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
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
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! 🧪
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
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.
Really fantastic ECM and spheroid modeling in @physicell.bsky.social. Great work! 🧪
"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
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
Congrats on some terrific work!!
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...
We're thrilled we're all together on it!
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! 🧪
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
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. :-)
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...
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
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.
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 ...
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
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.
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.
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)
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
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)
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.
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.
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.
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?
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 ...
A graphical interface for developing and running PhysiCell models in the cloud, using the model grammar without any coding.
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