Pathway Databases

directly accessible from CellDesigner's database menu:

• PANTHER Pathway database
• BioModels.Net

Models built with CellDesigner

CellDesigner Ver.4

• RB/E2F: Calzone L, Gelay A, Zinovyev A, Radvanyl F & Barillot E, Mol Syst Biol. 2008.4; Epub 2008 Mar 4, doi:10.1038/msb.2008.7
• A general map of iron metabolism and tissue-specific subnetworks, Mol. BioSyst. 2009 5,422-443, doi:10.1039/b816714c
• Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase. Patil et al. BMC Syst Biol (2010) vol. 4 pp. 137
• Hormone Receptor-Mediated Signaling Network in L{beta}T2 Cells: A Pathway-Based Web-Accessible Knowledgebase. Fink et al. Gonadotropin-Releasing Molecular endocrinology (Baltimore, Md) (2010) pp.
• budding yeast cell cycle Kaizu K et al, Mol Syst Biol (2010) vol. 6(1)
• mTOR signaling network. Caron et al. Molecular Systems Biology (2010) vol. 6 pp. 453
• Rheumatoid Artritis map Wu G et al, 2010, PLoS ONE

Models created by CellDesigner Ver.3

• PANTHER database
• RB/E2F pathway
  published online in Molecular Systems Biology http://www.nature.com/msb/journal/v4/n1/full/msb20087.html

Models created by CellDesigner Ver.2

• Metabolic Syndrome
  (adipocyte, hepatocyte, skeletal muscle cell, pancreatic beta cell)
• Molecular Interaction map of Macrophage
• EGFR(=Epidermal Growth Factor Receptor) pathway map
• Toll-Like Receptor signaling network
• Yeast Map

SBML models which can be retrieved to CellDesigner:

• SBML models for KEGG
• SBML models from Reactome
• SBML Model Repository


• systems-biology.org model repository
• BioModels.Net Simulation Results

Sample Files

• Samples for "The Process Diagram: Rationale and Description".