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PhysiCell Project. @physicell.bsky.social · 29/07/2025

This modeling grammar is fully supported in recent releases of PhysiCell including online studios on nanohub and galaxy! Links to online studios in a moment. @galaxyproject.bsky.social

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PhysiCell Project. @physicell.bsky.social · 29/07/2025

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

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Reposted by PhysiCell Project.

Paul Macklin @mathcancer.bsky.social · 29/07/2025

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! 🧪

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Sandy Anderson @sandyanderson.bsky.social · 15/07/2025

Today’s morning plenary and John Jungck Prize lecture is from @smbmathbiology.bsky.social former president, Fred Adler (@dendroicap.bsky.social) on "Education, Bureaucracy and Corruption". He manages to discuss some of his virus work with former @mathonco.bsky.social member Anna Miller! #SMB2025

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PhysiCell Project. @physicell.bsky.social · 15/07/2025

Hello, #SMB2025! If you’d like PhysiCell stickers, please find Paul Macklin (@mathcancer.bsky.social). I’ll try to get stickers to Randy Heiland ( @rheiland.bsky.social ) and John Metzcar (@jmetzcar.bsky.social) as well.

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Reposted by PhysiCell Project.

Paul Macklin @mathcancer.bsky.social · 09/04/2025

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

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Adam MacLean @adamlmaclean.bsky.social · 15/07/2025

"Patients should be their own control" - great & pithy takeaway from @sandyanderson.bsky.social in his talk on the adoption of adaptive therapies in the clinic #SMB2025 #MathOnco

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David Basanta @cancerevo.org · 04/04/2025

Unexpected treat today @moffittnews.bsky.social Innovator's of Tomorrow symposium with Jeanette Johnson, working with @fertiglab.bsky.social and developing on @physicell.bsky.social to create an #ABM for #pancreatic #cancer forecasting

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Fabian Spill @fabianspill.bsky.social · 09/04/2025

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.org

Frontiers | A hybrid computational model of cancer spheroid growth with ribose-induced collagen stiffening

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PhysiCell Project. @physicell.bsky.social · 13/02/2025

We're thrilled we're all together on it!

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PhysiCell Project. @physicell.bsky.social · 13/02/2025

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! 🧪

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PhysiCell Project. @physicell.bsky.social · 21/01/2025

PhysiCell 1.14.2 is released! 🧪 * bug fixes * better support for the cell behavior grammar / rules * prep work for future PhysiGym * new script to more easily add PhysiCell Studio See download links at: physicell.org/Downloads.html

physicell.org

PhysiCell Project Website: Downloads

PhysiCell Project Website

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

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. :-)

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

We were favoring Physicell3D, but the simpler Physicell stuck. We switched to camel case (PhysiCell) to emphasize the word parts. By Dec 2014, we were using PhysiCell in proposals and abstracts. In 2015 PhysiCell appeared in talks and @biorxivpreprint.bsky.social: www.biorxiv.org/content/10.1...

biorxiv.org

Agent-based simulation of large tumors in 3-D microenvironments

Multicellular simulations of tumor growth in complex 3-D tissues, where data come from high content in vitro and bioengineered experiments, have gained significant attention by the cancer modeling com...

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

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

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

CATE : cell and tissue environment -- but cate.org is taken SCATE : simulated cell and tissue environment -- scate.org taken catde : cell and tissue development environment (but not taken) But catde wasn't a super appealing name to say.

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

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 ...

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

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

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

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.

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

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.

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

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)

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

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

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

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)

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

Moreover, the word "cell" had a lot of collision with the cellular telephony space. Things like CellModel and CellSim were often taken by cellular network projects.

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

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.

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

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.

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

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?

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

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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Jeanette Johnson @jeanettejohnson.bsky.social · 22/09/2023

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

A graphical interface for developing and running PhysiCell models in the cloud, using the model grammar without any coding.

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GigaByte Journal @gigabytejournal.bsky.social · 03/07/2024

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.org

PhysiCell Studio: a graphical tool to make agent-based modeling more accessible

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Reposted by PhysiCell Project.

Ashlee N. Ford Versypt @fordversyptlab.bsky.social · 25/11/2024

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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Reposted by PhysiCell Project.

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 18/12/2024

Start&Stop - a PhysiCell and PhysiBoSS 2.0 add-on for interactive simulation control www.biorxiv.org/content/10.1101/202…

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PhysiCell Project. @physicell.bsky.social · 16/01/2025

(Oh, please tag us at @physicell.bsky.social to get our attention. Xitter-style @PhysiCell is alas an incomplete tag.)

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Marco Ruscone @drmarcoruscone.bsky.social · 14/01/2025

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 · 15/01/2025

Thanks for reading along! Stay tuned for more history tomorrow!

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PhysiCell Project. @physicell.bsky.social · 15/01/2025

By 2020, PhysiBoSS was integrated into the PhysiCell main release as the first officially supported addon. @vincent-noel.fr and @drmarcoruscone.bsky.social have joined us as core developers. None of this would have happened without an early preprint and open source release!

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PhysiCell Project. @physicell.bsky.social · 15/01/2025

Institut Curie (L Calzone, E Barrilot, V Noël, M Ruscone, ...), Barcelona Supercomputing Center (A Montagud, A Valencia, M Ponce de Leon ...), Toulouse (V Pancaldi) and others! @vincent-noel.fr @drmarcoruscone.bsky.social cone.bsky.social @verapancaldi.bsky.social @arnaumontagud.bsky.social

cone.bsky.social

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PhysiCell Project. @physicell.bsky.social · 15/01/2025

Moreover, it was the start of an amazing collaboration! This integration came to be known as PhysiBoSS (PhysiCell + PhysiBoSS), and it was the start of a growing collaboration that has come to involve ... academic.oup.com/bioinformati...

academic.oup.com

PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling

AbstractMotivation. Due to the complexity and heterogeneity of multicellular biological systems, mathematical models that take into account cell signalling

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PhysiCell Project. @physicell.bsky.social · 15/01/2025

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.)

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PhysiCell Project. @physicell.bsky.social · 15/01/2025

In April 2017, we had an answer: Gaelle Letort (from Institut Curie) reached out to say they were integrating MaBoSS (their Boolean network simulator) into our PhysiCell agents. Score a win for @biorxivpreprint.bsky.social and open source! After seeing this first community interest, we dove all-in

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PhysiCell Project. @physicell.bsky.social · 15/01/2025

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.

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PhysiCell Project. @physicell.bsky.social · 15/01/2025

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! 🧪

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Dani cRabaiotti 🦀 @danirabaiotti.bsky.social · 10/02/2024

Welcome to the Science feed! Please read our FAQs for instructions for how to be added as a contributor: bossett.io/science-feed/ Mod introductory posts linked below⬇️ Use the test tube emoji on posts you want to appear in the feed🧪 Please like the feed and make sure you follow our feed rules:

Science Feed Rules:
🧪 No misinformation
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