Modular microenvironment components reproduce vascular dynamics de novo in a multi-scale agent-based model: VASCULAR FUNCTION

Published: 15 July 2021| Version 2 | DOI: 10.17632/rgtddfyp97.2
Jessica Yu


Data and results for `VASCULAR FUNCTION` simulations. Simulations of cancerous cells in colony and tissue contexts with pattern and various graph layouts with degradation by cancerous cells and vascular remodeling. Each condition is run for 15 days (21600 ticks) with 10 replicates (random seeds 0 - 9). Cancerous cells (max_height x 1.5, meta_pref x 1.5, migra_threshold x 0.5) are introduced to the center of the environment after a 1 day delay. Snapshots are taken every 0.5 days (720 ticks). The data folder contains .tar.xz compressed replicate sets. The data.graph folder contains .tar.xz compressed replicate sets for .GRAPH output. The results folder contains .pkl files of data parsed into arrays. Simulations are labeled as: [context]_[sites]_[layout] - [context] - C = colony context, cancerous cells only - CH = tissue context, cancerous cells and healthy cells - [sites] - PATTERN = site architecture defined by pattern - GRAPH = site architecture defined by graph layout - [layout] - simulations with PATTERN do not have a layout label - Lav = line root graph with one artery and one vein (L11) - Lava = line root graph with two arteries and one vein (L21) - Lvav = line root graph with one artery and two veins (L12) - Sav = single root graph with one artery and one vein (S11) - Savav = single root graph with two arteries and two veins (S22)


Steps to reproduce

Simulations generated using ARCADE v2.3 (available at using the following setup files: - VASCULAR_FUNCTION_C_PATTERN.xml - VASCULAR_FUNCTION_CH_PATTERN.xml - VASCULAR_FUNCTION_C_GRAPH.xml - VASCULAR_FUNCTION_CH_GRAPH.xml For GRAPH simulations, checkpoints for each root layout are first simulated using ROOT_LAYOUTS.xml setup file. All setup files are available at


Natural Sciences