Model design choices impact biological insight: Unpacking the broad landscape of spatial-temporal model development decisions: CELL VARIABILITY

Published: 4 March 2024| Version 1 | DOI: 10.17632/dvrs8zsngb.1
Jessica Yu


Data and results for CELL VARIABILITY simulations. Simulations of cancerous cells in colony and tissue contexts with and without age and volume variability. 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 0.125 days (180 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]_[age]_[volume] - [context] - C = colony context, cancerous cells only - CH = tissue context, cancerous cells and healthy cells - [age] - A0 = deterministic age (all initial ages set to zero) - A1 = stochastic age (ages drawn from uniform distribution) - [volume] - V0 = deterministic volume (all initial volumes set to average volume) - V1 = stochastic volume (volumes drawn from normal distribution)


Steps to reproduce

Simulations generated using ARCADE v2.4 (available at using the following setup files: - CELL_VARIABILITY_C.xml - CELL_VARIABILITY_CH.xml All setup files are available at


Agent-Based Modeling, Computational Biology