iiinova — where your digital self keeps evolving

Vincent Noël @vincent-noel.fr · 09/09/2026

📍 VI SysBioRio — Nov 3–6, UFRJ, Rio de Janeiro. Registration is open! I'll be talking about personalizing multiscale models with #PhysiBoSS — using bulk RNA-seq, scRNA-seq, and spatial transcriptomics data. More information 👉 www.even3.com.br/vi-sysbiorio...

even3.com.br

VI International Course on Theoretical and Applied Aspects of Systems Biology (VI SysBioRio)

VI International Course on Theoretical and Applied Aspects of Systems Biology (VI SysBioRio) - Centro Brasileiro de Pesquisas Físicas - terça-feira, 3 de novembro de 2026

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Vincent Noël @vincent-noel.fr · 16/03/2026

Nesta quarta-feira as 16h, eu terei a honra de apresentar meu trabalho sobre a construção de modelos multiescala num webinário da área de Física biológica, da Sociedade Brasileira de Física. Access through Zoom: us02web.zoom.us/j/8586171834... Or YouTube: www.youtube.com/live/1F63k3T...

youtube.com

Webinário da BIO - Construção de Modelos Multiescala para Biologia de Sistemas

YouTube video by Sociedade Brasileira de Física

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Computational System Biology of Cancer @sysbiocurie.bsky.social · 10/06/2025

Last week to register ! Don't miss this great opportunity

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Vincent Noël @vincent-noel.fr · 12/05/2025

Two PhD positions to work on important and cool topics. And to make it even better, with some very nice and good people.

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Computational System Biology of Cancer @sysbiocurie.bsky.social · 18/03/2025

We are welcoming applications to the 8th edition of the International Curie Course on Computational Systems Biology of Cancer, to be held in Paris, September 22-26, 2025. This year the focus will be on multimodal data analysis and network modelling to master cancer hallmarks. 👇 tinyurl.com/57d4ed2v

training.institut-curie.org

Computational Systems Biology of Cancer - 8th edition - Multimodal data analysis and network modelling to master cancer hallmarks | Institut Curie Advanced Training

The course will gather leading speakers from different fields in cancer systems biology, in cancer research and in clinics. The invited speakers will expose various approaches for omics, imaging, clin...

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Paul Macklin @mathcancer.bsky.social · 20/01/2025

PhysiCell 1.14.2 will release later this afternoon. Mostly bugfixes and minor refinements, but also exciting new work by Elmar Bucher prepping for a future "PhysiGym" addon for RL etc. Major thanks to @danielrbergman.bsky.social for numerous PRs! Watch @physicell.bsky.social for the release.

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Marco Ruscone @drmarcoruscone.bsky.social · 14/01/2025

At the #Hanami High Level Symposium, my friend and colleagues Adam Smelko is presenting our new @PhysiCell formulation that allows for stretchable cellular membrane! We are still working on this, but I hope we will be able to give you updates vero soon!

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PhysiCell Project. @physicell.bsky.social · 15/01/2025

A fun FYI: PhysiCell was first publicly presented in 2015, with first open source release in 2016. So let's call 2025 our 10th anniversary! 🧪

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Vincent Noël @vincent-noel.fr · 25/11/2024

Thanks a lot for the kind words Ashlee! Very happy that our tutorial is useful. And of course, we are always available to answer questions and happy to clarify any points!

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Scholar Goggler bot @scholargoggler.bsky.social · 17/11/2024

Some word clouds based on publications by @vincent-noel.fr. Popular topics: cell, models, signaling.

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Vincent Noël @vincent-noel.fr · 08/11/2024

Many thanks to Marco Ruscone and Laurence Calzone for all their work that went into this tutorial, and to Andrea Checcoli, @rheiland.bsky.social, Emmanuel Barillot, @mathcancer.bsky.social for helping us build, test, write, and review everything! Feedback welcome !

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Vincent Noël @vincent-noel.fr · 08/11/2024

To conclude, this tutorial shows that #PhysiBoSS modeling doesn't require C++ coding skills, and is now simpler thanks to #PhysiCell Studio (even for advanced users). We hope this work will help a larger community to get into the multiscale modeling world.

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Vincent Noël @vincent-noel.fr · 08/11/2024

Finally, we show a complete rewrite of @MRuscone cancer invasion model, removing most of the C++ code, and replacing it with the new mapping system. A larger scale, real-world example of how to use the latest #PhysiBoSS functionalities!

