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...
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
Last week to register ! Don't miss this great opportunity
Two PhD positions to work on important and cool topics. And to make it even better, with some very nice and good people.
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
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.
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!
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! 🧪
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!
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
Some word clouds based on publications by @vincent-noel.fr. Popular topics: cell, models, signaling.
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 !
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.
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!
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.).
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!
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!
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 !
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👇
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
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...
PhysiCell is now on BlueSky! 🧪
bsky.app/profile/phys...
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 !
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.
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!
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.).
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!
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!
PhysiBoSS
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 👇
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
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/
