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

Published: 4 March 2024| Version 1 | DOI: 10.17632/96jtpmnrgt.1
Jessica Yu


Data and results for NUTRIENT DYNAMICS simulations. Simulations of cancerous cells in colony and tissue contexts with different nutrient levels of blood glucose and temporal nutrient concentration dynamics. 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]_[level]_[profile] - [context] - C = colony context, cancerous cells only - CH = tissue context, cancerous cells and healthy cells - [level] - BASAL = basal blood glucose concentration - LOW = low blood glucose concentration (half basal value) - HIGH = high blood glucose concentration (double basal value) - [profile] - constant = constant glucose levels - pulse = pulses of glucose every two days - cycle = cyclic glucose with three peaks a day


Steps to reproduce

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


Agent-Based Modeling, Computational Biology