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Vincent Noël @vincent-noel.fr · 08/11/2024

Third example had to be an immune example, since this is the most important application for #PhysiBoSS! We describe DCs, attracted by the CCL21 gradient toward the lymph node. There, they activate naive T-cells which differentiate in TH1,TH17 and Tregs (model from Corral et al.).

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Vincent Noël @vincent-noel.fr · 08/11/2024

The second has been one of our goals with #PhysiBoSS for a long time: a signaling-controlled cell cycle model. Using the #Boolean model from Sizek et al., we link the cyclins to the transitions of the phases of the cell cycle. With that, we can reproduce the effect of mutants!

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Vincent Noël @vincent-noel.fr · 08/11/2024

The first example is inspired by the TNF example of the original #PhysiBoSS. It shows how to quickly map a substrate concentration to a Boolean input, and an output to #PhysiCell's apoptosis and necrosis. It simulates long vs pulsatile treatment, necrotic core, and clonality!

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Vincent Noël @vincent-noel.fr · 08/11/2024

In this tutorial, the user only needs to use #PhysiCell studio to build, parametrize, simulate and explore the simulation results! We implemented full PhysiBoSS compatibility in the studio, so that you can add your signaling model, and explore the #Boolean state of every cell in the results !

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Vincent Noël @vincent-noel.fr · 08/11/2024

Our #PhysiBoSS tutorial is now available at Briefings in Bioinformatics: academic.oup.com/bib/article/.... Learn how to build #multiscale models with #Boolean intracellular signaling, without any code, using #PhysiCell Studio! Showing three simple examples, and an update of Ruscone's invasion model👇

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Paul Macklin @mathcancer.bsky.social · 16/10/2024

Congratulations to Cicely Macnamara, Robyn Shuttleworth, @vincent-noel.bsky.social, and Marco Ruscone for publishing PhysiMeSS in @gigabytejournal.bsky.social! A beautiful community contribution to the @physicell.bsky.social ecosystem! Tremendous work!! 🧪 gigabytejournal.com/articles/136

gigabytejournal.com

PhysiMeSS - a new physiCell addon for extracellular matrix modelling

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PhysiCell Project. @physicell.bsky.social · 16/09/2024

PhysiCell 1.14.0 is released! Key features include improved cell behavior grammar (including better phagocytosis, effector attack, and cell damage), better initialization, and more! 🧪 Release notes and downloads: github.com/MathCancer/P...

github.com

Release Version 1.14.0 · MathCancer/PhysiCell

PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D Multicellular Systems Versions: 1.14.0 - Release dates: 15 September 2024 - 1.14.0 : 15 September 2024 Overview: PhysiCell is a flex...

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Paul Macklin @mathcancer.bsky.social · 16/09/2024

PhysiCell is now on BlueSky! 🧪 bsky.app/profile/phys...

bsky.app

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Vincent Noël @vincent-noel.fr · 04/07/2024

Many thanks to Marco Ruscone and Laurence Calzone for all their work that went into this tutorial, and to Andrea Checcoli, Randy Heiland, Emmanuel Barillot, and @mathcancer.bsky.social for helping us build, test, write, and review everything! Feedback welcome !

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Vincent Noël @vincent-noel.fr · 04/07/2024

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Vincent Noël @vincent-noel.fr · 04/07/2024

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Vincent Noël @vincent-noel.fr · 04/07/2024

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Vincent Noël @vincent-noel.fr · 04/07/2024

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Vincent Noël @vincent-noel.fr · 04/07/2024

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Vincent Noël @vincent-noel.fr · 04/07/2024

Our #PhysiBoSS tutorial is finally available as a preprint: arxiv.org/abs/2406.18371! Learn how to build #multiscale models with #Boolean intracellular signaling, without any code, using #PhysiCell Studio. Showing 3 simple examples, and an update of @MRuscone invasion model 👇

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Anne Carpenter @drannecarpenter.bsky.social · 16/01/2024

Read our essay in Nat Cell Bio: "Bringing computation to biology by bridging the last mile" We argue to shift resources/rewards towards creating user-friendly software to bridge computation and biology - it yields huge returns! @shantanuxsingh.bsky.social Free author link: rdcu.be/dv82F

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Anaïs Baudot @anaisbaudot.bsky.social · 22/01/2024

Open #PhD position in the team! Modelling organoid digital twins to study muscle genetic diseases. With @eremy3 and in @centuri_ls interdisciplinary framework! centuri-livingsystems.org/phd2024-15/

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Vincent Noël @vincent-noel.fr · 06/01/2024

Final days for applying to the #systembiology course organised by @hallben.bsky.social and Anna Niarakis ! I'll be teaching #MaBoSS stuff there. Don't miss it !

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