Model design choices impact biological insight: Unpacking the broad landscape of spatial-temporal model development decisions: SYSTEM REPRESENTATION
Description
Data and results for SYSTEM REPRESENTATION simulations. Simulations of cancerous cells in colony and tissue contexts using rectangular or hexagonal geometry in 2D and 3D. Each condition is run for 15 days (21600 ticks) with 50 replicates (random seeds 0 - 49). 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 .csv.xz files of compressed parsed data. Simulations are labelled as: [context]_[dimension]_[geometry] - [context] - C = colony context, cancerous cells only - CH = tissue context, cancerous cells and healthy cells - [dimension] - 2D = 2D simulation (radius = 34, margin = 6, height = 1) - 3D = 3D simulation (radius = 26, margin = 6, height = 51) - [geometry] - rect = rectangular geometry - hex = hexagonal geometry
Files
Steps to reproduce
Simulations generated using ARCADE v2.4 (available at https://github.com/bagherilab/ARCADE) using the following setup files: - SYSTEM_REPRESENTATION_C.xml - SYSTEM_REPRESENTATION_CH.xml All setup files are available at https://github.com/bagherilab/arcade_modeling_choices.