Lecture 3: Pathway Generation Tool I: Lecture 3: Pathway Generation Tool I: CellDesigner: A modeling tool of biochemical CellDesigner: A modeling tool of biochemical networks networks Y.Z. Chen Y.Z. Chen Department of Pharmacy Department of Pharmacy National University of Singapore National University of Singapore Tel: 65-6616-6877; Email: Tel: 65-6616-6877; Email: [email protected][email protected]; Web: ; Web: http://bidd.nus.edu.sg http://bidd.nus.edu.sg Content Content • CellDesigner overview CellDesigner overview • Introduction of systems biology platforms and Introduction of systems biology platforms and software used by Celldesigner software used by Celldesigner • CellDesigner versions and features CellDesigner versions and features
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Lecture 3: Pathway Generation Tool I: CellDesigner: A modeling tool of biochemical networks Y.Z. Chen Department of Pharmacy National University of Singapore.
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Lecture 3: Pathway Generation Tool I:Lecture 3: Pathway Generation Tool I:CellDesigner: A modeling tool of biochemical networks CellDesigner: A modeling tool of biochemical networks
Y.Z. ChenY.Z. ChenDepartment of PharmacyDepartment of Pharmacy
National University of SingaporeNational University of Singapore Tel: 65-6616-6877; Email: Tel: 65-6616-6877; Email: [email protected]@nus.edu.sg ; Web: ; Web: http://bidd.nus.edu.sghttp://bidd.nus.edu.sg
ContentContent
• CellDesigner overviewCellDesigner overview
• Introduction of systems biology platforms and software used by Introduction of systems biology platforms and software used by CelldesignerCelldesigner
• CellDesigner versions and featuresCellDesigner versions and features
• 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 (what is ODE?) .
• 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.
Systems Biology Markup LanguageSystems Biology Markup LanguageSName
Systems Biology Markup LanguageSystems Biology Markup LanguageRules
Systems Biology Markup LanguageSystems Biology Markup LanguageDefinition of rule and derived types
Systems Biology Markup LanguageSystems Biology Markup LanguageMathematical functions
Systems Biology Markup LanguageSystems Biology Markup LanguageRate law functions
Systems Biology Markup LanguageSystems Biology Markup LanguageRate law functions
Systems Biology Markup LanguageSystems Biology Markup LanguageRate law functions
Systems Biology Markup LanguageSystems Biology Markup LanguageRate law functions
Systems Biology Markup LanguageSystems Biology Markup LanguageSymbols
Systems Biology Markup LanguageSystems Biology Markup LanguageSymbols
Systems Biology Markup LanguageSystems Biology Markup LanguageSymbols
Systems Biology Markup LanguageSystems Biology Markup LanguageSymbols
The SBML ODE Solver LibraryThe SBML ODE Solver Library• A programming library and a command-line application for
symbolic and numerical analysis of a system of ordinary differential equations (ODEs) derived from a chemical reaction network encoded in the Systems Biology Markup Language (SBML).
• Written in ANSI/ISO C and distributed under the terms of the GNU Lesser General Public License (LGPL)
• The package employs libSBML's AST (Abstract Syntax Tree) for formula representation to construct ODE systems, their Jacobian matrix and other derivatives
• SUNDIALS' version of CVODE is incorporated for numerical integration and sensitivity analysis of stiff and non-stiff ODE systems.
The SBML ODE Solver LibraryThe SBML ODE Solver Library• The native API provides fine-grained interfaces to all
internal data structures, symbolic operations and numerical routines, enabling the construction of powerful and efficient analytic applications, hybrid solvers or multi-scale models with interfaces to non SBML data sources.
• Optional modules based on Graphviz and XMGrace allow a quick inspection of a model's structure and dynamics.
• All functionalities are accessible directly via a command-line application and several example programs.
• Applications using SOSlib: CellDesigner, SBMLodeSolveR, SOSlib integration server, PyLESS