Vincent Noël

Vincent Noël

@vincent-noel.fr

Computational Biologist at Institut Curie, visiting at the Faculty of Medicine of the University of São Paulo. Modeling and simulating biological systems with multiscale frameworks. #MaBoSS, #PhysiBoSS developer

606 followers822 following23 posts

Vincent Noël
@vincent-noel.fr

🏆 Poster/abstract deadline: Oct 15. The two best posters each win a full fee waiver to publish in npj Systems Biology and Applications. I'll be talking about personalizing multiscale models with PhysiBoSS (bulk RNA-seq, scRNA-seq, spatial transcriptomics).

Vincent Noël
@vincent-noel.fr

📍 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.brVI 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

Vincent Noël reposted

Paul Macklin
@mathcancer.bsky.social

Really excited to share our new @cellpress.bsky.social Cell paper with @fertiglab.bsky.social and colleagues. 1/n www.cell.com/cell/fulltex... @jktgfoundation.bsky.social @itcrtraining.bsky.social @smbmathbiology.bsky.social #mathbio #mathonco @mathonco.bsky.social @deniswirtz.bsky.social

cell.comHuman interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratoriesWe developed a plain text modeling language—a cell behavior hypothesis grammar—to easily build virtual cell models and connect them to data, helping scientists to unlock the hidden dynamics of tissues...

Vincent Noël reposted

Computational System Biology of Cancer
@sysbiocurie.bsky.social

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

Computational System Biology of Cancer@sysbiocurie.bsky.social

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.orgComputational Systems Biology of Cancer - 8th edition - Multimodal data analysis and network modelling to master cancer hallmarks | Institut Curie Advanced TrainingThe 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...
Vincent Noël
@vincent-noel.fr

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

Arnau Montagud@arnaumontagud.bsky.social

📢 Exciting news! We will soon open two PhD positions at @i2sysbio.bsky.social @csic.es, in research projects in collaboration with the @bsc-cns.bsky.social. Both are related to tools to simulate biological tissues. Here’s the description of the open positions. #PhDpositions #PhDOpportunities 👇

Vincent Noël reposted

Computational System Biology of Cancer
@sysbiocurie.bsky.social

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

Vincent Noël reposted

Marco Ruscone
@drmarcoruscone.bsky.social

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!

Vincent Noël
@vincent-noel.fr

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!

Ashlee N. Ford Versypt@fordversyptlab.bsky.social

I'm so thankful for this post! I saw it just as two different collaborators were asking us to do things with our ABMs that we hadn't done before. Your tutorials and demos were so clear! Coupling with MaBoSS and PhysiCell Studio is also great and intuitive!

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Vincent Noël
@vincent-noel.fr

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

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.).

Vincent Noël
@vincent-noel.fr

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

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!

Vincent Noël
@vincent-noel.fr

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!

Vincent Noël
@vincent-noel.fr

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 !

Vincent Noël reposted

Paul Macklin
@mathcancer.bsky.social

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.comPhysiMeSS - a new physiCell addon for extracellular matrix modellingPhysiMeSS - a new physiCell addon for extracellular matrix modelling

Vincent Noël reposted

PhysiCell Project.
@physicell.bsky.social

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.comRelease Version 1.14.0 · MathCancer/PhysiCellPhysiCell: 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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Vincent Noël
@vincent-noel.fr

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.

View full thread
Vincent Noël
@vincent-noel.fr

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.).

Vincent Noël
@vincent-noel.fr

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!

Vincent Noël
@vincent-noel.fr

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!

Vincent Noël
@vincent-noel.fr

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!

Vincent Noël
@vincent-noel.fr

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 !

Ben Hall@hallben.bsky.social

Applications are now open for our advanced course in #systemsbiology! We will cover developing logical and executable models for understanding human disease. keynotes by Henning Hermjakob, Julio Saez Rodriguez, and Jasmin Fisher! coursesandconferences.wellcomeconnectingscience.org/event/comput...

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