CellDesigner.org

Simulation Example 1:
Hypothetical single-gene oscillatory circuit in a eukaryotic cell

Here we try to simulate the model of a hypothetical single-gene oscillatory circuit in a eukaryotic cell using the SBML ODE Solver directly invoked via CellDesigner's Simulation menu. This model was proposed by Michael Hucka, Andrew Finney, Herbert Sauro, Hamid Bolouri, et al. in [1]. Please refer the paper for more detailed information.

Model to simulate

In this model, the nucleus of the cell is represented as one compartment and the surrounding cell cytoplasm as another compartment.

Model file"Single_Gene.xml" to download

Simulation Step by Step

1. Set the value and formulas

  1. "Species" list: Set the initial value
    2. type positionTo
    Compartment    		 id name compartment quantity type initial
    Quantity    		 substance
    Units    		 spatialSize
    Units    		 hasOnly
    Substance
    Units    		 b.c. charge constants
    SIMPLE_MOLECULE inside s1 src c2 Amount 0 FALSE TRUE 0 FALSE
    SIMPLE_MOLECULE inside s2 waste c2 Amount 0 FALSE TRUE 0 FALSE
    PROTEIN inside s3 RNAP c2 Amount 0.66 FALSE FALSE 0 FALSE
    RNA inside s4 RNAnuc c2 Amount 96 FALSE FALSE 0 FALSE
    RNA inside s5 mRNAnuc c2 Amount 0.003 FALSE FALSE 0 FALSE
    RNA inside s6 mRNAcyt c1 Amount 3.8 FALSE FALSE 0 FALSE
    RNA inside s7 RNAcyt c1 Amount 0.005 FALSE FALSE 0 FALSE
    PROTEIN inside s8 P c1 Amount 20 FALSE FALSE 0 FALSE
    PROTEIN inside s9 AA c1 Amount 90.465 FALSE FALSE 0 FALSE
  2. Set the parameters.
    scope
    id
    name
    value
    units
    constant
    local:Reaction(re1) Vi 10 TRUE
    local:Reaction(re1) Ki 0.6 TRUE
    local:Reaction(re2) Vkd 1 TRUE
    local:Reaction(re3) Vm1 50 TRUE
    local:Reaction(re3) Km1 1 TRUE
    local:Reaction(re6) Vm2 50 TRUE
    local:Reaction(re6) Km2 0.5 TRUE
    local:Reaction(re7) Vm3 50 TRUE
    local:Reaction(re7) Km3 80 TRUE
    local:Reaction(re8) Vm4 50 TRUE
    local:Reaction(re8) Km4 1 TRUE
    local:Reaction(re9) k1 100 TRUE
    local:Reaction(re10) k2 100 TRUE
  3. Set the Kinetic Law at "math" column in "Raction" list.
    4. type
    id
    name
    reversible
    fast
    reactants
    products
    modifiers
    math
    STATE_TRANSITION re1 FALSE FALSE s1 s3 s8 Vi/(1+s8/Ki)
    STATE_TRANSITION re2 FALSE FALSE s3 s2 Vkd*s3
    STATE_TRANSITION re3 FALSE FALSE s4 s5 s3 Vm1*s3*s4/(s4+Km1)
    STATE_TRANSITION re6 FALSE FALSE s6 s7 Vm2*s6/(s6+Km2)
    STATE_TRANSITION re7 FALSE FALSE s9 s8 s6 Vm3*s6*s9/(s9+Km3)
    STATE_TRANSITION re8 FALSE FALSE s8 s9 Vm4*s8/(s8+Km4)
    TRANSPORT re9 FALSE FALSE s5 s6 k1*s5
    TRANSPORT re10 FALSE FALSE s7 s4 k2*s7

2. Run Simulator

  1. Select "Simulation" - "Control Panel " menu of CellDesigner.
    The ControlPanel screen appears.
  2. Set [End Time] and [Number of Points].
  3. Click [Execute] button at the bottom.

    You can also conduct "change initial quantities of the species and parameters ", "change amount at the specific time for simulation", "parameter scan", "interactive simulation" on the Control Panel.
  4. To save the plot image, select [File]-[Save Image/Print] menu of the ControlPanel.
    The Image Config Dialog window will appear.
  5. Click [Config] button to specify the detail appearance of the plot image, such as title, legend and background colors.
  6. Click [Save Image]. The image can be saved in BMP, PNG, TIFF, PNM, and JPEG.
  7. Click [Print] to print the image as specified.

References

  1. Hucka, M.; Finney, A.; Sauro, H.M.; Bolouri, H.; Doyle, J.C.; Kitano, H. et al. The Systems Biology Markup Language(SBML): A Medium for Representation and Exchange of Biochemical Network Models. Bioinformatics. 19. 524-531. 2003.

 

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