Supporting code for the article:

J Yu and N Bagheri. (2024). Model design choices impact biological insight: Unpacking the broad landscape of spatial-temporal model development decisions. PLoS Computational Biology. doi: 10.1371/journal.pcbi.1011917

Setup files

The setups directory contains all the setup files used for running simulations. Simulations were run using ARCADE v2.4.

Note that simulations for CELL_VARIABILITY use modified code that updates the cell toJSON method to include cell age.

Simulation data

Raw simulation data and results are available on Mendeley Data:

• SYSTEM REPRESENTATION . https://doi.org/10.17632/bh5w3tzsjc
• CELL VARIABILITY . https://doi.org/10.17632/dvrs8zsngb
• NUTRIENT DYNAMICS . https://doi.org/10.17632/96jtpmnrgt

Pipeline notebooks

Parse simulation outputs

The parse_simulation_outputs notebook provides the functions and scripts for parsing simulation files (.json) into compressed csvs (.csv.xz). These parsed results are included with the raw simulation data.

Analyze data & results

The analyze_data_results notebook provides functions and scripts for running basic analysis on simulation data and parsed results. All resulting .json and .csv files are provided in the analysis directory.

Generate figure inputs

The generate_figure_inputs notebook walks through all the steps necessary to generate figure input files from raw data, parsed files, and basic analysis files. All resulting files are provided in the analysis directory. Refer to figure section in notebook for more details.

To view figures, start a local HTTP server from the root folder, which can be done using Python or PHP:

$ python3 -m http.server
$ php -S 127.0.0.1:8000

Note that the links in the notebook to figures assume the local port 8000; if your server is running on a different port, the links to the figures from the notebook will not work. Instead, you can navigate to http://localhost:XXXX/ where XXXX is the port number and follow links to the figures.

Run ANOVA tests

The run_anova_tests notebook works through the process of running ANOVA for each of the simulation sets. ANOVA results are compiled into three files (included in the analysis directory) and used to generate the anova_summary figures.