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

Published: 15-07-2021| Version 3 | DOI: 10.17632/2n3mnkz7yc.3
Contributor:
Jessica Yu

Description

Data and results for `SITE ARCHITECTURE` simulations. Simulations of cancerous cells in colony and tissue contexts with different source (points and grids), pattern, and graph site layouts. 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 results folder contains .pkl files of data parsed into arrays. Simulations are labeled as: [context]_[sites]_[configuration] - [context] - C = colony context, cancerous cells only - CH = tissue context, cancerous cells and healthy cells - [sites] - SOURCE = sites architecture defined by point (or set of points) sources - PATTERN = site architecture defined by pattern - GRAPH = site architecture defined by graph layout - [configuration] - SOURCE - constant = every point is a source, equivalent to constant source - point# = point source located at position # from center - grid# = grid of point sources with # spacing in both the x and y directions - xAyB = grid of point sources with A spacing in the x direction and B spacing in the y direction - nosite = no point is a source - PATTERN - simulations with PATTERN do not have a configuration label - GRAPH - 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)

Files

Steps to reproduce

Simulations generated using ARCADE v2.3 (available at https://github.com/bagherilab/ARCADE) using the following setup files: - SITE_ARCHITECTURE_C_SOURCE.xml - SITE_ARCHITECTURE_CH_SOURCE.xml - SITE_ARCHITECTURE_C_PATTERN.xml - SITE_ARCHITECTURE_CH_PATTERN.xml - SITE_ARCHITECTURE_C_GRAPH.xml - SITE_ARCHITECTURE_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 https://github.com/bagherilab/arcade_vascular_dynamics.