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

Congrats on some terrific work!!

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

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.