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Content CellDesigner overview

Lecture 3: Pathway Generation Tool I: CellDesigner: A modeling tool of biochemical networks Y.Z. Chen Department of Pharmacy National University of Singapore Tel: 65-6616-6877; Email: phacyz@nus.edu.sg ; Web: http://bidd.nus.edu.sg. Content CellDesigner overview

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Content CellDesigner overview

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  1. Lecture 3: Pathway Generation Tool I:CellDesigner: A modeling tool of biochemical networks Y.Z. ChenDepartment of PharmacyNational University of SingaporeTel: 65-6616-6877; Email: phacyz@nus.edu.sg ; Web: http://bidd.nus.edu.sg • Content • CellDesigner overview • Introduction of systems biology platforms and software used by Celldesigner • CellDesigner versions and features

  2. What is Celldesigner?

  3. What is Celldesigner?

  4. 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)

  5. 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.

  6. Systems 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

  7. Systems Biology Graphical Notation

  8. Systems Biology Graphical Notation Link to SBGN webpage, online document

  9. Systems Biology Graphical Notation Step 1: Block diagram

  10. Systems Biology Graphical Notation Step 2: Molecular Interaction Map

  11. Systems Biology Graphical Notation Step 3: Edinburgh Notation

  12. Systems Biology Graphical Notation Step 3: Edinburgh Notation

  13. Systems Biology Graphical Notation

  14. Systems Biology Graphical Notation

  15. Systems Biology Graphical Notation Please read this online manual as part of your homework

  16. Systems Biology Graphical Notation

  17. Systems Biology Graphical Notation

  18. Systems Biology Graphical Notation

  19. Systems Biology Markup Language

  20. Systems 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)

  21. Systems Biology Markup Language

  22. Systems Biology Markup Language

  23. Systems Biology Markup Language

  24. Systems Biology Markup Language Please read SBML manual

  25. Systems Biology Markup Language SName

  26. Systems Biology Markup Language Rules

  27. Systems Biology Markup Language Definition of rule and derived types

  28. Systems Biology Markup Language Mathematical functions

  29. Systems Biology Markup Language Rate law functions

  30. Systems Biology Markup Language Rate law functions

  31. Systems Biology Markup Language Rate law functions

  32. Systems Biology Markup Language Rate law functions

  33. Systems Biology Markup Language Symbols

  34. Systems Biology Markup Language Symbols

  35. Systems Biology Markup Language Symbols

  36. Systems Biology Markup Language Symbols

  37. The 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.

  38. The 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

  39. Celldesigner Versions

  40. Celldesigner Versions

  41. Celldesigner Features

  42. Celldesigner Features

  43. Celldesigner Features

  44. Celldesigner Features

  45. Celldesigner Features

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