Randy Heiland

Can you say more about how you'd like to change the initial cell positions? As you've probably learned, they are currently done in the setup_tissue() in the custom_modules/cancer_immune_3D.cpp. And it calls create_cell_sphere_positions which creates the cells' positions.

For starters try running that model with the full output flag to false. Just save the SVG. On Wed, Jan 10, 2024 at 9:06 AM Steven S ssummey@users.sourceforge.net wrote: g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 I ran the heterogeneity-sample project as well and it ran smoothly. I realize the simulation from the literature had several custom modules and adjusted settings for their model; however, when running that simulation, I noticed the output file sizes were considerably large for the time-steps...

Let's start with something simpler. Can you provide your terminal output when compiling and trying to run the "template" project, i.e., these commands: make reset make template make project You might also provide "g++ --version"

This is quite specialized. Do you have a model that doesn't require Boost?

Check out Furkan's presentation from last summer's workshop: https://github.com/physicell-training/ws2023/blob/main/agenda.md#advanced-session-4-intracellular-with-libroadrunner-introduction If you've downloaded PhysiCell, you could try building/running the ode-energy-sample: (base) M1P~/dev/PhysiCell_V1.13.1$ make ode-energy-sample ... You may need to step through the PhysiCell setup slides also linked on the above agenda, if you haven't yet.

Hi Cyrene, Unfortunately, yes. Although quite different, perhaps the PhysiCell Studio could help with whatever you are trying to accomplish? https://www.biorxiv.org/content/10.1101/2023.10.24.563727v1

You're correct that there's no built-in functionality to handle electric charges. I'm not sure if you're referring to neuron signaling or other bioelectric phenomena. Michael Levin (Tufts U.) is known for such research. You have at least two options for providing such functionality (without modifying the core code): 1) write custom C++ functions, or 2) use intracellular modeling, e.g., SBML/ODEs.

We haven't maintained documentation describing all of the sample projects as well as we'd like. But you're right, the rather dated User Guide has some, as does the 2018 method paper in PloS CompBio for PhysiCell. Perhaps some of the most detailed docs are found in the "About" pages of our online nanoHUB models, e.g., https://nanohub.org/tools/pc4cancerbots (nanoHUB requires a free registration account to run the models). If you do create an account on nanoHUB, in your dashboard, do a search for "PhysiCell"...