CellDesigner Documents / Papers using CellDesigner Models

CellDesigner is a modeling tool of biochemical networks with graphical user interface. It is designed to be SBW (Systems Biology Workbench) compliant, and support SBML (Systems Biology Markup Language) format.


Developers Documents

Related Papers & Documentation


  1. Funahashi, A., Tanimura, N., Morohashi, M., and Kitano, H., CellDesigner: a process diagram editor for gene-regulatory and biochemical networks, BIOSILICO, 1:159-162, 2003
  2. Funahashi, A., Jouraku, A., Matsuoka, Y., Kitano, H., Integration of CellDesigner and SABIO-RK, In Silico Biol. 2007;7(2 Supple):S81-90
  3. Funahashi, A.; Matsuoka, Y.; Jouraku, A.; Morohashi, M.; Kikuchi, N.; Kitano, H."CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks" Proceedings of the IEEE Volume 96, Issue 8, Aug. 2008 Page(s):1254 - 1265
    [doi 10.1109/JPROC.2008.925458] Abstract  | Full Text: PDF (1379 KB)

Graphical Notation

  1. Kitano, H.et al. "Using process diagram for the graphical representation of biological networks", Nature Biotechnology 23(8), 961-966 (2005)
  2. Kitano, H.. "The Process Diagram: Rational and Definition" - [ pdf ] [ html ]
  3. Kitano, H.. A graphical notation for biochemical networks. BIOSILICO. 1. 169-176. 2003.


  1. Le Novere et al., Systems Biology Graphical Notation. Nature Biotech. 2009 [doi:10.1038/nbt1558]


  1. M. Hucka; A. Finney; B.J. Bornstein; S.M. Keating; B.E. Shapiro; J. Matthews; B.L. Kovitz; M.J. Schilstra; A. Funahashi; J.C. Doyle; and H. Kitano Evolving a lingua franca and associated software infrastructure for computational systems biology: theSystemsBiologyMarkupLanguage(SBML) project. IEE Systems Biology. 1:41-53, 2004
  2. Hucka, M.; Finney, A.; Sauro, H.M.; Bolouri, H.; Doyle, J.C.; Kitano, H. et al. The Systems Biology Markup Language(SBML): A Medium for Representation and Exchange of Biochemical Network Models. Bioinformatics. 19. 524-531. 2003.


  1. Simulation of SBML file with Mathematica using MathSBML
  2. Simulation with Jarnac 2.0


  1. Huaiyu Mi, Betty Lazareva-Ulitsky, Rozina Loo, Anish Kejariwal, Jody Vandergriff, Steven Rabkin, Nan Guo, Anushya Muruganujan, Olivier Doremieux, Michael J. Campbell, Hiroaki Kitano and Paul D. Thomas.The PANTHER database of protein families, subfamilies, functions and pathways. Nucl. Acids. Res., 2005. 31:334-341.
  2. Mi H, Guo N, Kejariwal A, Thomas PD., PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways.Nucleic Acids Res. 2007 Jan;35(Database issue):D247-52. Epub 2006 Nov 27

Models buit with CellDesigner

  1. Oda K, Matsuoka Y, Funahashi A, Kitano H., A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol. 2005;1:2005.0010. Epub 2005 May 25
  2. Oda, K.; Kimura, T, Matsuoka, Y.; Funahashi, A.; Muramatsu, M.; Kitano, H. Molecular Interaction Map of Macrophage . AfCS Research Reports. 2004.
  3. Oda K. and Kitano H., A comprehensive map of the toll-like receptor signaling network. Mol Sys Bio (2006) vol. 2 doi:10.1038/msb4100057
  4. Dampier, W & Tozeren, A. Signaling perturbations induced by invading H.pylori proteins in the host epithelial cells: A mathematical modeling approach. Journal of Theoretical Biology 248, 130-144 (2007)
  5. Calzone L, Gelay A, Zinovyev A, Radvanyl F & Barillot E, A comprehensive modular map of molecular interactions in RB/E2F pathway, Mol Syst Biol. 2008.4; Epub 2008 Mar 4, doi:10.1038/msb.2008.7
  6. Hower V, Mendes P, Torti FM, Laubenbacher R, Akman S, Shulaev V, Torti SV, A general map of iron metabolism and tissue-specific subnetworks, Mol. BioSyst. 2009 5,422-443, doi:10.1039/b816714c
  7. Wu G, Zhu L, Dent JE, Nardini C, 2010 A Comprehensive Molecular Interaction Map for Rheumatoid Arthritis. PLoS ONE 5(4): e10137. doi:10.1371/journal.pone.0010137
  8. Patil et al. Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase. BMC Syst Biol (2010) vol. 4 pp. 137
  9. Fink et al. Gonadotropin-Releasing Hormone Receptor-Mediated Signaling Network in L{beta}T2 Cells: A Pathway-Based Web-Accessible Knowledgebase. Molecular endocrinology (Baltimore, Md) (2010) pp.
  10. Kaizu K et al, A comprehensive molecular interaction map of the budding yeast cell cycle. Mol Syst Biol (2010) vol. 6(1)
  11. Caron et al. A comprehensive map of the mTOR signaling network. Molecular Systems Biology (2010) vol. 6 pp. 453

CellDesigner Plugins

  1. Andreas Draeger , Nadine Hassis , Jochen Supper , Adrian Schroeder and Andreas Zell, SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks, BMC Systems Biology 2008, 2:39doi:10.1186/1752-0509-2-39,
  2. John L. Van Hemert; Julie A. Dickerson, PathwayAccess: CellDesigner Plugins for Pathway Databases
    Bioinformatics 2010; doi: 10.1093/bioinformatics/btq423
    PMID: 20647521
  3. Mi et al. BioPAX Support in CellDesigner. Bioinformatics (2011) pp.

CellDesigner Related Utilities

  1. Zinovyev A., Viara E., Calzone L., Barillot E. BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics 2007 doi: 10.1093/bioinformatics/btm553
  2. Viswanathan GA., Nudelman G., Patil S., Sealfon SC., BioPP: a tool for web-publication of biological networks, BMC Bioinformatics. 2007 May 22;8:168.
  3. Matsuoka Y., Ghosh S., Kikuchi N., Kitano H., Payao : A Community Platform for SBML Pathway Model Curation. Bioinformatics 2010 doi:10.1093/bioinformatics/btq143
  4. Florez LA., Lammers CR., Michna R., Stuke J., CellPublisher: a web platform for the intuitive visualization and sharing of metabolic, signaling and regulatory pathways, Bioinformatics 2010 doi: 10.1093/bioinformatics/btq585
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