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CS 572 Fall 2013 Lecture 6 Tool for setting up kinetic simulations

CS 572 Fall 2013 Lecture 6 Tool for setting up kinetic simulations. Example 2: second order and enzymatic reactions. t02.py. Cell Designer is tool for creating and sharing models. Early version. When used in conjunction with Systems Biology Workbench, Cell designer will

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CS 572 Fall 2013 Lecture 6 Tool for setting up kinetic simulations

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  1. CS 572 Fall 2013 Lecture 6 Tool for setting up kinetic simulations

  2. Example 2: second order and enzymatic reactions

  3. t02.py

  4. Cell Designer is tool for creating and sharing models Early version

  5. When used in conjunction with Systems Biology Workbench, Cell designer will (1) prepare MATLAB files to solve ODEs (2) save your model as an XML file in systems biology markup language (Hucka et al, Bioinformatics 19 (2004) 524 SourceForge.net

  6. http://celldesigner.org/help/Install/ With Cell Designer, you draw the network

  7. Boris network drawn in Cell Designer Cell Designer sets up the tables of reactants, reactions, and parameters

  8. As you draw Cell Designer creates an SBML file

  9. id defined in order that species is added to graph To get a particular order for spices id (e.g. Boris table I), put all species on graph before reactions

  10. Directions of arrows correspond to rate laws in Boris Table II Reactions added to the model in numerical order

  11. reactions listed in the same order as Boris Table II Species id used to define reactants and products. User decides names of rate parameters User has option to define each rate law (i.e. “math”)

  12. Put in the value of rate constants. These values are different from Boris Table II to make number per cell the dynamic variable

  13. Choose MATLAB from options offered by Systems Biology Workbench

  14. Supplement MATLAB m-files as needed to make graphs in Figure 4A of Boris paper.

  15. MATLAB main program assigns initial values, sets time span, calls solver, and plots results

  16. More recent versions of Cell Designer have more features http://celldesigner.org/help/Install/

  17. sim1: an example in tutorial

  18. Standard elements for pathway design

  19. Built in simulator lets you run your model

  20. MAPK cascade (with feedback) in SBGN Denotes enzyme MKK = MAPK kinase; example MEK MKKK= MAPK kinase kinase: example RAF ERK is an example of MAPK

  21. Model of MAPK cascade with feedback can oscillate

  22. Model Sharing

  23. CellDesigner 4.1 supports “stochastic” simulations Concentrations used in ODE method are average quantities. When number of molecules is small, fluctuations become important. Stochastic method: discrete time steps reaction rates  probabilities choose next reaction by random numbers update number of molecules after each reaction

  24. Questions on lecture 6 What is Systems Biology Markup Language (SBML)? What is Systems Biology Graphis Notation (SBGN)? Contrast Cell Designer and Reactor with respect the following: model creation, rate law specification parameter input, ODE generation and solution model sharing.

  25. More questions on lecture 6 Contrast ODE-based and stochastic simulations of signaling kinetics. Under what condition is stochastic simulation needed? Give examples of enzymes MAPK, MKK, and MKKK. In SBNG, how do one show that E is an enzyme in reaction A  B (draw) What type of enzymes reverse phosphorylation cascades?

  26. Cell Designer: You draw the network Dr. Miller: Here's the link for CellDesigner: http://celldesigner.org/ It contains everything you need about it. If you need any help about installation and how to use it, please let me know. Best wishes, Shuangshuang

  27. Down load the Systems Biology Workbench before installing Cell Designer Can be accomplished using folder “windows install for students” on class web page • Extract sbw-1.0.5-src • Run sbw-1.0.5-win-full (you will be ask to install java VM) • Run CDInstall-2-2-win (choose option install with SBW 2.0)

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