compucell software current capabilities and research plan rajiv chaturvedi jesús a. izaguirre with...
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CompuCell SoftwareCompuCell Software
Current capabilities and Research Plan
Rajiv ChaturvediJesús A. Izaguirre
With Patrick M. Virtue
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ObjectiveObjectiveIntroduction to integrated Potts model simulation and visualization package called CompuCellShow simulation results (application to macrophage and bacteria movement)Present a Research and Development plan to
Model chicken limb growthModel Integration (Potts and Reaction Diffusion)
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Talk OutlineTalk OutlinePreliminary results:
Current model and software capabilities Macrophage simulation results
Research 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
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Movie from experimentsMovie from experimentshttp://www.nd.edu/~icsb
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Problem schematicProblem schematicMacrophage and bacterium
wbc
bacterium
•Periodic boundary conditions on square lattice
•Gradient fields in medium
•Linear field from left to right
•Radial field originating from bacteria
•Update field after each move
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Results: Model DescriptionResults: Model DescriptionHamiltonians:
VolumeSurfaceInteractionChemotaxis
Multiple gradients of chemical fieldLinearRadial distribution of concentration from a source
Field implementationCurrent limitation: Field as action at a distance rather than diffusing through lattice
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Results:Results: Initial and boundary Initial and boundary conditionsconditions
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 sourcePeriodic boundary conditions on lattice edges
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Results: Verification and Results: Verification and validationvalidation
Verification: Potts model for multiple fluctuating cells without chemotaxis HamiltonianPotts model for moving cells with linear gradient
Validation Qualitative studies (visual inspection) for patterns formed and those observed
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Results: SoftwareResults: Software
Software: Interactive (integrated with visualization)Stand-alone
Visualization: Uses VTK (visualization tool kit) libraries Movie creation capabilitiesImage manipulation: rotate, zoom, sectionVisualization done by Patrick Virtue
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Results: GUIResults: GUI Allows user to define initial conditions
Cells of arbitrary shape on a lattice Visualization properties for cells
Future integration with CompuCell discussed below
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Results: GuiResults: GuiGUI:
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Results: VisualizationResults: VisualizationVisualization 3D hydra burst:
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Results: Software Results: Software extensibilityextensibility
Object Oriented design: caters for reuse and extensibility by
Hierarchy of classes: General to specificAbstractionEncapsulation
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Computational engines running multiscale simulations (ellipses)
Potts Reaction diffusion
Data Communication
Experimental data
Computational engine running Analysis
Visualization Engine
High Level Architecture for Integrated PSE
GUI
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Results: Software Results: Software extensibilityextensibility
Addition of new hamiltonians (at programming level):
Derive new hamiltonian from abstract Hamiltonian classEncapsulate its data, mimic methods of other HamiltoniansTotal Hamiltonian (a subclass of Hamiltonian) takes care of Energy calculationsIn modeling code, create objects of various types of Hamiltonians, add them to TotalHamiltonian object
Addition of new fields: similarAddition of new boundary conditions
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Results: SoftwareResults: 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
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Results: cell movement in Results: cell movement in gradient gradient
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Talk OutlineTalk OutlineOverview: Integrated Problem Solving EnvironmentPreliminary results: bacteriophage problem
Current model and software capabilitiesBacteriophage simulation results
Research and Development planModeling
Steps to Chicken limb bud R-D integration
Software Integration of other models (eg., Reaction Diffusion) GUI designed for generality Visualization
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Research Plan: Cell SortingResearch Plan: Cell SortingProblem 0: (Cell sorting in the presence of a gradient)
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Research Plan: CondensationResearch Plan: CondensationProblem 1: (Cell condensation in the presence of reaction-diffusion)
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Research Plan: Limb bud Research Plan: Limb bud growthgrowth
Problem 2:
Full of 3D cells No activity in
Progress zone
TimeProgress Zone
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Research Plan: Limb bud Research Plan: Limb bud growthgrowth
Problem 1 and 2:
K steps of Reaction Diffusion in a lattice
Potts model movement, cells as moving sources
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R&D plan: Limb bud R&D plan: Limb bud growthgrowth
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
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R&D plan: Limb bud R&D plan: Limb bud growthgrowth
Software Extension needed/desired: Front end:
Integration and extension of GUIAutomated tuning of parameters (software detects param ranges where desired behavior is obtained)
Computational backend:Integration with reaction-diffusion code Handling multiple grids (hierarchy of grids, interpolation)Clustering algorithms to detect pattern formationMore efficient solvers (for 3D)
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Issue of accuracyIssue of accuracyA working definition of “good” simulation for various simulations needs to be defined.
Verification: Solving the model rightVerification against known analytical solutions
(analytical results for statistical variables in stochastic models)Quantifying accuracy of results against grid size
Validation: Solving the right model: basis of comparing results to experiments
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Integrated Problem Solving EnvironmentIntegrated 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 visualizationConfiguration files to specify initial conditions and simulation parametersRecommender system (to assist user)GUI to allow for user inputsAbility to allow user to choose models (in the long run) through a GUI