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|---|---|---|---|
BIOMD0000000037
|
<?xml version="1.0" encoding="UTF-8"?>
<sedML xmlns="http://sed-ml.org/sed-ml/level1/version4" xmlns:sbml="http://www.sbml.org/sbml/level2" level="1" version="4">
<listOfModels>
<model id="BIOMD0000000037_url" language="urn:sedml:language:sbml" source="BIOMD0000000037_url.xml"/>
</listOfModels>
<listOfSimulations>
<uniformTimeCourse id="auto_ten_seconds" initialTime="0" outputStartTime="0" outputEndTime="10" numberOfSteps="1000">
<algorithm name="ODE solver" kisaoID="KISAO:0000694"/>
</uniformTimeCourse>
</listOfSimulations>
<listOfTasks>
<task id="task1" modelReference="BIOMD0000000037_url" simulationReference="auto_ten_seconds"/>
</listOfTasks>
<listOfDataGenerators>
<dataGenerator id="auto_time_for_task1" name="Time">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_time_for_task1_var </ci>
</math>
<listOfVariables>
<variable id="auto_time_for_task1_var" symbol="urn:sedml:symbol:time" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_Pfr">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_Pfr__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_Pfr__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Pfr']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_Pr">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_Pr__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_Pr__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Pr']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_Xi">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_Xi__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_Xi__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Xi']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_Xa">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_Xa__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_Xa__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Xa']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_prepreS">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_prepreS__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_prepreS__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='prepreS']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_preS">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_preS__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_preS__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='preS']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_Ya">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_Ya__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_Ya__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Ya']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_S">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_S__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_S__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='S']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_Gluc">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_Gluc__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_Gluc__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Gluc']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_Yi">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_Yi__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_Yi__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Yi']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_V">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_V__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_V__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='V']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_Pi">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_Pi__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_Pi__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='Pi']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_compartment">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_compartment__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_compartment__x" target="/sbml:sbml/sbml:model/sbml:listOfCompartments/sbml:compartment[@id='compartment']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_Photoreceptor_activation">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_Photoreceptor_activation__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_Photoreceptor_activation__x" target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='Photoreceptor_activation']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_Photoreceptor_inactivation">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_Photoreceptor_inactivation__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_Photoreceptor_inactivation__x" target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='Photoreceptor_inactivation']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_Transducer_activation">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_Transducer_activation__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_Transducer_activation__x" target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='