Week 1 – BUILDING IMMUNE DIGITAL TWINS
*Monday 15 May 2023*
09:00 Introduction to the workshop by the organizers, Anna Niarakis and Reinhard Laubenbacher
10:00 Is the time right for building IDTs?- R. Laubenbacher, University of Florida
10:45 Discussion with the keynote speaker
11:00 Coffee Break
11:15 Executable biology – Applications, challenges and state of the art (Jasmin Fisher, PhD, UCL, UK)
12:00 Discussion with the keynote speaker
12:15 Lunch break
14:00 How do we imagine IDTs? What would be the most promising IDT applications? How far are we? Is an executable human Immune system feasible?Challenges of the human Immune System - what can we model? What can we measure? What would be an ideal IDT? Chairwoman Anna Niarakis, Discussion panel: Jasmin Fisher UCL Yaron Ilan University of Jerousalem Nicolas Gaudenzio Genoskin Gary An University of Vermont Larner College of Medicine Franck Augé, Sanofi
15:30 Coffee break
16:00 Open discussion with all participants and closing remarks of the first day
16:45 Feedback from the students’ group taking notes of the day
17:00 Happy hour + poster session
Tuesday 16 May 2023
09:00 Coffee
09:30 Coordination with the students’ teams
10:00 James Glazier - TBA
10:45 Discussion with the keynote speaker
11:00 Coffee Break
11:15 Gaetane Nocturne, MD, PhD MCU-PH, Hopitaux Universitaires Paris-Sud: Autoimmunity - when the immune system targets itself
12:00 Discussion with the keynote speaker
12:15 Lunch break
14:00 Nicola Gaudenzio - Predicting injectable drugs immunogenicity using Genoskin data generation platforms.
14:30 Q&A
15:00 Networking
16:00 The Genopole Biocluster - Christophe Lanneau
16:40 Discussion with the speaker
17:00 Transfert
18:00 Genopole social event - visit and buffet
21:00 Back to the hotels
Wednesday 17 May 2023
09:00 Coffee
09:30 Coordination with the students’ teams
10:00 Yaron Ilan University of Jerusalem - Enhancing digital twin accuracy with biological noise
10:45 Discussion with the keynote speaker
11:00 Coffee Break
11:15 Mustafa Kammash, ETH Zurich - Novel Approaches for Controlling Human System-Level Responses and the Role of Models
12:00 Discussion with the keynote speaker
12:15 Lunch break
14:00 François Fages, Lifeware, INRIA Saclay - Algorithms of life
14:20 Q&A
14:30 Kitware presentation - Brian Helba
14:50 Q&A
15:00 Coffee break
15:15 Discussion panel: Challenges of modelling and controling the immune system - do we need new maths? new methods? Chairman: Reinhard Laubenbacher, discussion panel James Glazier, University of Indiana Mustafa Khammash, ETH Zurich Brian Helba, Kitware François Fages, INRIA Saclay Lorenzo Veschini King’s College London
16:30 Coffee break
16:45 Wrap up of the day -Feedback from the students’ group taking notes of the day
17:00 End
19:00 Social event – dinner
Thursday 18 May 2023
09:00 Coffee
09:30 Coordination with the students’ teams
10:00 Emmanuel Barillot, Andrei Zinovyev - Institut Curie, France -Evotec- IDTs in oncology
10:45 Discussion with the keynote speaker
11:00 Coffee Break
11:15 Anabelle Balesta, INSERM and Institut Curie - Chronobiology and cancer
12:00 Discussion with the keynote speaker
12:15 Lunch break
14:00 Asmund Flobak, NTNU - Personalized and precision medicine
14:45 Discussion with the keynote speaker
15:00 Coffee break
15:15 Discussion panel: Can we envision IDTs in the clinic? How far are we? What needs to be done to move forward faster? Chairman: François Fages Emmanuel Barillot, Institut Curie, France Annabelle Balesta, INSERM and Institut Curie Asmund Flobak, NTNU Mustafa Khammash, ETH Zurich Andrei Zinovyev, Evotec
