1. CompuCell3D: A Morphogenesis simulation package
Nan Chen and Mark Alber
2/20/2006

2. Topics Introduction to CompuCell3D Cellular Potts Model
Framework of CompuCell3D
Usage of CompuCell3D
Future Plans

3. Introduction to CompuCell3D

4. CompuCell3D overview
Morphogenesis simulation package based on Cellular Potts Model (CPM)
Capable of modeling cell clustering as well as growth, division, death, intracellular adhesion, and volume and surface area constraints
Partial differential equation models for external chemical fields which can model reaction-diffusion
Cell type automata provides a method for categorizing cells by behavior into types and algorithms for changing cell type
Chemotaxis and haptotaxis

5. CompuCell3D overview
Framework design allow scientists to focus on simulation development
Visualization tool (CompCell Player)
Standard input (XML) make the package easy to use
Minimize the amount of coding required
Flexible simulation framework
Software design Pattern and Plug in feature
Easy to extend and add new features

6. CompuCell3D Applications
Cell sorting
Limb bud growth
Amoeba migration
Dictyostelium discoideum
Somites formation

7. Cell Sorting
Simple set-up of the Cellular Potts Model (CPM) (a) Initial condition, (b-d) results for various bond-strength settings between dark cells, light cells and the surrounding medium.

8. Limb bud growth
Left. Skeletal Pattern formation: Time-series of chick limb-bud development. Right. 3D cell condensation and patterning into skeletal elements- humerus, ulna+radius, and digits in a chicken limb.

9. Cellular Potts Model

10. Cellular Potts Model
Cell structure is discretized into a cell map, each number in the above cell map corresponds to one cell.

11. Cellular Potts Model
System Hamiltonian consists of adhesion energy, volume energy and chemical energy
Transition probability, W, is determined by the change of free energy due to orientation alteration. DG, according to above equation.

12. Cellular Potts Model Energy minimization formalism
extended by Graner and Glazier, 1992
DAH: Contact energy depending on cell types (differentiated cells)
Extensions:
J_cell_cell is type dependent
Other terms: Cell volume, Chemotaxis/Haptotaxis
Metropolis algorithm: probability of configuration change

13. Framework of CompuCell3D

14. Information flow chart for CompuCell3D
CompuCellPlayer
XML input
User
CompuCell3D Kernal

15. CompuCellPlayer Visualization tool Using QT Lib 3D Visualization
2D Cross-section
Zooming, rotating, translating
Picture Generation
pause a simulation

16. CompuCell3D - XML input <Potts> Potts Model
<Dimensions x=“51" y=“51" z="21"/>
<Steps>10</Steps>
<Temperature>2</Temperature>
<Flip2DimRatio>1</Flip2DimRatio>
</Potts>
Potts Model
Defination
<Plugin Name="Volume">
<TargetVolume>64</TargetVolume>
<LambdaVolume>0.05</LambdaVolume>
</Plugin>
Volume
volume
volumeEnergy(cell)
<Plugin Name="Surface">
<TargetSurface>77</TargetSurface>
<LambdaSurface>0.05</LambdaSurface>
</Plugin>
Surface
area
surfaceEnergy(cell)
<Plugin Name="Contact">
<Energy Type1="Medium" Type2="Medium">0</Energy>
<Energy Type1="Light" Type2="Medium">0</Energy>
<Energy Type1="Dark" Type2="Medium">0.1</Energy>
<Energy Type1="Light" Type2="Light">0.5</Energy>
<Energy Type1="Dark" Type2="Dark">3.0</Energy>
<Energy Type1="Light" Type2="Dark">0.5</Energy>
</Plugin>
Contact
contactEnergy(
cell1, cell2)

17. CompuCell3D Structure
Steppables are executed once per Monte Carlo step and once before and after the main loop. They are the main hooks for initialization and rendering.
Initialization()
Steppables.Start()
For each Monte Carlo step:
For flip attempt:
if(flip):
CellChangeWatcher(cell)
Automatons.Update(cell)
Steppers.step()
Steppabless.step()
Steppables.finish()
CompuCell3D Program Flow
Plugins are loaded at runtime. They are the main way of adding new features to CompuCell. They can be Steppables, Steppers, CellChangeWatchers, or Automatons.
CellChangeWatchers are executed once per each successful spin flip. They are useful for adjusting values that depend on the number of lattice points in a cell.
Automatons enable cell state to change their state as the simulation evolves.
Steppers are executed once per spin flip attempt. They are the main hooks for energy functions.

