CellDesigner and Virtual Cell

Leang Chhun and Chanchala Kaddi

Georgia Institute of Technology

29 June, 2006

Goal

• Describe two simulation tools– CellDesigner and Virtual Cell

• Brief tutorials of each– Separate case study

CellDesigner• Free download; no registration required• SBML compliant

– standardized technology

• Can be run on multiple platforms– Windows– MacOS X– Linux– FreeBSD

• Graphical Notation, Mathematical Notation• www.celldesigner.org

Case Study

• Belousov-Zhabotinsky (BZ) Reaction– Oscillating reaction– Does not follow equilibrium thermodynamic

behavior– Traces concentrations

• BrO3

• HOBr• Cerium(IV)• Br

• HBrO2

Steps to Complete Model

• Create the physical model

• Add other information– Reaction equations

– Reaction rates

– Parameters

• Simulate model

• Analyze results

LayoutComponent Icons

Physical Model

Parameters

Creating the Model

• Compartments

• Species

• Reaction arrows

Physical Model

CellDesigner Model of Belousov-Zhabotinsky Reaction

Compartment

Species

ReactionArrows

Add Information

• Reaction equations– Concentration of species

– Rate constants

• Initial parameters

Parameters

Definitions of species, reactions, etc.

Initial valuesof species

Reactionequations

Reaction rateconstants

Simulation/Results

• Simulation>Control Panel

• Define end time and number of points

• Execute

• Directly plotted

Control PanelEnd time,# of points

Parameter values

Output Plot

Results

CellDesigner results of BZ Reaction (Run time: 1000s, # of steps: 100

Oscillation patterns

CellDesigner Summary

• Models biochemical networks– GUI

– SBML

• Graphical and mathematical notation

• Select different species types

• SBML ODE solver

Virtual Cell

• Free but must be registered user

• Can only be run from website

• Run as Java Applet or Java Application– Requires Java Runtime Environment

• 3 components: – Modeling framework

– Mathematics framework

– Internet based

• www.vcell.org

Case Study

• Online tutorials

• Used to show capabilities of software

• Models calcium channels and pumps through membranes

• Facilitated calcium diffusion in epithelial cells

• http://www.vcell.org/login/facil_ca_dif.pdf

Creating the Model

• Add compartments/membranes– Select feature tool and label membrane and

compartment

• Add species– Defined in parts of compartments

Physical Model

Biomodel of Facilitated Calcium Diffusion

Pointer

Membrane

Species

Add Information

• Reaction equations (case specific)– Add flux across membranes

– Add flux equation to flux icon

• Initial parameters

Virtual Cell Flux diagram

Add Application

• Case specific– Add geometry

associated with case study

Simulation

• Application window>Simulations

• Run

• Results saved to online database

• View results

Time ScrollGeometry (Cell)

Species

Virtual Cell

• Change in concentration of CaB

1sec

5sec

3sec

10sec

Virtual Cell Summary

• Models biochemical networks; java interface

• Graphical and mathematical interfaces.

• General species, features tools.

• Several ODE solvers

Comparison

CellDesigner Virtual Cell

Ease of Use: No tutorials Several tutorials

Simulations: GUIs; SBML, No SBML SBW

Databases: Biomodels.net KEGG

Comparison

CellDesigner Virtual Cell

Geometries: N/A 2D & 3D

Electrical: N/A Membrane

Mapping Potentials, Stimuli

ODE Solvers: SBML ODE Euler, Runge-

Kutta, etc.

Drawbacks

• CellDesigner– Concentration plots

only– Only one ODE solver

• Virtual Cell– Internet connection

required– Not SBML based

Positive Features

• CellDesigner– Concentration plots– GUI, graphical

notation– SBML compliant

• Virtual Cell– 3D visual aid– Electrical mapping– Multiple ODE

solvers