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HPC/Exascale Centre of Excellence in Personalised Medicine - PerMedCoE

Deliverables

Risk analysis mid-term report

List of identified risks prioritised and with adequate mitigation and contingency plans This Deliverable will also feed on WP5

Risk analysis final report

Final report on risks related to the PerMedCoE’s activity, including the list of identified risks and any actions implemented during the project

Final tools release

Final 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 cases

Based 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 cases

This 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 report

Interim 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 development

This 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 training

Final 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 ready

A 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 plans

Detailed 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 reports

The 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 release

Release 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 report

Final 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 report

We 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 functionalities

Final catalogue of building blocks and use case workflows.

Software best practices and optimisation final report

Final 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 release

Release 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 workflow

Report 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 plan

Report 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 infrastructure

Proposal 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 release

Release of all code developed with documentation and usecase tests contributed by UKHD

Second PerMed technology observatory release and benchmark report

We 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 report

We 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 and

Risk 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 engagement

Report 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 Report

Report 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 plan

This 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 engagement

First report on User communities identification and engagement

Project Handbook

Overview of the administrative procedures of the project to ensure efficient implementation and highquality delivery of results including a risk assessment and management strategy

Data Management Plan

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

Publications

Patient-specific Boolean models of signalling networks guide personalised treatments

Author(s): 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
Published in: Computational and Systems Biology, 2022, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.72626

Modeling the extracellular matrix in cell migration and morphogenesis: A guide for the curious biologist

Author(s): 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
Published in: Frontiers in Cell and Developmental Biology, Issue Volume 12 , 2024, 2024
Publisher: Frontiers
DOI: 10.3389/fcell.2024.1354132

PhysiBoss 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks

Author(s): Miguel Ponce-de-Leon, Arnau Montagud, Vincent Noël, Annika Meert, Gerard Pradas, Emmanuel Barillot, Laurence Calzone and Alfonso Valencia
Published in: NPJ Systems Biology and Applications, Issue V 9, article 54, Oct 30, 2023, 2023, ISSN 2056-7189
Publisher: Nature
DOI: 10.1038/s41540-023-00314-4

Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models

Author(s): St. Elmo Wilken; Mathieu Besançon; Miroslav Kratochvíl; Chilperic Armel Foko Kuate; Christophe Trefois; Wei Gu; Oliver Ebenhöh
Published in: Metabolic Engineering, Issue Volume 74, November 2022, 2022, Page(s) 72-82, ISSN 1096-7176
Publisher: Academic Press
DOI: 10.1101/2022.07.11.499575

WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically

Author(s): Vincent Noël, Marco Ruscone, Gautier Stoll, Eric Viara, Andrei Zinovyev, Emmanuel Barillot, Laurence Calzone
Published in: Frontiers in Molecular Biosciences, 2021, ISSN 2296-889X
Publisher: Frontiers
DOI: 10.3389/fmolb.2021.754444

Systems Biology at the giga-scale: large multi-scale models of complex, heterogeneous multicellular systems

Author(s): Arnau Montagud, Miguel Ponce de León, Alfonso Valencia
Published in: Current Opinion in Systems Biology Journal, Issue Volume 28, December 2021, 100385, 2021, ISSN 2452-3100
Publisher: Elsevier
DOI: 10.1016/j.coisb.2021.100385

Modeling signaling pathways in biology with MaBoSS: from one single cell to a dynamic population of heterogeneous interacting cells

Author(s): Laurence Calzone, Vincent Noël, Emmanuel Barillot, Guido Kroemer, Gautier Stoll
Published in: Computational and Structural Biotechnology Journal, 2022, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2022.10.003

COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

Author(s): 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
Published in: Molecular Systems Biology, 17(10):e10387. Nature Publishing Group, Issue 27, 2021, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202110387

Optimizing dosage-specific treatments in a multi-scale model of a tumor growth

Author(s): Miguel Ponce-de-Leon,Arnau Montagud, Charilaos Akasiadis, Janina Schreiber, Thaleia Ntiniakou and Alfonso Valencia
Published in: Systems Modeling: Approaches and Applications, 2022, ISSN 2296-889X
Publisher: Frontiers Media S.A.

Drug-Target identification in COVID-19 disease mechanisms using computational systems biology approaches

Author(s): Niarakis et al.
Published in: Frontiers in Immunology, Issue Vol 14, 13 February 2024, 2024, ISSN 1664-3224
Publisher: Frontiers in Immunology
DOI: 10.3389/fimmu.2023.1282859

COBREXA.jl: constraint-based reconstruction and exascale analysis

Author(s): 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
Published in: Bioinformatics, Issue Volume 38, Issue 4, 15 February 2022, 2021, Page(s) 1171–1172, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab782

Multiscale model of the different modes of cancer cell invasion

Author(s): Marco Ruscone; Arnau Montagud; Philippe Chavrier; Olivier Destaing; Isabelle Bonnet; Andrei Zinovyev; Emmanuel Barillot; Vincent Noël; Laurence Calzone
Published in: Bioinformatics, Issue Volume 39, Issue 6, June 2023, 2023, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.1101/2022.10.07.511296

UPMaBoSS: A Novel Framework for Dynamic Cell Population Modeling

Author(s): Gautier Stoll, Aurélien Naldi, Vincent Noël, Eric Viara, Emmanuel Barillot, Guido Kroemer, Denis Thieffry, Laurence Calzone
Published in: Frontiers in Molecular Biosciences, Issue Vol 9, 02 March 2022, 2022, ISSN 2296-889X
Publisher: Frontiers
DOI: 10.3389/fmolb.2022.800152

BioFVM-X: an MPI+OpenMP 3-D simulator for biological systems

Author(s): Saxena, Gaurav; Ponce De Leon, Miguel; Montagud, Arnau; Vicente Dorca, David; Valencia, Alfonso
Published in: Part of the Lecture Notes in Computer Science book series (LNCS, volume 12881), Issue 1, 2021, ISBN 978-3-030-85633-5
Publisher: Springer
DOI: 10.1007/978-3-030-85633-5_18

Lessons learned from a Performance Analysis and Optimization of a multiscale cellular simulation

Author(s): Huebl, Axel / Silvano, Cristina / Robinson, Timothy / Clascà, Marc / Garcia-Gasulla, Marta / Montagud, Arnau / Caballero, José / Valencia, Alfonso
Published in: PASC '23: Platform for Advanced Scientific Computing ConferenceProceedings of the Platform for Advanced Scientific Computing Conference, Issue Article 4, 26 June 2023, 2023, ISBN 979-8-4007-0190-0
Publisher: ACM Digital Library
DOI: 10.1145/3592979.3593403

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