CellDesigner uses Process Diagram Notation (Kitano 2005) to illustrate molecular events and biochemical reactions of pathways, and it automatically creates a computational representation that is compatible with the Systems Biology Markup Language (SBML, Hucka 2003).

• PANTHER Tutorial - quick startup guide on drawing pathways using CellDesigner (pdf, ppt)
• For additional details, please reference Help page from CellDesigner.

If you still have questions, send email to pathcuration@pantherdb.org for further support. An online webex tutorial can be scheduled.

Examples of Reactions

• Binding_inhibition (jpg, xml)
• G_protein_activation (jpg, xml)
• Ion_channel (jpg, xml)
• Ligand_receptor_binding (jpg, xml)
• Protease_cleavage (jpg, xml)
• Protein_degradation (jpg, xml)
• Protein_phosphorylation (jpg, xml)
• Transcription_regulation (jpg, xml)
• Transporter (jpg, xml)

References for CellDesigner and SBML

• Kitano, H.et al. (2005) Using process diagram for the graphical representation of biological networks. Nature Biotechnology 23(8), 961-966.
• Funahashi, A., Tanimura, N., Morohashi, M., and Kitano, H. (2003) CellDesigner: a process diagram editor for gene-regulatory and biochemical networks, BIOSILICO, 1:159-162.
• Kitano, H. The Process Diagram: Rational and Definition
• Hucka, M.; Finney, A.; Sauro, H.M.; Bolouri, H.; Doyle, J.C.; Kitano, H. et al. (2003) The Systems Biology Markup Language (SBML): A Medium for Representation and Exchange of Biochemical Network Models. Bioinformatics. 19. 524-531.