Agent-based models predict emergent behavior of heterogeneous cell populations in dynamic microenvironments: DEFAULT

Published: 21 July 2021| Version 1 | DOI: 10.17632/wzs7pxkgb9.1
Contributor:
Jessica Yu

Description

Data and results for `DEFAULT` simulations. Simulations of default conditions. For colony, only cancerous cells are simulated for 15 days (21600 ticks) with 51 replicates (random seeds 0 - 50). Cells are introduced to the center of the constant source environment after a 1 day delay. For tissue, only healthy cells are simulated for 15 days (21600 ticks) with 51 replicates (random seeds 0 - 50). Cells are introduced to every location of the constant source environment at the start of the simulation. For the random simulations, cell agents use a random state rule set simulated for 15 days (21600 ticks) with 50 replicates (random seeds 0 - 49). 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: [case]_[initialization] - [case] - C = cancer cells only - H = healthy cells only - random = randomized state rules - [initialization] - only randomized state rules have this label - R1 = initialized to radius 1 - R5 = initialized to radius 5

Files

Steps to reproduce

Simulations generated using ARCADE v2.2 (available at https://github.com/bagherilab/ARCADE) using the following setup files: - DEFAULT_C.xml - DEFAULT_H.xml - DEFAULT_random.xml * Simulations with * used modified code; see article for details. All setup files are available at https://github.com/bagherilab/arcade_emergent_behavior.

Categories

Computational Biology

License