PhysiCell Project.

PhysiCell Project.

@physicell.bsky.social

Celebrating 10 years in 2025! Project home at https://physicell.org

496 followers19 following39 posts

PhysiCell Project.
@physicell.bsky.social

Major PhysiCell paper in Cell using a new, intuitive model grammar to create complex multicellular systems models with "plain language" cell hypotheses! 🧪 @cellpress.bsky.social @cp-cell.bsky.social @mathcancer.bsky.social @fertiglab.bsky.social #mathonco #mathbio #abm #opensource

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...

PhysiCell Project. reposted

Paul Macklin
@mathcancer.bsky.social

Nice writeup of our new @cp-cell.bsky.social article on an intuitive, plain language "grammar" to make simulation modeling of complex multicellular systems more accessible. Huge thx to Forest Ray and @genomeweb.bsky.social ! Joint work by @fertiglab.bsky.social, Genevieve Stein-O'Brien & team! 🧪

GenomeWeb@genomeweb.bsky.social

Computational Model Predicts Tissue-Specific Cell Activity Over Time

genomeweb.comComputational Model Predicts Tissue-Specific Cell Activity Over Time

PhysiCell Project. reposted

Paul Macklin
@mathcancer.bsky.social

Really fantastic ECM and spheroid modeling in @physicell.bsky.social. Great work! 🧪

Fabian Spill@fabianspill.bsky.social

Congrats Margherita for her new paper, where she investigated how cancer spheroids grow in collagen matrices with varying stiffness, implementing varying ECM properties in @physicell.bsky.social Thanks Tom Susan John and Pradeep for the collaboration www.frontiersin.org/journals/bio...

frontiersin.orgFrontiers | A hybrid computational model of cancer spheroid growth with ribose-induced collagen stiffening
PhysiCell Project.
@physicell.bsky.social

New paper for new PhysiCell capabilities! John Metzcar et al. (2025) created a very accessible framework to integrate ECM structure into cell agent behaviors, particularly including contact guidance. Give it a look! 🧪

Paul Macklin@mathcancer.bsky.social

Congratulations to John Metzcar for his new paper modeling cell-ECM interactions in @physicell.bsky.social ! 🧪 This work helps provide an accessible means to have an intermediate level of ECM detail (density, orientation, anisotropy) affect cell migration and behavior. dx.doi.org/10.1007/s115...

dx.doi.orgA Simple Framework for Agent-Based Modeling with Extracellular Matrix - Bulletin of Mathematical BiologyExtracellular matrix (ECM) is a key component of the cellular microenvironment and critical in multiple disease and developmental processes. Representing ECM and cell-ECM interactions is a challenging...
PhysiCell Project.
@physicell.bsky.social

Continuing our 10-year celebration of PhysiCell with some more project history! :-) Today we'll talk about choosing a name 🧪 On Thanksgiving Day in 2014, I was with family at Disneyland sitting for the parade. I'm not as super big into the parade, so I started searching for our project name ...

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PhysiCell Project.
@physicell.bsky.social

I found the evolving pronunciation a bit funny. Since it's "physics" + "cells", I pronounce it like "Physics" without the "s", followed by cells. I've found that others pronounce it like "FizzyCell". But who am I to argue?? Come back tomorrow for more fun backstory. :-)

PhysiCell Project.
@physicell.bsky.social

Continuing our 10-year celebration of PhysiCell with some more project history! :-) Today we'll talk about choosing a name 🧪 On Thanksgiving Day in 2014, I was with family at Disneyland sitting for the parade. I'm not as super big into the parade, so I started searching for our project name ...

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PhysiCell Project.
@physicell.bsky.social

Then we thought through the functionality more Physicell -- physics-based cell simulator Or physicells Physicell3D -- no relevant hits biophysicell -- meant to sound like biophysical biophysicells -- biophysics-based cell simulator / biophysics-based cell system and other variants

PhysiCell Project.
@physicell.bsky.social

Continuing our 10-year celebration of PhysiCell with some more project history! :-) Today we'll talk about choosing a name 🧪 On Thanksgiving Day in 2014, I was with family at Disneyland sitting for the parade. I'm not as super big into the parade, so I started searching for our project name ...

