Celldesigner: a process diagram editor for gene-regulatory and biochemical networks. CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW). CellDesigner supports simulation and parameter scan by an integration with SBML ODE Solver, SBML Simulation Core and Copasi. By using CellDesigner, you can browse and modify existing SBML models with references to existing databases, simulate and view the dynamics through an intuitive graphical interface.

References in zbMATH (referenced in 21 articles )

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  1. Duintjer Tebbens, Jurjen; Matonoha, Ctirad; Matthios, Andreas; Papáček, Štěpán: On parameter estimation in an in vitro compartmental model for drug-induced enzyme production in pharmacotherapy. (2019)
  2. Hinze, Thomas: The Java environment for nature-inspired approaches (JENA): a workbench for biocomputing and biomodelling enthusiasts (2018)
  3. Shafaghati, Leila; Razaghi-Moghadam, Zahra; Mohammadnejad, Javad: A systems biology approach to understanding alcoholic liver disease molecular mechanism: the development of static and dynamic models (2017)
  4. Pardini, Giovanni; Milazzo, Paolo; Maggiolo-Schettini, Andrea: Component identification in biochemical pathways (2015)
  5. Pardini, Giovanni; Milazzo, Paolo; Maggiolo-Schettini, Andrea: An algorithm for the identification of components in biochemical pathways (2013)
  6. Samal, Satya Swarup; Errami, Hassan; Weber, Andreas: PoCaB: a software infrastructure to explore algebraic methods for bio-chemical reaction networks (2012)
  7. Hoppe, Andreas; Hoffmann, Sabrina; Gerasch, Andreas; Gille, Christoph; Holzhütter, Hermann-Georg: FASIMU: flexible software for flux-balance computation series in large metabolic networks (2011) ioport
  8. Jack, John; Păun, Andrei; Rodríguez-Patón, Alfonso: A review of the nondeterministic waiting time algorithm (2011) ioport
  9. Latendresse, Mario; Karp, Peter D.: Web-based metabolic network visualization with a zooming user interface (2011) ioport
  10. Albrecht, Mario; Kerren, Andreas; Klein, Karsten; Kohlbacher, Oliver; Mutzel, Petra; Paul, Wolfgang; Schreiber, Falk; Wybrow, Michael: On open problems in biological network visualization (2010)
  11. Barbuti, Roberto; Lepri, Daniela; Maggiolo-Schettini, Andrea; Milazzo, Paolo; Pardini, Giovanni; Rama, Aureliano: Simulation of Kohn’s molecular interaction maps through translation into stochastic CLS+ (2010)
  12. Likić, Vladimir A.; McConville, Malcolm J.; Lithgow, Trevor; Bacic, Antony: Systems biology: the next frontier for bioinformatics (2010)
  13. Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro: TinkerCell: Modular CAD Tool for Synthetic Biology (2009) arXiv
  14. Dogrusöz, Ugur; Cetintas, Ahmet; Demir, Emek; Babur, Ozgun: Algorithms for effective querying of compound graph-based pathway databases (2009) ioport
  15. Ghosh, Preetam; Ghosh, Samik; Basu, Kalyan; Das, Sajal: Parametric modeling of protein-DNA binding kinetics: a discrete event based simulation approach (2009)
  16. Hinze, Thomas; Faßler, Raffael; Lenser, Thorsten; Matsumaru, Naoki; Dittrich, Peter: Event-driven metamorphoses of P systems (2009)
  17. Jack, John; Păun, Andrei: Discrete modeling of biochemical signaling with memory enhancement (2009)
  18. Tran, Nam; Baral, Chitta: Hypothesizing about signaling networks (2009)
  19. Van Beek, Johannes H. G. M.; Hauschild, Anne-Christin; Hettling, Hannes; Binsl, Thomas W.: Robust modelling, measurement and analysis of human and animal metabolic systems (2009)
  20. Dampier, William; Tozeren, Aydin: Signaling perturbations induced by invading \textitH. pylori proteins in the host epithelial cells: a mathematical modeling approach (2007)

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