lecture 3: pathway generation tool i: celldesigner: a modeling tool of biochemical networks y.z....

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

mailto:[email protected]

http://bidd.nus.edu.sg/

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What is Celldesigner?What is Celldesigner?

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What is Celldesigner?What is Celldesigner?

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)

http://www.systems-biology.org/cd/

http://sbml.org/index.psp


http://128.208.17.155/research/sbwIntro.htm

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.

http://www.tbi.univie.ac.at/~raim/odeSolver/

http://en.wikipedia.org/wiki/Ordinary_differential_equation

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

http://sbgn.org/

http://sbgn.org/doku.php?id=current_working_draft_proposal

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Systems Biology Graphical NotationSystems Biology Graphical Notation

Systems Biology Graphical NotationSystems Biology Graphical NotationLink to SBGN webpage, online document

http://sbgn.org/

http://sbgn.org/doku.php?id=current_working_draft_proposal

Systems Biology Graphical NotationSystems Biology Graphical NotationStep 1: Block diagram

Systems Biology Graphical NotationSystems Biology Graphical NotationStep 2: Molecular Interaction Map

Systems Biology Graphical NotationSystems Biology Graphical NotationStep 3: Edinburgh Notation

Systems Biology Graphical NotationSystems Biology Graphical NotationPlease read this online manual as part of your homework

http://sbgn.cvs.sourceforge.net/*checkout*/sbgn/documents/specifications/Level1/sbgn-level1.pdf

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Systems Biology Markup LanguageSystems Biology Markup Language

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 LanguagePlease read SBML manual

http://sbml.org/specifications/sbml-level-1/version-2/html/sbml-level-1.html

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 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.

http://www.tbi.univie.ac.at/~raim/odeSolver/doc/api.html


http://en.wikipedia.org/wiki/ISO_C#ANSI_C_and_ISO_C

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

Celldesigner VersionsCelldesigner Versions

Celldesigner FeaturesCelldesigner Features

lecture 3: pathway generation tool i: celldesigner: a modeling tool of biochemical networks y.z....

Documents

software systems

intuitive graphical

existing sbml models

generegulatory networks

metabolic networks

computational models

biochemical networksnetworks

drawing generegulatory