16:30 Coffee break
16:45 Wrap up of the day -Feedback from the students’ group taking notes of the day
17:00 Group Photo
Friday 19 May 2023
09:00 Coffee
09:30 Coordination with the students’ teams
10:00 Crowdsourcing examples: The COVID 19 Disease Map initiative - Can we crowdsource the mapping of the Human Immune System? Anna Niarakis, University of Evry Paris Saclay & INRIA Saclay
10:45 Discussion with the speaker
11:00 Coffee Break
11:15 REACTOME and BioModels resources - Rahuman Sheriff
12:00 Discussion with the speaker
12:15 Lunch break
14:00 Brief project presentations and break out sessions Projects/ use cases: Rheumatoid Arthritis Infectious pneumonia Cancer Inflammation Sepsis Break out sessions - Generic Immune Digital Twin Breakout session 1 - Conceptual design of the Human Immune System Breakout session 2 - Designing an IDT system (on/ off, multiscale, federated, mechanistic, AI, wearable etc) Breakout session 3 - What is required to parametrize, validate and personalize an IDT? Breakout session 4 - What are the needed infrastructure and resources to build an IDT? Breakout session 5 - What are the existing resources that we could use to accelerate the IDT building?
15.00 Coffee break
15:15 Working Groups: projects, proceedings, conceptual work (mind maps)
16:45 Wrap up of the day
17:00 End
Week 2 – BUILDING IMMUNE DIGITAL TWINS
Monday 22 May 2023
09:00 Coffee
09:30 Gary An, University of Vermont - Modelling Sepsis and the Immune System response
10:15 Coffee Break
10:30 Julio Saez Rodriguez - Combining omics and prior knowledge to help us building IDTs
11:15 Discussion with the speakers
12:00 Lunch break
14:00 Vassili Soumelis, Owkin -Systems immunology for mechanistic studies and target discovery
14:45 Q&A
15:00 Coffee break
15:30 Innovation in academia and private sector - How can we work together to accelerate building IDTs and bringing them to the clinics and decision-making? Chairman: Gary An Discussion panel: Vassili Soumelis, Owkin Julio Saez Rodriguez - Heidelberg University Serkawt Khola, EvoPlexus Medics Alexander Kulesza, Novadiscovery
16:30 Coffee break
16:45 Wrap up of the day -Feedback from the students’ group taking notes of the day
17:00 End
Tuesday 23 May 2023
09:00 Coffee
09:30 Coordination with the students’ teams
10:00 Tomas Helikar - Digital Twin Innovation Hub: Towards a General Purpose Immune Digital Twin
10:45 Discussion with the speaker
11:00 Coffee Break
11:15 Irene Vignon Clementel, INRIA Saclay - Mathematical models for simulations of human biological processes - challenges and state of the art
12:00 Q&A
12:15 Lunch break
14:00 Discussion panel: Data integration and translational medicine - how can we contextualize/ personalize the models? What type of data? What amount of data? Which computational capacities? Chair: Markus Rehberg, Sanofi Germany Arnau Montagud, Barcelona Supercomputing Center (BSC), Spain Laurence Calzone, Institut Curie Tomas Helikar, Nebraska Lincoln Irene Vignon Clementel
15:00 Coffee break
15:15 Alexander Kulesza/ Shiny Martis - Novadiscovery Exploring virtual twins and developing in silico clinical trials on Jinkō
16:00 Discussion with the speaker
16:15 Coffee break
16:30 Working groups
18:00 End
19:00 Social event – dinner
Wednesday 24 May 2023
09:00 Coffee
09:30 Yves Balkanski, IPa Deputy Director - presentation of the Institute Pascal
