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vincent-noel.fr
Vincent Noël
@vincent-noel.fr
580 followers 810 following 18 posts
Research scientist in the Computational System Biology of Cancer team at Institut Curie, Visiting Scientist in São Paulo Modeling and simulating biological systems with multiscale frameworks. #MaBoSS, #PhysiBoSS developer
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vincent-noel.fr
Vincent Noël @vincent-noel.fr · Nov 8
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👇
2 7 25
Reposted by Vincent Noël
mathcancer.bsky.social
Paul Macklin @mathcancer.bsky.social · Jul 28
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
Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories
We 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...
www.cell.com
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Reposted by Vincent Noël
sysbiocurie.bsky.social
Computational System Biology of Cancer @sysbiocurie.bsky.social · Jun 10
Last week to register ! Don't miss this great opportunity
sysbiocurie.bsky.social
Computational System Biology of Cancer @sysbiocurie.bsky.social · Mar 18
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
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...
training.institut-curie.org
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vincent-noel.fr
Vincent Noël @vincent-noel.fr · May 12
Two PhD positions to work on important and cool topics. And to make it even better, with some very nice and good people.
arnaumontagud.bsky.social
Arnau Montagud @arnaumontagud.bsky.social · May 6
📢 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
👇
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Reposted by Vincent Noël
sysbiocurie.bsky.social
Computational System Biology of Cancer @sysbiocurie.bsky.social · Mar 18
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
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...
training.institut-curie.org
2 2
Reposted by Vincent Noël
mathcancer.bsky.social
Paul Macklin @mathcancer.bsky.social · Jan 20
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.
1 7 11
Reposted by Vincent Noël
drmarcoruscone.bsky.social
Marco Ruscone @drmarcoruscone.bsky.social · Jan 14
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!
2 6 11
Reposted by Vincent Noël
physicell.bsky.social
PhysiCell Project. @physicell.bsky.social · Jan 15
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! 🧪
1 6 10
vincent-noel.fr
Vincent Noël @vincent-noel.fr · Nov 25
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!
fordversyptlab.bsky.social
Ashlee N. Ford Versypt @fordversyptlab.bsky.social · Nov 25
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!
2
Reposted by Vincent Noël
scholargoggler.bsky.social
Scholar Goggler bot @scholargoggler.bsky.social · Nov 17
Some word clouds based on publications by @vincent-noel.fr. Popular topics: cell, models, signaling.
Cloud of words in various colors and sizes based on a Google Scholar profile. Some of the largest words include cell models boolean networks signaling cycle modeling biology cells hybrid pathways biochemical cancer computational dynamic dynamical framework population rasmapk adrenocortical analysis application designing heterogeneous insights interacting k-ras-driven kinetic logical maboss
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vincent-noel.fr
Vincent Noël @vincent-noel.fr · Nov 8
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-noel.fr
Vincent Noël @vincent-noel.fr · Nov 8
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.
1 6
vincent-noel.fr
Vincent Noël @vincent-noel.fr · Nov 8
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!
1 3
vincent-noel.fr
Vincent Noël @vincent-noel.fr · Nov 8
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-noel.fr
Vincent Noël @vincent-noel.fr · Nov 8
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!
1 3
vincent-noel.fr
Vincent Noël @vincent-noel.fr · Nov 8
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!
1 3
vincent-noel.fr
Vincent Noël @vincent-noel.fr · Nov 8
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 !
1 4
vincent-noel.fr
Vincent Noël @vincent-noel.fr · Nov 8
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👇
2 7 25
Reposted by Vincent Noël
mathcancer.bsky.social
Paul Macklin @mathcancer.bsky.social · Oct 16
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
PhysiMeSS - a new physiCell addon for extracellular matrix modelling
PhysiMeSS - a new physiCell addon for extracellular matrix modelling
gigabytejournal.com
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Reposted by Vincent Noël
physicell.bsky.social
PhysiCell Project. @physicell.bsky.social · Sep 16
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...
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...
github.com
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Reposted by Vincent Noël
mathcancer.bsky.social
Paul Macklin @mathcancer.bsky.social · Sep 16
PhysiCell is now on BlueSky! 🧪

bsky.app/profile/phys...
bsky.app
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vincent-noel.fr
Vincent Noël @vincent-noel.fr · Jul 4
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 !
2
vincent-noel.fr
Vincent Noël @vincent-noel.fr · Jul 4
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.
1 2
vincent-noel.fr
Vincent Noël @vincent-noel.fr · Jul 4
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!
1
vincent-noel.fr
Vincent Noël @vincent-noel.fr · Jul 4
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.).
1
vincent-noel.fr
Vincent Noël @vincent-noel.fr · Jul 4
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!
1