Transducer_activation']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_Transducer_inactivation">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_Transducer_inactivation__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_Transducer_inactivation__x" target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='Transducer_inactivation']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_preS_formation">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_preS_formation__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_preS_formation__x" target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='preS_formation']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_S_generation">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_S_generation__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_S_generation__x" target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='S_generation']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_Glucose_sensor_inactivation">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_Glucose_sensor_inactivation__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_Glucose_sensor_inactivation__x" target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='Glucose_sensor_inactivation']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_S_formation">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_S_formation__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_S_formation__x" target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='S_formation']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_V_formation">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_V_formation__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_V_formation__x" target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='V_formation']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_S_degradation">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_S_degradation__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_S_degradation__x" target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='S_degradation']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_V_degradation">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_V_degradation__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_V_degradation__x" target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='V_degradation']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
<dataGenerator id="auto_dg_for_task1_Photoreceptor_decay">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_Photoreceptor_decay__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_Photoreceptor_decay__x" target="/sbml:sbml/sbml:model/sbml:listOfReactions/sbml:reaction[@id='Photoreceptor_decay']" taskReference="task1"/>
</listOfVariables>
</dataGenerator>
</listOfDataGenerators>
<listOfOutputs>
<report id="autogen_report_for_task1" name="Auto-generated report for task1, including all symbols in SBML with mathematical meaning, both constant and variable.">
<listOfDataSets>
<dataSet id="autogen_time_for_task1" label="Time" dataReference="auto_time_for_task1"/>
<dataSet id="autogen_task1_Pfr" label="Pfr" dataReference="auto_dg_for_task1_Pfr"/>
<dataSet id="autogen_task1_Pr" label="Pr" dataReference="auto_dg_for_task1_Pr"/>
<dataSet id="autogen_task1_Xi" label="Xi" dataReference="auto_dg_for_task1_Xi"/>
<dataSet id="autogen_task1_Xa" label="Xa" dataReference="auto_dg_for_task1_Xa"/>
<dataSet id="autogen_task1_prepreS" label="prepreS" dataReference="auto_dg_for_task1_prepreS"/>
<dataSet id="autogen_task1_preS" label="preS" dataReference="auto_dg_for_task1_preS"/>
<dataSet id="autogen_task1_Ya" label="Ya" dataReference="auto_dg_for_task1_Ya"/>
<dataSet id="autogen_task1_S" label="S" dataReference="auto_dg_for_task1_S"/>
<dataSet id="autogen_task1_Gluc" label="Gluc" dataReference="auto_dg_for_task1_Gluc"/>
<dataSet id="autogen_task1_Yi" label="Yi" dataReference="auto_dg_for_task1_Yi"/>
<dataSet id="autogen_task1_V" label="V" dataReference="auto_dg_for_task1_V"/>
<dataSet id="autogen_task1_Pi" label="Pi" dataReference="auto_dg_for_task1_Pi"/>
<dataSet id="autogen_task1_compartment" label="compartment" dataReference="auto_dg_for_task1_compartment"/>
<dataSet id="autogen_task1_Photoreceptor_activation" label="Photoreceptor_activation" dataReference="auto_dg_for_task1_Photoreceptor_activation"/>
<dataSet id="autogen_task1_Photoreceptor_inactivation" label="Photoreceptor_inactivation" dataReference="auto_dg_for_task1_Photoreceptor_inactivation"/>
<dataSet id="autogen_task1_Transducer_activation" label="Transducer_activation" dataReference="auto_dg_for_task1_Transducer_activation"/>
<dataSet id="autogen_task1_Transducer_inactivation" label="Transducer_inactivation" dataReference="auto_dg_for_task1_Transducer_inactivation"/>
<dataSet id="autogen_task1_preS_formation" label="preS_formation" dataReference="auto_dg_for_task1_preS_formation"/>
<dataSet id="autogen_task1_S_generation" label="S_generation" dataReference="auto_dg_for_task1_S_generation"/>
