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CompuCell Software
Current capabilities and
Research Plan
Rajiv Chaturvedi
Jesús A. Izaguirre
With Patrick M. Virtue
Objective
Introduction
to integrated Potts model simulation and
visualization package called CompuCell
Show simulation results (application to macrophage and
bacteria movement)
Present a Research and Development plan to
Model chicken limb growth
Model Integration (Potts and Reaction Diffusion)

Talk Outline
Preliminary


Current model and software capabilities
Macrophage simulation results
Research


results:
and Development plan
Modeling
 Cell condensation in 2D
 Chicken limb bud in 2D
 R-D integration
 (Flock modeling)
Software
 Integration of other models (eg., Reaction Diffusion)
 GUI designed for generality
 3-d simulation an dvisualization
Movie from experiments
http://www.nd.edu/~icsb
Problem schematic
Macrophage and bacterium
•Periodic boundary
conditions on square
lattice
•Gradient fields in
medium
•Linear field
from left to right
wbc
bacterium
•Radial field
originating from
bacteria
•Update field after
each move
Results: Model Description
Hamiltonians:
Volume
Surface
Interaction
Chemotaxis

Multiple
gradients of chemical field
Linear
Radial distribution of concentration from a source

Field
implementation
Current limitation: Field as action at a distance rather than
diffusing through lattice

Results: Initial and boundary conditions
SubDomains

in software <-> Cells in the model:
Experimented with 2 and 3 cells in the lattice
Boundaries:
The pixels of the changing bacteria boundary act as source
Periodic boundary conditions on lattice edges

Results: Verification and validation
Verification:
Potts model for multiple fluctuating cells without
chemotaxis Hamiltonian
Potts model for moving cells with linear gradient

Validation
Qualitative studies (visual inspection) for patterns
formed and those observed

(Show animated gif)
Results: Software
Software:
Interactive (integrated with visualization)
Stand-alone

Visualization:
Uses VTK (visualization tool kit) libraries
Movie creation capabilities
Image manipulation: rotate, zoom, section
Visualization done by Patrick Virtue

Results: GUI
Allows user to define initial
conditions

Cells of arbitrary shape on a
lattice
 Visualization properties for cells

Future integration with
CompuCell discussed below

Results: Gui
GUI:
Results: Visualization
Visualization
3D hydra burst:
Results: Software
extensibility
Object
Oriented design: caters for reuse and
extensibility by
Hierarchy of classes: General to specific
Abstraction
Encapsulation

GUI
Visualization
Engine
Data Communication
Potts
Computational
engine running
Analysis
Reaction diffusion
Computational engines running
multiscale simulations (ellipses)
Experimen
tal data
High Level Architecture for Integrated PSE
Results: Software
extensibility
Addition
of new hamiltonians (at programming level):
Derive new hamiltonian from abstract Hamiltonian class
Encapsulate its data, mimic methods of other Hamiltonians
Total Hamiltonian (a subclass of Hamiltonian) takes care of
Energy calculations
In modeling code, create objects of various types of
Hamiltonians, add them to TotalHamiltonian object

Addition
of new fields: similar
Addition of new boundary conditions
Results: Software

Input:




Command line
prompts
File input (and from
GUI)
Initial conditions


Lattice
Cells


Positions and sizes
Parameters

Constraints params…
Output:



Runtime
visualization
Movies
Post processing
mode
Results: cell movement in gradient
(Show animated gif)
Talk Outline
Overview:
Integrated Problem Solving Environment
Preliminary results: bacteriophage problem
Current model and software capabilities
Bacteriophage simulation results

Research
and Development plan
Modeling
 Steps to Chicken limb bud
 R-D integration
Software
 Integration of other models (eg., Reaction Diffusion)
 GUI designed for generality
 Visualization

Research Plan: Cell Sorting
Problem
0: (Cell sorting in the presence of a gradient)
Research Plan: Condensation
Problem
1: (Cell condensation in the presence of
reaction-diffusion)
Research Plan: Limb bud growth
Problem
2:
Time
Full of 3D cells
No activity in
Progress zone
Progress Zone
Research Plan: Limb bud growth
Problem
1 and 2:
K steps of Reaction Diffusion in a lattice
Potts model movement, cells as moving sources
R&D plan: Limb bud growth
Model
extension needed:
Diffusive gradients
 Reaction diffusion equations to solve
 Extra cellular matrix characterization (field)
 Progress zone characterization (in Potts model)
 Set of reasonable initial/boundary conditions, and
parameters for Potts model validation
 3 D potts
 3 D RD

R&D plan: Limb bud growth
Software
Front
Extension needed/desired:
end:
Integration
and extension of GUI
Automated tuning of parameters (software detects param
ranges where desired behavior is obtained)
Computational
Integration
backend:
with reaction-diffusion code
Handling multiple grids (hierarchy of grids, interpolation)
Clustering algorithms to detect pattern formation
More efficient solvers (for 3D)
Issue of accuracy
A
working definition of “good” simulation for various
simulations needs to be defined.

Verification: Solving the model right
Verification
against known analytical solutions
(analytical
Quantifying
results for statistical variables in stochastic models)
accuracy of results against grid size
Validation: Solving the right model: basis of comparing results to
experiments

Integrated Problem Solving Environment
Grand
aim: The end user must be able to focus on
Biology/ Physics problems rather than software/
programming.
Runtime and post processing visualization
Configuration files to specify initial conditions and
simulation parameters
Recommender system (to assist user)
GUI to allow for user inputs
Ability to allow user to choose models (in the long
run) through a GUI