View full thread
PhysiCell Project.
@physicell.bsky.social

Leaning back towards functional names ... Multicellular simulation system : McSimSys (abm plus fvm) And names emphasizing open source (compared to some closed-source binaries in Germany at the time): OpenBioSims - open source bio simulation system OpenBAMS! open biological agent model system

PhysiCell Project.
@physicell.bsky.social

OpenMcSim : open multicellular simulator abcats - agent based cell and tissue simulator OpenVCATS - open virtual cell and tissue simulators - agent based cell and tissue simulator But still too awkward and chunky ...

PhysiCell Project.
@physicell.bsky.social

Continuing our 10-year celebration of PhysiCell with some more project history! :-) Today we'll talk about choosing a name 🧪 On Thanksgiving Day in 2014, I was with family at Disneyland sitting for the parade. I'm not as super big into the parade, so I started searching for our project name ...

View full thread
PhysiCell Project.
@physicell.bsky.social

And more zany thoughts: Broth (No witty abbreviation) Water (No witty abbrevation) Cream of Cellery (or Mushroom or something) Some we steered away from because we wanted to make clear that we're not only for cancer modeling. Others because good luck being the top google hit for water.

PhysiCell Project.
@physicell.bsky.social

We worried that zany naming schemes could force us to needlessly contort future projects to fit a theme like backronyms, and they could backfire and make the projects sound like a joke. We steered back towards simple, functional names that clearly describe what the codes do.

PhysiCell Project.
@physicell.bsky.social

Continuing our 10-year celebration of PhysiCell with some more project history! :-) Today we'll talk about choosing a name 🧪 On Thanksgiving Day in 2014, I was with family at Disneyland sitting for the parade. I'm not as super big into the parade, so I started searching for our project name ...

View full thread
PhysiCell Project.
@physicell.bsky.social

Some of our earlier floated names were a bit chunky but very functional (continued): Biomechanical Individual Based Simulator (BIBSim) Biomechanical MultiCellular Simulator (BMCSim)Reducsion: A REaction DiffUsion ConveCTION (ConveCSION) Finite Volume Method code

PhysiCell Project.
@physicell.bsky.social

Other names were a bit zanier: The overarching project is called SoopCanS: Scalable Object Oriented Programming for Cancer Simulations It contains the follow "cans": Cellery: A Cellular Agent Based Model TumorIC: Tumor Initial Conditions (AKA the snapshot generator)

PhysiCell Project.
@physicell.bsky.social

Continuing our 10-year celebration of PhysiCell with some more project history! :-) Today we'll talk about choosing a name 🧪 On Thanksgiving Day in 2014, I was with family at Disneyland sitting for the parade. I'm not as super big into the parade, so I started searching for our project name ...

View full thread
PhysiCell Project.
@physicell.bsky.social

Some of our earlier floated names were a bit chunky but very functional CAGEMED: Cellular AGEnt based MEthoD CabMerlot: Cellular Agent Based Model .... MultiCellular Systems Simulator (MCSSim) Mechanical MultiCellular Simulator (MMCSim) Biomechanical Agent Based Simulator (BiABSim)

PhysiCell Project.
@physicell.bsky.social

Continuing our 10-year celebration of PhysiCell with some more project history! :-) Today we'll talk about choosing a name 🧪 On Thanksgiving Day in 2014, I was with family at Disneyland sitting for the parade. I'm not as super big into the parade, so I started searching for our project name ...

View full thread
PhysiCell Project.
@physicell.bsky.social

We got into a good discussion on what makes a good project name. We regarded Biocellion and CompuCell3D as great names -- unique, easy to say, and very clear purposes. Biocellion is particularly brilliant: biology, billion cells, and cells all suggested in one word. CompuCell3D als very clear.

PhysiCell Project.
@physicell.bsky.social

On the other hand, other projects used a common or existing word that was hard to find on google (sorry, Chaste), or used weird symbols that are harder to type and search for. So, we wanted to avoid names like that. Any name should also have an open web domain.

