A simple framework for agent-based modeling with extracellular matrix: Simulation results

Data for "A simple framework for agent-based modeling with extracellular matrix"

Metzcar, J., Duggan, Ben S., Fischer, B., Murphy, M., Heiland, R., Macklin, P. A simple framework for agent-based modeling with extracellular matrix. bioRxiv. doi: 10.1101/2022.11.21.514608

Link to preprint

This repository contains the data for each subfigure (and video) in the preprint cited and linked abvoe, as well as the original figures and videos themselves. We have tried to include original model file (PhysiCell_settings.xml or other *.xml file) used to generate each results with each file set as well as the code (see python scripts) to make images and videos that appear in the pre-print - both within the files and base modules and examples in a separate folder.

The data can be regenerated using release 2.0, 2.1, and 2.2.1. Release 2.1 is recommended for reproducing more exactly the results for the fibrosis, invasive carcinoma, and series of leader-follower results as the results archived here were produced using a set of two random number generators (one from PhysiCell and one from BioFVM). 2.2.1, used to produce the invasive cellular front results, consolidates the use of random number generators to just one (the PhysiCell one). As such, in 2.2.1, the random number generator seed may need changed to produce stochastic replicates, even when multithreading.

The following file sets are in this download:

Fig2_SM_3_simple_tests.zip

Has results for Figure 2 and SM Figure 3

Fig3_fibrosis.zip

Results from fibrosis simulation (originally Figure 3, now Figure 4)

Fig4_invasive_carcinoma.zip

Results from invasive carcinoma simulation (originally Figure 4, now Figure 5)

Fig5_collective_migration_initial_tests.zip

Results from initial leader follower model development (originally Figure 5, now Figure 6)

Fig6_instant_remodeling.zip

Results from instant remodeling leader follower model scenariods (originally Figure 6, now Figure 7)

Fig7b_leader_follower.zip

Results from leader-follower collective migration scenario (origianlly Figure 7b, now Figure 8b)

images_and_vidoes_for_paper.zip

has all the images, videos, and some figures from the main body of the paper and the supplmental material. Updated in this version.

Invasive_cellular_front.zip

Has results for each ECM scenario: random, parallel, and perpindicular orientations and mixed ECM conditions. New to this data repository.

python_imaging.zip

Base modules and examples for producing images (tested on Python 3.9). Updated in in this verison

SM_Fig_4b_leader_follower_decreased_remodeling.zip

stochastic_replicates.zip

Contains stochastic replicates for the collective migration, fibrosis, and invasive carcinoma models and source code for all.

stochastic_replicates_invasive_cellular_front.zip

Contains stochastic replicates for the invasive cellular front scenarios. New to this data repository.