CC3D-Breast-Duct

Twedit Usage Guide

Opening Twedit

1. Open terminal.
2. Type cd CompuCell3D/.
3. Type ./twedit++.command.
4. Select 'CC3D project'.
5. Choose 'Open project'.
6. Click on the .cc3d file to open.

The project is now open in Twedit.

Coding in Twedit

• Click on 'CC3D Python' on the top bar for prebuilt blocks of code.
• Remember to save your work using Ctrl + S or Cmd + S.
• You can comment out parts of the code using Ctrl + / or Cmd + /.

Running Simulation

Using Twedit

• Right-click on the folder in the left section of Twedit.
• Select 'Open in Player'.

Using Terminal

1. Open terminal.
2. Type cd CompuCell3D/.
3. Type ./compucell3d.command.
4. Open the folder to run the simulation.

Editing Code Guidelines

Notes on Modifying IF Statements

• mcs: Time step of the simulation when the event starts.
• random.random(): Generates a number between 0.0 and 1.0. To make an event more likely, increase the threshold.
• cell.volume: Controls the size the cells must be for an event to happen.

XML File

Initial Position and Area of Cells:

• Found in the UniformInitializer block.
• Example: To remove macrophages, comment out the corresponding code in UniformInitializer of type MAC.

Contact Energies Between Cells:

• Located in the Contact block.
• Example: Setting the contact energy between Medium and LUM to indicate non-attraction.

Adding a New Cell Type:

• Located in the CellType block.
• Ensure to add respective values for its contact energies.

Python Steppables File

ConstraintInitializer Class:

• Sets target volume for each cell type.
• Change the coefficient multiplied by the constant (cellVol) to adjust volumes.

BreastDuctSim Class:

• Contains code for the cell killer.

GrowthSteppable Class:

• Manages growth rate of cells, primarily EPI cells.
• Increase target volume increment to boost growth rate.

MitosisSteppable Class:

• Governs cell proliferation.
• Modify the proliferation rates as described in the initial notes.

CellMovementSteppable Class:

• Manages movement of MAC cells.
• Refer to comments in the class for editing guidance.

PositionPlotSteppable Class:

• Used for testing CellMovementSteppable.
• Avoid editing as it doesn't impact the simulation.

FocalPointPlasticity Class:

• Intended for making MEM impermeable, but not used in current versions.

Main Python File

• Avoid editing unless adding new classes to the Python steppable file.