18. Quickstart Guide of CompuCell3D

19. Installation
For testing purpose, you could directly install binary package
Easy to install
For development purpose, you could download source code and compile it
Your computer needs to have automake, autoconfigure, autohead, libtool package
You could find this package from simtk.org

20. Your first example-Foam simulation
Mcs 0
Mcs 50
Mcs 100

21. Your first example 1 2 3 4 <CompuCell3D> <Potts>
<Dimensions x="101" y="101" z="1"/>
<Anneal>0</Anneal>
<Steps>100</Steps>
<Temperature>5</Temperature>
<Flip2DimRatio>1</Flip2DimRatio>
<Boundary_y>Periodic</Boundary_y>
<Boundary_x>Periodic</Boundary_x>
<FlipNeighborMaxDistance>1.75</FlipNeighborMaxDistance>
</Potts>
<Plugin Name="CellType">
<CellType TypeName="Medium" TypeId="0"/>
<CellType TypeName="Foam" TypeId="1"/>
</Plugin>
<Plugin Name="Contact">
<Energy Type1="Foam" Type2="Foam">20</Energy>
<Energy Type1="Medium" Type2="Medium">100</Energy>
<Energy Type1="Medium" Type2="Foam">100</Energy>
<Depth>1.5</Depth>
<Steppable Type="PIFInitializer">
<PIFName>Foam_1.pif</PIFName>
</Steppable>
</CompuCell3D> 1 2 3 4

22. Setting for Potts Model
<Dimensions x="101" y="101" z="1"/>
<Anneal>0</Anneal>
<Steps>100</Steps>
<Temperature>5</Temperature>
<Flip2DimRatio>1</Flip2DimRatio>
<Boundary_y>Periodic</Boundary_y>
<Boundary_x>Periodic</Boundary_x>
<FlipNeighborMaxDistance>1.75</FlipNeighborMaxDistance>
</Potts>

23. Setting for Cell type and Contact energy
<Plugin Name="CellType">
<CellType TypeName="Medium" TypeId="0"/>
<CellType TypeName="Foam" TypeId="1"/>
</Plugin>
<Plugin Name="Contact">
<Energy Type1="Foam" Type2="Foam">20</Energy>
<Energy Type1="Medium" Type2="Medium">100</Energy>
<Energy Type1="Medium" Type2="Foam">100</Energy>
<Depth>1.5</Depth>

24. PIF File <Steppable Type="PIFInitializer">
<PIFName>Foam_1.pif</PIFName>
</Steppable>
1 Foam
2 Foam
3 Foam
4 Foam
5 Foam
6 Foam
7 Foam
8 Foam
9 Foam

25. PIF Generator ./FoamInit.pl -r5 -i60 -ofoaminit1.pif -z2 -m10
Lattice dimension: x_max=301 y_max=301 z_max=1
<Dimensions x="301" y="301" z="1"/>

26. Change temperature 5 500 <Potts>
<Dimensions x="101" y="101" z="1"/>
<Anneal>0</Anneal>
<Steps>1000</Steps>
<Temperature>500</Temperature>
<Flip2DimRatio>1</Flip2DimRatio>
<Boundary_y>Periodic</Boundary_y>

27. Change Contact energy Mcs 100 Mcs 0 Mcs 50
<Plugin Name="Contact">
<Energy Type1="Foam" Type2="Foam">200</Energy>
<Energy Type1="Medium" Type2="Medium">1</Energy>
<Energy Type1="Medium" Type2="Foam">1</Energy>
<Depth>1.5</Depth>
</Plugin>

28. Order of Neighbor 5 4 3 2 1 x <Potts>
<Dimensions x="101" y="101" z="1"/>
<Anneal>0</Anneal>
<Steps>100</Steps>
<Temperature>5</Temperature>
<Flip2DimRatio>1</Flip2DimRatio>
<Boundary_y>Periodic</Boundary_y>
<Boundary_x>Periodic</Boundary_x>
<FlipNeighborMaxDistance>1.75</FlipNeighborMaxDistance>
</Potts>
<Plugin Name="Contact">
<Energy Type1="Foam" Type2="Foam">20</Energy>
<Energy Type1="Medium" Type2="Medium">100</Energy>
<Energy Type1="Medium" Type2="Foam">100</Energy>
<Depth>1.5</Depth>
</Plugin>

