lecture 3: pathway generation tool i: celldesigner: a modeling tool of biochemical networks y.z....
TRANSCRIPT
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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
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What is Celldesigner?What is Celldesigner?
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What is Celldesigner?What is Celldesigner?
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What is CellDesigner?What is CellDesigner?
• 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)
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What is CellDesigner?What is CellDesigner?
• 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.
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Systems Biology Graphical NotationSystems Biology Graphical Notation• A visual notation for network diagrams
• To help standardize a graphical notation for computational models in systems biology
• A natural complement to SBML
Link to
SBGN webpage
online document
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Systems Biology Graphical NotationSystems Biology Graphical Notation
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Systems Biology Graphical NotationSystems Biology Graphical NotationLink to SBGN webpage, online document
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Systems Biology Graphical NotationSystems Biology Graphical NotationStep 1: Block diagram
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Systems Biology Graphical NotationSystems Biology Graphical NotationStep 2: Molecular Interaction Map
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Systems Biology Graphical NotationSystems Biology Graphical NotationStep 3: Edinburgh Notation
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Systems Biology Graphical NotationSystems Biology Graphical NotationStep 3: Edinburgh Notation
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Systems Biology Graphical NotationSystems Biology Graphical Notation
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Systems Biology Graphical NotationSystems Biology Graphical Notation
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Systems Biology Graphical NotationSystems Biology Graphical NotationPlease read this online manual as part of your homework
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Systems Biology Graphical NotationSystems Biology Graphical Notation
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Systems Biology Graphical NotationSystems Biology Graphical Notation
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Systems Biology Graphical NotationSystems Biology Graphical Notation
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Systems Biology Markup LanguageSystems Biology Markup Language
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Systems Biology Markup LanguageSystems Biology Markup Language• A computer-readable format for representing models of biochemical
reaction networks.
• Applicable to metabolic networks, cell-signaling pathways, regulatory networks, and many others.
• Supported by over 120 software systems (as of Jan 2008)
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Systems Biology Markup LanguageSystems Biology Markup Language
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Systems Biology Markup LanguageSystems Biology Markup Language
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Systems Biology Markup LanguageSystems Biology Markup Language
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Systems Biology Markup LanguageSystems Biology Markup LanguagePlease read SBML manual
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Systems Biology Markup LanguageSystems Biology Markup LanguageSName
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Systems Biology Markup LanguageSystems Biology Markup LanguageRules
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Systems Biology Markup LanguageSystems Biology Markup LanguageDefinition of rule and derived types
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Systems Biology Markup LanguageSystems Biology Markup LanguageMathematical functions
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Systems Biology Markup LanguageSystems Biology Markup LanguageRate law functions
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Systems Biology Markup LanguageSystems Biology Markup LanguageRate law functions
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Systems Biology Markup LanguageSystems Biology Markup LanguageRate law functions
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Systems Biology Markup LanguageSystems Biology Markup LanguageRate law functions
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Systems Biology Markup LanguageSystems Biology Markup LanguageSymbols
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Systems Biology Markup LanguageSystems Biology Markup LanguageSymbols
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Systems Biology Markup LanguageSystems Biology Markup LanguageSymbols
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Systems Biology Markup LanguageSystems Biology Markup LanguageSymbols
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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.
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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
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Celldesigner VersionsCelldesigner Versions
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Celldesigner VersionsCelldesigner Versions
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Celldesigner FeaturesCelldesigner Features
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Celldesigner FeaturesCelldesigner Features
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Celldesigner FeaturesCelldesigner Features
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Celldesigner FeaturesCelldesigner Features
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Celldesigner FeaturesCelldesigner Features