<dataSet id="autogen_task1_Glucose_sensor_inactivation" label="Glucose_sensor_inactivation" dataReference="auto_dg_for_task1_Glucose_sensor_inactivation"/>
<dataSet id="autogen_task1_S_formation" label="S_formation" dataReference="auto_dg_for_task1_S_formation"/>
<dataSet id="autogen_task1_V_formation" label="V_formation" dataReference="auto_dg_for_task1_V_formation"/>
<dataSet id="autogen_task1_S_degradation" label="S_degradation" dataReference="auto_dg_for_task1_S_degradation"/>
<dataSet id="autogen_task1_V_degradation" label="V_degradation" dataReference="auto_dg_for_task1_V_degradation"/>
<dataSet id="autogen_task1_Photoreceptor_decay" label="Photoreceptor_decay" dataReference="auto_dg_for_task1_Photoreceptor_decay"/>
</listOfDataSets>
</report>
<plot2D id="autogen_plot_for_task1" name="Auto-generated plot for task1, including all species.">
<xAxis name="Time" type="linear"/>
<yAxis name="Species" type="linear"/>
<listOfCurves>
<curve id="autogen_curve_task1_Pfr" name="Pfr" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_Pfr"/>
<curve id="autogen_curve_task1_Pr" name="Pr" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_Pr"/>
<curve id="autogen_curve_task1_Xi" name="Xi" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_Xi"/>
<curve id="autogen_curve_task1_Xa" name="Xa" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_Xa"/>
<curve id="autogen_curve_task1_prepreS" name="prepreS" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_prepreS"/>
<curve id="autogen_curve_task1_preS" name="preS" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_preS"/>
<curve id="autogen_curve_task1_Ya" name="Ya" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_Ya"/>
<curve id="autogen_curve_task1_S" name="S" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_S"/>
<curve id="autogen_curve_task1_Gluc" name="Gluc" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_Gluc"/>
<curve id="autogen_curve_task1_Yi" name="Yi" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_Yi"/>
<curve id="autogen_curve_task1_V" name="V" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_V"/>
<curve id="autogen_curve_task1_Pi" name="Pi" logX="false" xDataReference="auto_time_for_task1" logY="false" yDataReference="auto_dg_for_task1_Pi"/>
</listOfCurves>
</plot2D>
</listOfOutputs>
</sedML>
|
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
<model id="id_uxiu">
<listOfUnitDefinitions>
<unitDefinition id="id_l1oz">
<listOfUnits>
<unit kind="second" multiplier="3600"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="id_akl9" size="1"/>
</listOfCompartments>
<listOfSpecies>
<species id="id_mvl4" compartment="id_akl9" initialAmount="0"/>
<species id="id_dpcy" compartment="id_akl9" initialAmount="10"/>
<species id="id_thh2" compartment="id_akl9" initialAmount="0"/>
<species id="id_5qqo" compartment="id_akl9" initialAmount="200"/>
<species id="id_0wnr" compartment="id_akl9" initialAmount="0"/>
<species id="id_3u0u" compartment="id_akl9" initialAmount="0.9"/>
<species id="id_kbri" compartment="id_akl9" initialAmount="30"/>
<species id="id_0338" compartment="id_akl9" initialAmount="0"/>
<species id="id_29af" compartment="id_akl9" initialAmount="0" boundaryCondition="true"/>
<species id="id_xesb" compartment="id_akl9" initialAmount="0"/>
<species id="id_1sty" compartment="id_akl9" initialAmount="6"/>
<species id="id_k4hs" compartment="id_akl9" initialAmount="0"/>
</listOfSpecies>
</model>
</sbml>
|
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
<model id="id_uxiu">
<listOfUnitDefinitions>
<unitDefinition id="id_l1oz">
<listOfUnits>
<unit kind="second" multiplier="3600"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="id_akl9" size="1"/>
</listOfCompartments>
<listOfSpecies>
<species id="id_mvl4" compartment="id_akl9" initialAmount="0"/>
<species id="id_dpcy" compartment="id_akl9" initialAmount="10"/>
<species id="id_thh2" compartment="id_akl9" initialAmount="0"/>
<species id="id_5qqo" compartment="id_akl9" initialAmount="200"/>
<species id="id_0wnr" compartment="id_akl9" initialAmount="0"/>
<species id="id_3u0u" compartment="id_akl9" initialAmount="0.9"/>
<species id="id_kbri" compartment="id_akl9" initialAmount="30"/>
<species id="id_0338" compartment="id_akl9" initialAmount="0"/>
<species id="id_29af" compartment="id_akl9" initialAmount="0" boundaryCondition="true"/>
<species id="id_xesb" compartment="id_akl9" initialAmount="0"/>
<species id="id_1sty" compartment="id_akl9" initialAmount="6"/>
<species id="id_k4hs" compartment="id_akl9" initialAmount="0"/>
</listOfSpecies>
<listOfParameters>
<parameter id="id_4mb1" value="0.1"/>
<parameter id="id_3y6k" value="0.1"/>
<parameter id="id_kedp" value="0.8"/>
<parameter id="id_2xy5" value="0.2"/>
<parameter id="id_eabx" value="0.1"/>
<parameter id="id_u5k1" value="50"/>
<parameter id="id_wmo5" value="1"/>
<parameter id="id_z2o5" value="1"/>
<parameter id="id_2klh" value="0.1"/>
<parameter id="id_d7ie" value="30"/>
<parameter id="id_sd1v" value="1"/>
<parameter id="id_j382" value="0"/>
</listOfParameters>
<listOfReactions>
<reaction id="id_up2t" reversible="false">
