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

Published: 15 July 2021| Version 2 | DOI: 10.17632/p8yzkdccg7.2
Contributor:
Jessica Yu

Description

Data and results for `VESSEL COLLAPSE` simulations. Simulations of cancerous cells in tissue context with realistic vasculature (single root with two arteries and two veins). Different variations of the vasculature are produced using random seeds 0 - 9 and assigned letters from A - J, respectively. Each condition is run for 22 days (31680 ticks) with 10 replicates (random seeds 0 - 9) for each of the 10 vasculature variations, for 100 total simulations per parameter value. 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). Parameters (degradation rate and stabilization fraction) are varied from 0.0 to 1.0 (increments of 0.1). For stabilization fraction simulations, stabilization step is set to day 8 (11520 ticks). Note that simulations with stabilization fraction use modified code. 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 compressed .csv files with parsed metrics for each simulation and .csv files with all simulation metrics consolidated into a single file. Simulations are labeled as: [parameter]_[value]_[graph] - [parameter] - degradation = degradation rate - stabilized = stabilization fraction - [value] - ### = parameter value (###/100) - [graph] - A = single root graph with two arteries and two veins, seed 0 - B = single root graph with two arteries and two veins, seed 1 - ... - J = single root graph with two arteries and two veins, seed 9

Files

Steps to reproduce

Simulations generated using ARCADE v2.3 (available at https://github.com/bagherilab/ARCADE) using the following setup files: - VESSEL_COLLAPSE_degradation.xml - VESSEL_COLLAPSE_stabilized.xml Checkpoints for the root layout are simulated using ROOT_LAYOUTS.xml. The Savav layout is then expanded by converting seed to structures, then duplicating for each seed (i.e. multiple replicates given with the same layout). For example: Savav_00 becomes Savav_A_degradation_*, Savav_01 becomes Savav_B_degradation_*, etc. where * indicates seeds 0 - 9. For the stabilized simulations, which uses modified code, new checkpoints need to be saved and expanded as above: Savav_00 becomes Savav_A_stabilized_*, Savav_01 becomes Savav_B_stabilized_*, etc. where * indicates seeds 0 - 9. Note that the VESSEL_COLLAPSE_stabilized simulations uses slightly modified code; see article for details. All setup files are available at https://github.com/bagherilab/arcade_vascular_dynamics.

Categories

Natural Sciences

License