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PhysiCell Project. @physicell.bsky.social · Jul 29

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 · Jul 29

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 · 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 PhysiCell Project.

Paul Macklin @mathcancer.bsky.social · Jul 29

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 · Jul 29

Computational Model Predicts Tissue-Specific Cell Activity Over Time

www.genomeweb.com

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Reposted by PhysiCell Project.

Sandy Anderson @sandyanderson.bsky.social · Jul 15

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 · Jul 15

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 · Apr 9

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

Fabian Spill @fabianspill.bsky.social · Apr 9

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...

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

www.frontiersin.org

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Reposted by PhysiCell Project.

Adam MacLean @adamlmaclean.bsky.social · Jul 14

"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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Reposted by PhysiCell Project.

David Basanta @cancerevo.org · Apr 4

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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PhysiCell Project. @physicell.bsky.social · Apr 9

Congrats on some terrific work!!

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Reposted by PhysiCell Project.

Fabian Spill @fabianspill.bsky.social · Apr 9

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...

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

www.frontiersin.org

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PhysiCell Project. @physicell.bsky.social · Feb 13

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

PhysiCell Project. @physicell.bsky.social · Feb 13

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 · Feb 13

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...

A Simple Framework for Agent-Based Modeling with Extracellular Matrix - Bulletin of Mathematical Biology

Extracellular 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...

dx.doi.org

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PhysiCell Project. @physicell.bsky.social · Jan 21

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 Project Website: Downloads

PhysiCell Project Website

physicell.org

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PhysiCell Project. @physicell.bsky.social · Jan 16

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 · Jan 16

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...

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...

www.biorxiv.org

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PhysiCell Project. @physicell.bsky.social · Jan 16

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 · Jan 16

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 · Jan 16

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 · Jan 16

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 · Jan 16

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 · Jan 16

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 · Jan 16

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 · Jan 16

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 · Jan 16

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 · Jan 16

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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