10:00 Coffee break
10:15 Working Groups
11:00 Laurence Calzone - Gautier Stoll: MaBoSS, PopMaBoSS
12:00 Q&A
12:15 Lunch break
14:00 Vincent Noel - Arnau Montagud: PhysiBoSS, use of multiscale modeling tools in biomedical projects
15:00 Coffee break + Meet the speakers: Informal discussion on modeling the human immune system
16:45 Wrap up of the day
17:00 Happy hour + poster session
Thursday 25 May 2023
09:00 Coffee
09:15 Working Groups
10:45 Coffee break
11:00 Anna Niarakis - Sylvain Soliman: Automated Inference of Boolean Networks
12:00 Q&A
12:15 Lunch break
14:00 Pedro Monteiro, University of Lisbon - The CoLoMoTo notebook
15:00 Q&A
15:15 Coffee break
15:30 Tomas Helikar Cell Collective
16:00 Q&A
16:15 Coffee break + Meet the speakers: Informal discussion on modelling the human immune system
16:45 Wrap up of the day
17:00 Michael Blinov-Simulation and analysis of biochemical networks and their dynamics-COPASI, VCell and rule-based
18:00 End
Friday 26 May 2023
09:00 Coffee
09:15 Working Groups : projects, proceedings, conceptual work (mind maps)
10:15 Brian Helba-KITWARE Europe
10:45 Coffee break
11:00 TJ Sego - CompuCell3D
11:45 Discussion with the speaker
12:00 Break
14:00 EvoPlexus Medics - Serkawt Khola
15:00 Q&A
15:15 Coffee break
15:30 Working Groups : projects, proceedings, conceptual work (mind maps) Presentations of the working groups
16:45 Wrap up of the day
17:30 End
Week 3 – BUILDING IMMUNE DIGITAL TWINS
Monday 29 May 2023
09:00 Coffee
09:30 Selected presentations from participants :
Eirini Tsirvouli
Leonard Harris
Michael Blinov
Francesco Messina
10:45 Coffee break
11:00 Maria Rodriguez Martinez - ML models of the immune system
11:45 Discussion with the speaker
12:00 Lunch break
14:00 Drafting of the paper – working groups
14:45 Coffee break
15:00 Benjamin Hall, UCL (remote) - Modelling cancer phenotype determination and evolution with BioModelAnalyzer
16:00 Working Groups : projects, proceedings, conceptual work (mind maps)
18:00 End
Tuesday 30 May 2023
09:00 Coffee
09:30 Kristin Reiche, How far away are we from virtual twins for patients treated with advanced therapy medicinal products?”
10:15 Discussion with the speaker
10h30 Coffee break
11:00 Dagmar Waltemath, Professor of medical informatics (MILA), University of Greifswald – Data stewardship: creating, preparing, using, storing, and archiving data for IDTs-remote
11:45 Discussion with the speaker
12:00 Lunch break
14:00 KITWARE presentation - Rachel Clipp
15:00 Coffee break
15:15 Selected presentations from participants
Sahar Aghakhani
Naouel Zerrouk
Sacha E Silva Saffar
Lorenzo Veschini
Niloofar Nikaein
16:15 Networking, drafting, working groups
18:00 End
19:00 Social dinner – Le gramophone
Wednesday 31 May 2023
09:00 Coffee – drafting
10:00 Liebet Gueris - EDITH: building the ecosystem for digital twins in healthcare
10:45 Coffee break
11:00 Groups presentations and brainstorming
12:15 Lunch break
14:00 Drafting the white paper
15:00 Coffee break + Networking + Group work
17:00 Happy hour + poster session
Thursday 01 June 2023
09:00 Coffee
09:30 Drafting the white paper
10:45 Coffee break
11:00 Drafting the white paper
12:15 Lunch break
14:00 Dirk Drasdo talk TBA
15:45 Q&A
16:00 Coffee break
16:15 Yves Balkanski talk-IPa Deputing Director-Scenarios And Uncertainty When Predicting Future Climate
Friday 02 June 2023
09:00 Coffee
09:30 Drafting the white paper
10:45 Coffee break
11:00 Drafting the white paper
12:15 Lunch break
14:00 Getting ready to go!!
