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 or 2.1 (recommended). 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 Fig4_invasive_carcinoma.zip Fig5_collective_migration_initial_tests.zip Fig6_instant_remodeling.zip Fig7b_leader_follower.zip 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 python_imaging.zip Base modules and examples for producing images (tested on Python 3.9) README 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.