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CellDesigner and Virtual Cell

Leang Chhun and Chanchala Kaddi Georgia Institute of Technology 29 June, 2006. CellDesigner and Virtual Cell. Goal. Describe two simulation tools CellDesigner and Virtual Cell Brief tutorials of each Separate case study. CellDesigner. Free download; no registration required

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CellDesigner and Virtual Cell

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  1. Leang Chhun and Chanchala Kaddi Georgia Institute of Technology 29 June, 2006 CellDesigner and Virtual Cell

  2. Goal • Describe two simulation tools • CellDesigner and Virtual Cell • Brief tutorials of each • Separate case study

  3. 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

  4. Case Study • Belousov-Zhabotinsky (BZ) Reaction • Oscillating reaction • Does not follow equilibrium thermodynamic behavior • Traces concentrations • BrO3 • HOBr • Cerium(IV) • Br • HBrO2

  5. Steps to Complete Model • Create the physical model • Add other information • Reaction equations • Reaction rates • Parameters • Simulate model • Analyze results

  6. Layout Component Icons Parameters Physical Model

  7. Creating the Model • Compartments • Species • Reaction arrows

  8. Physical Model Compartment Reaction Arrows Species CellDesigner Model of Belousov-Zhabotinsky Reaction

  9. Add Information • Reaction equations • Concentration of species • Rate constants • Initial parameters

  10. Parameters Initial values of species Reaction equations Reaction rate constants Definitions of species, reactions, etc.

  11. Simulation/Results • Simulation>Control Panel • Define end time and number of points • Execute • Directly plotted

  12. Control Panel End time, # of points Output Plot Parameter values

  13. Results Oscillation patterns CellDesigner results of BZ Reaction (Run time: 1000s, # of steps: 100

  14. CellDesigner Summary • Models biochemical networks • GUI • SBML • Graphical and mathematical notation • Select different species types • SBML ODE solver

  15. 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

  16. 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

  17. Creating the Model • Add compartments/membranes • Select feature tool and label membrane and compartment • Add species • Defined in parts of compartments

  18. Physical Model Pointer Membrane Species Biomodel of Facilitated Calcium Diffusion

  19. Add Information • Reaction equations (case specific) • Add flux across membranes • Add flux equation to flux icon • Initial parameters Virtual Cell Flux diagram

  20. Add Application • Case specific • Add geometry associated with case study

  21. Simulation Time Scroll • Application window>Simulations • Run • Results saved to online database • View results Geometry (Cell) Species

  22. Virtual Cell • Change in concentration of CaB 1sec 3sec 5sec 10sec

  23. Virtual Cell Summary • Models biochemical networks; java interface • Graphical and mathematical interfaces. • General species, features tools. • Several ODE solvers

  24. Comparison CellDesignerVirtual Cell Ease of Use: No tutorials Several tutorials Simulations: GUIs; SBML, No SBML SBW Databases: Biomodels.net KEGG

  25. Comparison CellDesignerVirtual Cell Geometries: N/A 2D & 3D Electrical: N/A Membrane Mapping Potentials, Stimuli ODE Solvers: SBML ODE Euler, Runge- Kutta, etc.

  26. CellDesigner Concentration plots only Only one ODE solver Virtual Cell Internet connection required Not SBML based Drawbacks

  27. CellDesigner Concentration plots GUI, graphical notation SBML compliant Virtual Cell 3D visual aid Electrical mapping Multiple ODE solvers Positive Features

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