality delivery of results including a risk assessment and management strategy
The data management plan for the use cases to organise the efficient curation preservation and provision of access to data collected or produced under the project and the plans for the management of the softwareservice outcomes of the Joint Research Activities of the project It will include policies defined in T23 in terms of security and archiving with regards to file transfer schemas
Pubblicazioni
Autori:
Arnau Montagud, Jonas Béal, Luis Tobalina, Pauline Traynard, Vigneshwari Subramanian, Bence Szalai, Róbert Alföldi, László Puskás, Alfonso Valencia, Emmanuel Barillot, Julio Saez-Rodriguez, Laurence Calzone
Pubblicato in:
Computational and Systems Biology, 2022, ISSN 2050-084X
Editore:
eLife Sciences Publications
DOI:
10.7554/elife.72626
Autori:
Rebecca M. Crossley, Samuel Johnson, Erika Tsingos, Zoe Bell, Massimiliano Berardi, Margherita Botticelli, Quirine J. S. Braat, John Metzcar, Marco Ruscone, Yuan Yin, and Robyn Shuttleworth
Pubblicato in:
Frontiers in Cell and Developmental Biology, Numero Volume 12 , 2024, 2024
Editore:
Frontiers
DOI:
10.3389/fcell.2024.1354132
Autori:
Miguel Ponce-de-Leon, Arnau Montagud, Vincent Noël, Annika Meert, Gerard Pradas, Emmanuel Barillot, Laurence Calzone and Alfonso Valencia
Pubblicato in:
NPJ Systems Biology and Applications, Numero V 9, article 54, Oct 30, 2023, 2023, ISSN 2056-7189
Editore:
Nature
DOI:
10.1038/s41540-023-00314-4
Autori:
St. Elmo Wilken; Mathieu Besançon; Miroslav Kratochvíl; Chilperic Armel Foko Kuate; Christophe Trefois; Wei Gu; Oliver Ebenhöh
Pubblicato in:
Metabolic Engineering, Numero Volume 74, November 2022, 2022, Pagina/e 72-82, ISSN 1096-7176
Editore:
Academic Press
DOI:
10.1101/2022.07.11.499575
Autori:
Vincent Noël, Marco Ruscone, Gautier Stoll, Eric Viara, Andrei Zinovyev, Emmanuel Barillot, Laurence Calzone
Pubblicato in:
Frontiers in Molecular Biosciences, 2021, ISSN 2296-889X
Editore:
Frontiers
DOI:
10.3389/fmolb.2021.754444
Autori:
Arnau Montagud, Miguel Ponce de León, Alfonso Valencia
Pubblicato in:
Current Opinion in Systems Biology Journal, Numero Volume 28, December 2021, 100385, 2021, ISSN 2452-3100
Editore:
Elsevier
DOI:
10.1016/j.coisb.2021.100385
Autori:
Laurence Calzone, Vincent Noël, Emmanuel Barillot, Guido Kroemer, Gautier Stoll
Pubblicato in:
Computational and Structural Biotechnology Journal, 2022, ISSN 2001-0370
Editore:
Elsevier
DOI:
10.1016/j.csbj.2022.10.003
Autori:
Marek Ostaszewski; Anna Niarakis; Anna Niarakis; Alexander Mazein; Inna Kuperstein; Inna Kuperstein; Robert Phair; Aurelio Orta-Resendiz; Vidisha Singh; Sara Sadat Aghamiri; Marcio Luis Acencio; Enrico Glaab; Andreas Ruepp; Gisela Fobo; Corinna Montrone; Barbara Brauner; Goar Frishman; Luis Cristobal Monraz Gomez; Luis Cristobal Monraz Gomez; Julia Somers; Matti Hoch; Shailendra K. Gupta; Julia Sc
Pubblicato in:
Molecular Systems Biology, 17(10):e10387. Nature Publishing Group, Numero 27, 2021, ISSN 1744-4292
Editore:
Nature Publishing Group
DOI:
10.15252/msb.202110387
Autori:
Miguel Ponce-de-Leon,Arnau Montagud, Charilaos Akasiadis, Janina Schreiber, Thaleia Ntiniakou and Alfonso Valencia
Pubblicato in:
Systems Modeling: Approaches and Applications, 2022, ISSN 2296-889X
Editore:
Frontiers Media S.A.
Autori:
Niarakis et al.
Pubblicato in:
Frontiers in Immunology, Numero Vol 14, 13 February 2024, 2024, ISSN 1664-3224
Editore:
Frontiers in Immunology
DOI:
10.3389/fimmu.2023.1282859
Autori:
Miroslav Kratochvíl, Laurent Heirendt, St Elmo Wilken, Taneli Pusa, Sylvain Arreckx, Alberto Noronha, Marvin van Aalst, Venkata P Satagopam, Oliver Ebenhöh, Reinhard Schneider, Christophe Trefois, Wei Gu
Pubblicato in:
Bioinformatics, Numero Volume 38, Numero 4, 15 February 2022, 2021, Pagina/e 1171–1172, ISSN 1367-4803
Editore:
Oxford University Press
DOI:
10.1093/bioinformatics/btab782
Autori:
Marco Ruscone; Arnau Montagud; Philippe Chavrier; Olivier Destaing; Isabelle Bonnet; Andrei Zinovyev; Emmanuel Barillot; Vincent Noël; Laurence Calzone
Pubblicato in:
Bioinformatics, Numero Volume 39, Numero 6, June 2023, 2023, ISSN 1367-4811
Editore:
Oxford University Press
DOI:
10.1101/2022.10.07.511296
Autori:
Gautier Stoll, Aurélien Naldi, Vincent Noël, Eric Viara, Emmanuel Barillot, Guido Kroemer, Denis Thieffry, Laurence Calzone
Pubblicato in:
Frontiers in Molecular Biosciences, Numero Vol 9, 02 March 2022, 2022, ISSN 2296-889X
Editore:
Frontiers
DOI:
10.3389/fmolb.2022.800152
Autori:
Saxena, Gaurav; Ponce De Leon, Miguel; Montagud, Arnau; Vicente Dorca, David; Valencia, Alfonso
Pubblicato in:
Part of the Lecture Notes in Computer Science book series (LNCS, volume 12881), Numero 1, 2021, ISBN 978-3-030-85633-5
Editore:
Springer
DOI:
10.1007/978-3-030-85633-5_18
Autori:
Huebl, Axel / Silvano, Cristina / Robinson, Timothy / Clascà, Marc / Garcia-Gasulla, Marta / Montagud, Arnau / Caballero, José / Valencia, Alfonso
Pubblicato in:
PASC '23: Platform for Advanced Scientific Computing ConferenceProceedings of the Platform for Advanced Scientific Computing Conference, Numero Article 4, 26 June 2023, 2023, ISBN 979-8-4007-0190-0
Editore:
ACM Digital Library
DOI:
10.1145/3592979.3593403
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