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:

1. Select a pif file from the "Selection Simulation File" pulldown menu in the steering panel
2. Click the "Step" button
3. Click the "Play" button

To run another simulation, please follow these steps:

1. Click the "Stop" button
2. Click the "Step" Button
3. 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/

[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.

Researchers should cite this work as follows:

• Apanavicius, Joshua Alan, Juliano Ferrari Gianlupi (2022), "CC3D Slime Mold Simulation," https://nanohub.org/resources/slimemold. (DOI: 10.21981/AW1K-2T46).

  BibTex | EndNote

1. cc3d
2. CompuCell3D
3. tool:slimemold