ODE Model: Cell Cycle

Open in Morpheus

Persistent Identifier

Use this permanent link to cite or share this Morpheus model:


Introduction

This model is a simple three-species ODE model of the Xenopus embryonic cell cycle (Ferrell et al., 2011). It exhibits sustained limit cycle oscillations.

Time plots of ODE model of *Xenopus* embryonic cell cycle.
Time plots of ODE model of Xenopus embryonic cell cycle.

Description

One CellType is created that has three variables of Properties representing the concentrations of $\mathrm{APC}$, $\mathrm{Plk1}$, and $\mathrm{CDK1}$. These variables are coupled in a System of DiffEqns.

In the System, a number of Constants are defined, whose symbols are used in the DiffEqn. Note that the equations are entered in simple plain text.

The System uses the runga-kutta (4th order) solver for the differential equations and speficies a particular time step (here $ht = 10^{-2}$) which is interpreted in global time steps.

The global time is defined in the Time element and runs from StartTime to StopTime ($0$ to $25$). In this non-spatial model, Space defines a Lattice of size $(x,y,z)=(1,1,0)$.

Results are written to a file using the Analysis plugin Logger. The Logger also visualizes the time plot to screen (in interactive mode) or to PNG files (in local mode).

Things to try

  • Change the dynamics by altering System/time-scaling.

Reference

J. E. Ferrell Jr., T. Y. Tsai, Q. Yang: Modeling the Cell Cycle: Why Do Certain Circuits Oscillate?. Cell 144 (6): 874-885, 2011.

Model

Get this model via:

  • Morpheus-Link or
  • Morpheus GUI: ExamplesODECellCycle.xml or
  •  Download: CellCycle.xml
  • XML Preview

    <?xml version='1.0' encoding='UTF-8'?>
    <MorpheusModel version="3">
        <Description>
            <Title>Example-CellCycle</Title>
            <Details>James Ferrell, Tony Yu-Chen Tsai and Qiong Yang (2011) Modeling the Cell Cycle: Why Do Certain Circuits Oscillate?, Cell 144, p874-885. http://dx.doi.org/10.1016/j.cell.2011.03.006</Details>
        </Description>
        <Global/>
        <Space>
            <Lattice class="square">
                <Size symbol="size" value="1,1,0"/>
                <Neighborhood>
                    <Order>1</Order>
                </Neighborhood>
            </Lattice>
            <SpaceSymbol symbol="space"/>
        </Space>
        <Time>
            <StartTime value="0"/>
            <StopTime value="25"/>
            <TimeSymbol symbol="time"/>
        </Time>
        <CellTypes>
            <CellType class="biological" name="cells">
                <Property symbol="APC" value="0"/>
                <Property symbol="Plk1" value="0"/>
                <Property symbol="CDK1" value="0"/>
                <System solver="runge-kutta" time-scaling="1" time-step="1e-2">
                    <Constant symbol="n" value="8"/>
                    <Constant symbol="K" value="0.5"/>
                    <Constant symbol="α1" value="0.1"/>
                    <Constant symbol="α2" value="3.0"/>
                    <Constant symbol="α3" value="3.0"/>
                    <Constant symbol="β1" value="3.0"/>
                    <Constant symbol="β2" value="1.0"/>
                    <Constant symbol="β3" value="1.0"/>
                    <DiffEqn symbol-ref="CDK1">
                        <Expression>α1 - β1 * CDK1 * (APC^n) / (K^n + APC^n)</Expression>
                    </DiffEqn>
                    <DiffEqn symbol-ref="Plk1">
                        <Expression>α2*(1-Plk1) * ((CDK1^n) / (K^n + CDK1^n)) - β2*Plk1</Expression>
                    </DiffEqn>
                    <DiffEqn symbol-ref="APC">
                        <Expression>α3*(1- APC) * ((Plk1^n) / (K^n + Plk1^n)) - β3*APC</Expression>
                    </DiffEqn>
                </System>
            </CellType>
        </CellTypes>
        <CellPopulations>
            <Population size="0" type="cells">
                <InitCellLattice/>
            </Population>
        </CellPopulations>
        <Analysis>
            <Logger time-step="1e-2">
                <Restriction>
                    <Celltype celltype="cells"/>
                </Restriction>
                <Input>
                    <Symbol symbol-ref="APC"/>
                    <Symbol symbol-ref="CDK1"/>
                    <Symbol symbol-ref="Plk1"/>
                </Input>
                <Output>
                    <TextOutput file-format="csv"/>
                </Output>
                <Plots>
                    <Plot time-step="-1">
                        <Style style="lines" line-width="4.0"/>
                        <Terminal terminal="png"/>
                        <X-axis>
                            <Symbol symbol-ref="time"/>
                        </X-axis>
                        <Y-axis>
                            <Symbol symbol-ref="APC"/>
                            <Symbol symbol-ref="CDK1"/>
                            <Symbol symbol-ref="Plk1"/>
                        </Y-axis>
                    </Plot>
                    <Plot time-step="-1">
                        <Style style="lines" line-width="4.0"/>
                        <Terminal terminal="png"/>
                        <X-axis>
                            <Symbol symbol-ref="CDK1"/>
                        </X-axis>
                        <Y-axis>
                            <Symbol symbol-ref="APC"/>
                        </Y-axis>
                        <Color-bar>
                            <Symbol symbol-ref="Plk1"/>
                        </Color-bar>
                    </Plot>
                </Plots>
            </Logger>
        </Analysis>
    </MorpheusModel>
    
    

    Downloads

    Files associated with this model:

    Next