SBML Import: MAPK Signaling
Introduction
This model has been imported and automatically converted from SBML format by Morpheus. It shows oscillations in the MAPK signaling cascade (Kholodenko, 2000).
Description
Upon importing an SBML file, a Morpheus model is automatically created. A System of DiffEqns is generated, based on the function and reactions defined in the SBML file and defined as part of a CellType. Additionally, a Logger is generated to record and visualize the output.
Simulation details, such as StartTime and StopTime, as well as the time-step of System, need to be specified manually.
Things to try
- Browse the Biomodels database and try importing some SBML models.
Reference
B. N. Kholodenko: Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur. J. Biochem. 267 (6): 1583-1588, 2000.
Model
Get this model via:
Examples → ODE → MAPK_SBML.xml or
MAPK_SBML.xml
XML Preview
<?xml version='1.0' encoding='UTF-8'?>
<MorpheusModel version="3">
<Description>
<Title>BIOMD0000000010</Title>
<Details>Imported SBML model: http://www.ebi.ac.uk/biomodels-main/BIOMD0000000010
Kholodenko BN, Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades.</Details>
</Description>
<Global/>
<Space>
<Lattice class="linear">
<Size symbol="size" value="1 0 0"/>
<Neighborhood>
<Order>1</Order>
</Neighborhood>
</Lattice>
<SpaceSymbol symbol="space"/>
</Space>
<Time>
<StartTime value="0"/>
<StopTime symbol="stop" value="1.0"/>
<TimeSymbol symbol="time" name="time"/>
</Time>
<CellTypes>
<CellType class="biological" name="sbml_ct">
<System solver="runge-kutta-adaptive" time-scaling="4000" time-step="stop">
<Constant symbol="V1" value="2.5"/>
<Constant symbol="Ki" value="9"/>
<Constant symbol="n" value="1"/>
<Constant symbol="K1" value="10"/>
<DiffEqn symbol-ref="MKKK" name="gained from reactions">
<Expression> - V1 * MKKK / ((1 + pow(MAPK_PP / Ki, n)) * (K1 + MKKK)) + V2 * MKKK_P / (KK2 + MKKK_P)</Expression>
</DiffEqn>
<DiffEqn symbol-ref="MKKK_P" name="gained from reactions">
<Expression>V1 * MKKK / ((1 + pow(MAPK_PP / Ki, n)) * (K1 + MKKK)) - V2 * MKKK_P / (KK2 + MKKK_P)</Expression>
</DiffEqn>
<Constant symbol="V2" value="0.25"/>
<Constant symbol="KK2" value="8"/>
<Constant symbol="k3" value="0.025"/>
<Constant symbol="KK3" value="15"/>
<DiffEqn symbol-ref="MKK" name="gained from reactions">
<Expression> - k3 * MKKK_P * MKK / (KK3 + MKK) + V6 * MKK_P / (KK6 + MKK_P)</Expression>
</DiffEqn>
<DiffEqn symbol-ref="MKK_P" name="gained from reactions">
<Expression>k3 * MKKK_P * MKK / (KK3 + MKK) - uVol * k4 * MKKK_P * MKK_P / (KK4 + MKK_P) + uVol * V5 * MKK_PP / (KK5 + MKK_PP) - V6 * MKK_P / (KK6 + MKK_P)</Expression>
</DiffEqn>
<Constant symbol="k4" value="0.025"/>
<Constant symbol="KK4" value="15"/>
<DiffEqn symbol-ref="MKK_PP" name="gained from reactions">
<Expression>k4 * MKKK_P * MKK_P / (KK4 + MKK_P) - V5 * MKK_PP / (KK5 + MKK_PP)</Expression>
</DiffEqn>
<Constant symbol="V5" value="0.75"/>
<Constant symbol="KK5" value="15"/>
<Constant symbol="V6" value="0.75"/>
<Constant symbol="KK6" value="15"/>
<Constant symbol="k7" value="0.025"/>
<Constant symbol="KK7" value="15"/>
<DiffEqn symbol-ref="MAPK" name="gained from reactions">
<Expression> - k7 * MKK_PP * MAPK / (KK7 + MAPK) + V10 * MAPK_P / (KK10 + MAPK_P)</Expression>
</DiffEqn>
<DiffEqn symbol-ref="MAPK_P" name="gained from reactions">
<Expression> k7 * MKK_PP * MAPK / (KK7 + MAPK) - k8 * MKK_PP * MAPK_P / (KK8 + MAPK_P) + uVol * V9 * MAPK_PP / (KK9 + MAPK_PP) - V10 * MAPK_P / (KK10 + MAPK_P)</Expression>
</DiffEqn>
<Constant symbol="k8" value="0.025"/>
<Constant symbol="KK8" value="15"/>
<DiffEqn symbol-ref="MAPK_PP" name="gained from reactions">
<Expression>k8 * MKK_PP * MAPK_P / (KK8 + MAPK_P) - V9 * MAPK_PP / (KK9 + MAPK_PP)</Expression>
</DiffEqn>
<Constant symbol="V9" value="0.5"/>
<Constant symbol="KK9" value="15"/>
<Constant symbol="V10" value="0.5"/>
<Constant symbol="KK10" value="15"/>
</System>
<Constant symbol="uVol" value="1" name="compartment size"/>
<Property symbol="MKKK" value="90" name="Mos"/>
<Property symbol="MKKK_P" value="10" name="Mos-P"/>
<Property symbol="MKK" value="280" name="Mek1"/>
<Property symbol="MKK_P" value="10" name="Mek1-P"/>
<Property symbol="MKK_PP" value="10" name="Mek1-PP"/>
<Property symbol="MAPK" value="280" name="Erk2"/>
<Property symbol="MAPK_P" value="10" name="Erk2-P"/>
<Property symbol="MAPK_PP" value="10" name="Erk2-PP"/>
</CellType>
</CellTypes>
<CellPopulations>
<Population size="1" type="sbml_ct"/>
</CellPopulations>
<Analysis>
<Logger time-step="stop/200">
<Restriction>
<Celltype celltype="sbml_ct"/>
</Restriction>
<Input>
<Symbol symbol-ref="MAPK"/>
<Symbol symbol-ref="MAPK_P"/>
<Symbol symbol-ref="MAPK_PP"/>
<Symbol symbol-ref="MKK"/>
<Symbol symbol-ref="MKK_P"/>
<Symbol symbol-ref="MKK_PP"/>
<Symbol symbol-ref="MKKK"/>
<Symbol symbol-ref="MKKK_P"/>
</Input>
<Output>
<TextOutput/>
</Output>
<Plots>
<Plot time-step="-1">
<Style grid="true" style="lines" line-width="3.0"/>
<Terminal terminal="png"/>
<X-axis>
<Symbol symbol-ref="time"/>
</X-axis>
<Y-axis>
<Symbol symbol-ref="MAPK"/>
<Symbol symbol-ref="MAPK_P"/>
<Symbol symbol-ref="MAPK_PP"/>
<Symbol symbol-ref="MKK"/>
<Symbol symbol-ref="MKK_P"/>
<Symbol symbol-ref="MKK_PP"/>
<Symbol symbol-ref="MKKK"/>
<Symbol symbol-ref="MKKK_P"/>
</Y-axis>
</Plot>
</Plots>
</Logger>
</Analysis>
</MorpheusModel>
Downloads
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