Vincent Noël

@vincent-noel.bsky.social

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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
Paris, São Paulo

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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 👇

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!

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!

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.).

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!

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.

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

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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Vincent Noël

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/

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 !

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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