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 11 articles )

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  1. Pardini, Giovanni; Milazzo, Paolo; Maggiolo-Schettini, Andrea: Component identification in biochemical pathways (2015)
  2. Pardini, Giovanni; Milazzo, Paolo; Maggiolo-Schettini, Andrea: An algorithm for the identification of components in biochemical pathways (2013)
  3. Samal, Satya Swarup; Errami, Hassan; Weber, Andreas: PoCaB: a software infrastructure to explore algebraic methods for bio-chemical reaction networks (2012)
  4. Jack, John; Păun, Andrei; Rodríguez-Patón, Alfonso: A review of the nondeterministic waiting time algorithm (2011) ioport
  5. Albrecht, Mario; Kerren, Andreas; Klein, Karsten; Kohlbacher, Oliver; Mutzel, Petra; Paul, Wolfgang; Schreiber, Falk; Wybrow, Michael: On open problems in biological network visualization (2010)
  6. 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)
  7. Likić, Vladimir A.; Mcconville, Malcolm J.; Lithgow, Trevor; Bacic, Antony: Systems biology: the next frontier for bioinformatics (2010)
  8. Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro: TinkerCell: Modular CAD Tool for Synthetic Biology (2009) arXiv
  9. Ghosh, Preetam; Ghosh, Samik; Basu, Kalyan; Das, Sajal: Parametric modeling of protein-DNA binding kinetics: a discrete event based simulation approach (2009)
  10. Tran, Nam; Baral, Chitta: Hypothesizing about signaling networks (2009)
  11. 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)