29. Order of Neighbor 1.5 2.7 1.1 <Plugin Name="Contact">
<Energy Type1="Foam" Type2="Foam">20</Energy>
<Energy Type1="Medium" Type2="Medium">200</Energy>
<Energy Type1="Medium" Type2="Foam">200</Energy>
<Depth>1.1</Depth>
</Plugin>

30. Temperature effect on Low Order of Neighbor
<Depth>1.1</Depth>
Temperature 20
Temperature 5
<Potts>
<Dimensions x="101" y="101" z="1"/>
<Anneal>0</Anneal>
<Steps>100</Steps>
<Temperature>5</Temperature>
<Flip2DimRatio>1</Flip2DimRatio>
<Boundary_y>Periodic</Boundary_y>
<Boundary_x>Periodic</Boundary_x>
<FlipNeighborMaxDistance>1.1</FlipNeighborMaxDistance>
</Potts>

31. Cell Sorting
Initial

32. XML file for Cell Sorting
<CompuCell3D>
<Potts>
<Dimensions x="70" y="70" z="1"/>
<Anneal>10</Anneal>
<Steps>10000</Steps>
<Temperature>5</Temperature>
<Flip2DimRatio>1</Flip2DimRatio>
<FlipNeighborMaxDistance>1.75</FlipNeighborMaxDistance>
</Potts>
<Plugin Name="Volume">
<TargetVolume>9</TargetVolume>
<LambdaVolume>3.0</LambdaVolume>
</Plugin>
<Plugin Name="Surface">
<TargetSurface>16</TargetSurface>
<LambdaSurface>0.5</LambdaSurface>
<Plugin Name="CellType">
<CellType TypeName="Medium" TypeId="0"/>
<CellType TypeName="Condensing" TypeId="1"/>
<CellType TypeName="NonCondensing" TypeId="2"/>
<Plugin Name="Contact">
<Energy Type1="Medium" Type2="Medium">0</Energy>
<Energy Type1="NonCondensing" Type2="NonCondensing">14</Energy>
<Energy Type1="Condensing" Type2="Condensing">2</Energy>
<Energy Type1="NonCondensing" Type2="Condensing">11</Energy>
<Energy Type1="NonCondensing" Type2="Medium">16</Energy>
<Energy Type1="Condensing" Type2="Medium">16</Energy>
<Depth>1.75</Depth>
<Plugin Name="CenterOfMass"/>
<Steppable Type="OutputData"/>
<Steppable Type="BlobInitializer">
<Gap>0</Gap>
<Width>2</Width>
<CellSortInit>yes</CellSortInit>
<Radius>20-</Radius>
</Steppable>
</CompuCell3D> 1 2 3 4

33. Energy setting <Plugin Name="Volume">
<TargetVolume>9</TargetVolume>
<LambdaVolume>3.0</LambdaVolume>
</Plugin>
<Plugin Name="Surface">
<TargetSurface>16</TargetSurface>
<LambdaSurface>0.5</LambdaSurface>
<Plugin Name="CellType">
<CellType TypeName="Medium" TypeId="0"/>
<CellType TypeName="Condensing" TypeId="1"/>
<CellType TypeName="NonCondensing" TypeId="2"/>
<Plugin Name="Contact">
<Energy Type1="Medium" Type2="Medium">0</Energy>
<Energy Type1="NonCondensing" Type2="NonCondensing">14</Energy>
<Energy Type1="Condensing" Type2="Condensing">2</Energy>
<Energy Type1="NonCondensing" Type2="Condensing">11</Energy>
<Energy Type1="NonCondensing" Type2="Medium">16</Energy>
<Energy Type1="Condensing" Type2="Medium">16</Energy>
<Depth>1.75</Depth>

34. Initial structure setting
<Steppable Type="BlobInitializer">
<Gap>0</Gap>
<Width>2</Width>
<CellSortInit>yes</CellSortInit>
<Radius>20-</Radius>
</Steppable>

35. Future Plans We want to hear from you Shell language interface
As matlab, FemLab
Parallelizing