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Abstract
This is a recreation of work originally completed in 2011 by Niklas B. Semmler. [1] The purpose of this project is to re-create Semmler’s work using the newest version of Compucell3D (CC3D) [2] (3.4.x, originally writ-
ten using 3.3.x). Another goal is to add GUI elements that will allow non-programmers to access, run, modify, and hopefully learn something about slime molds and Compucell3D.
How to Run the Simulation:
Once CC3D launches please follow these steps to run the slime mold simulation:
- Select a pif file from the "Selection Simulation File" pulldown menu in the steering panel
- Click the "Step" button
- Click the "Play" button
To run another simulation, please follow these steps:
- Click the "Stop" button
- Click the "Step" Button
- Click the "Play" Button
Please see the following links if you are not familiar with CC3D:
Reference Manual: https://compucell3dreferencemanual.readthedocs.io/en/latest/
CC3D Tutorials: https://compucell3d.org/Tutorials
Python Scripting Manual: https://pythonscriptingmanual.readthedocs.io/en/latest/
References
[1] Niklas B. Semmler. Emergent Networks: A Slime Mold Simulation. 2011.
[2] Maciej H. Swat et al. “Chapter 13 - Multi-Scale Modeling of Tissues Using CompuCell3D”. In: Computational Methods in Cell Biology. Ed. by Anand R. Asthagiri and Adam P. Arkin. Vol. 110. Methods in Cell Biology. Academic Press, 2012, pp. 325–366. doi: https://doi.org/10.1016/B978-
0 - 12 - 388403 - 9 . 00013 - 8. url: https : / / www . sciencedirect . com /
science/article/pii/B9780123884039000138.
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