PhysiCell Project.
@physicell.bsky.social

Continuing our 10-year celebration of PhysiCell with some more project history! :-) Today we'll talk about choosing a name 🧪 On Thanksgiving Day in 2014, I was with family at Disneyland sitting for the parade. I'm not as super big into the parade, so I started searching for our project name ...

PhysiCell Project.
@physicell.bsky.social

In an email with Farzin Ghaffarizadeh and Sam Friedman (postdocs at the time) and Edwin Rosales (PhD student). Email chain started off as: Subject: Code names for open source? Let's try to decide today / tomorrow :-) MultiCellFVM and MultiCellABM BioFVM and BioABM Other ideas and combos?

PhysiCell Project. reposted

Jeanette Johnson
@jeanettejohnson.bsky.social

Replying to @jeanettejohnson.bsky.social

Another nice benefit of our approach is that we can combine the model grammar with graphical interfaces to easily write and test new models without writing code. This opens the world of simulation modeling to new communities. (Preprint by @rheiland soon!) 16/19

PhysiCell Project. reposted

GigaByte Journal
@gigabytejournal.bsky.social

New in our PhysiCell Ecosystem series is a GUI for building, simulating, and visualizing PhysiCell models. PhysiCell Studio: a graphical tool to make agent-based modeling more accessible doi.org/10.46471/gig... See also the introductory video: youtu.be/jkbPP1yDzME?...

doi.orgPhysiCell Studio: a graphical tool to make agent-based modeling more accessiblePhysiCell Studio: a graphical tool to make agent-based modeling more accessible

PhysiCell Project. reposted

Ashlee N. Ford Versypt
@fordversyptlab.bsky.social

Replying to @vincent-noel.fr

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!

PhysiCell Project. 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!

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PhysiCell Project.
@physicell.bsky.social

And what an amazing first win that was for all of us! We had considered adding intracellular networks MUCH later, but through teh power of preprints and open source, we were getting a jump together even before publication. (PhysiCell spent over a year in peer review.)

PhysiCell Project.
@physicell.bsky.social

While the seeds of PhysiCell were around and presented before (first as a DCIS model before generalizing), we chose the project name PhysiCell in December 2014 and consolidated pre-release code throughout 2015.

PhysiCell Project.
@physicell.bsky.social

In 2016, we released our code as open source (version 0.5.0!) and posted a preprint while working on our main method paper. We really had no idea if anybody would even look at it. journals.plos.org/ploscompbiol...

journals.plos.orgPhysiCell: An open source physics-based cell simulator for 3-D multicellular systemsAuthor summary This paper introduces PhysiCell: an open source, agent-based modeling framework for 3-D multicellular simulations. It includes a standard library of sub-models for cell fluid and solid ...
PhysiCell Project.
@physicell.bsky.social

Fantastic new paper by @fordversyptlab.bsky.social lab using @physicell.bsky.social !! 🧪

Ashlee N. Ford Versypt@fordversyptlab.bsky.social

Our newest paper is now online. Mohammad Aminul Islam, Ph.D. developed this followup to our earlier COVID-19 agent-based model and resulting lung fibrosis. Here, we studied COVID-19 with the renin-angiotensin system and patient-specific differences: www.sciencedirect.com/science/arti...

sciencedirect.comMathematical modeling of impacts of patient differences on renin-angiotensin system and applications to COVID-19 lung fibrosis outcomesPatient-specific premorbidity, age, and sex are significant heterogeneous factors that influence the severe manifestation of lung diseases, including …
PhysiCell Project.
@physicell.bsky.social

PhysiCell 1.14.1 is released! This introduced asymmetric cell division (thanks, @danielrbergman.bsky.social!), improved handling of conserved cell contents in phagocytosis and transformation, and numerous bug fixes. 🧪 #mathbio #mathonco #opensource github.com/MathCancer/P...

github.comRelease 1.14.1 · 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 1.14.1 : 13 December 2024 Ove...

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