CellDesigner and Virtual Cell

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This presentation from the BioMIBLab Summer 2006 Workshop is a comparison of two imaging bioinformatics tools.



A simulation tool that models biochemical networks.

Virtual Cell

A simulation tool that models biochemical networks with a Java interface.


  • Free download; no registration required
  • SBML compliant-standardized technology
  • Can be run on multiple platforms
  • Graphical Notation, Mathematical Notation
  • Can select different species types
Virtual Cell
  • Free but must be registered user
  • Can only be run from website
  • Requires Java Runtime Environment
  • 3 components
Modeling framework
Mathematics framework
Internet based
  • Graphical and mathematical interfaces.
  • General species, features tools.
  • Several ODE solvers
  • Has many tutorials

Full Presentation

CellDesigner and Virtual Cell PowerPoint Presentation


Cell Designer
"CellDesigner: a process diagram editor for gene-regulatory and biochemical networks" Funahashi, et al.

Support Documents

Control Panel Tutorial
Virtual Cell
Users Guide
Quick Start Guide
Facilitated Calcium Diffusion in the Intestinal Epithelial Cell
Creating a FRAP BioModel
Creating a FRAP binding BioModel
Membrane Potential


CellDesigner Homepage Virtual Cell Homepage