<listOfProducts>
<speciesReference species="id_kbri"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="id_k4hs"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> id_akl9 </ci>
<apply>
<divide/>
<ci> id_u5k1 </ci>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<power/>
<ci> id_k4hs </ci>
<cn type="integer"> 3 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="id_fkft" reversible="false">
<listOfReactants>
<speciesReference species="id_3u0u"/>
<speciesReference species="id_29af"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="id_xesb"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> id_eabx </ci>
<ci> id_3u0u </ci>
<ci> id_29af </ci>
<ci> id_akl9 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="id_rw19" reversible="false">
<listOfReactants>
<speciesReference species="id_mvl4"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="id_0338"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> id_akl9 </ci>
<ci> id_4mb1 </ci>
<ci> id_mvl4 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="id_5qj4" reversible="false">
<listOfReactants>
<speciesReference species="id_thh2"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="id_k4hs"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference species="id_3u0u"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> id_thh2 </ci>
<ci> id_sd1v </ci>
<ci> id_3u0u </ci>
<ci> id_akl9 </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="id_p7x7" reversible="false">
<listOfReactants>
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<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> id_5qqo </ci>
<ci> id_2xy5 </ci>
<ci> id_0wnr </ci>
<ci> id_akl9 </ci>
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<reaction id="id_ykd9" reversible="false">
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<speciesReference species="id_1sty"/>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> id_kedp </ci>
<ci> id_0wnr </ci>
<ci> id_akl9 </ci>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
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<ci> id_z2o5 </ci>
<ci> id_k4hs </ci>
<ci> id_akl9 </ci>
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<listOfProducts>
<speciesReference species="id_0wnr"/>
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<listOfModifiers>
<modifierSpeciesReference species="id_mvl4"/>
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<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> id_1sty </ci>
<ci> id_3y6k </ci>
<ci> id_mvl4 </ci>
<ci> id_akl9 </ci>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> id_dpcy </ci>
<ci> id_2klh </ci>
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<ci> id_kbri </ci>
<ci> id_wmo5 </ci>
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<times/>
<ci> id_akl9 </ci>
<apply>
<divide/>
<ci> id_d7ie </ci>
<apply>
<plus/>
<cn type="integer"> 1 </cn>
<apply>
<power/>
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<cn type="integer"> 3 </cn>
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</listOfReactions>
</model>
</sbml>
|
BIOMD0000000407
|
<?xml version="1.0" encoding="UTF-8"?>
<sedML xmlns="http://sed-ml.org/sed-ml/level1/version4" xmlns:sbml="http://www.sbml.org/sbml/level2/version4" level="1" version="4">
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_time_for_task1_var </ci>
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<dataGenerator id="auto_dg_for_task1_TNFR_E">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TNFR_E__x </ci>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TNF_E__x </ci>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TNF_TNFR_E__x </ci>
</math>
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<variable id="auto_dg_for_task1_TNF_TNFR_E__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='TNF_TNFR_E']" taskReference="task1"/>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TNFR__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_TNFR__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='TNFR']" taskReference="task1"/>
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<dataGenerator id="auto_dg_for_task1_RIP">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_RIP__x </ci>
</math>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TRADD__x </ci>
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<dataGenerator id="auto_dg_for_task1_TRAF2">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TRAF2__x </ci>
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<listOfVariables>
<variable id="auto_dg_for_task1_TRAF2__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='TRAF2']" taskReference="task1"/>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_FADD__x </ci>
</math>
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<variable id="auto_dg_for_task1_FADD__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='FADD']" taskReference="task1"/>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TNF_TNFR_TRADD__x </ci>
</math>
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<variable id="auto_dg_for_task1_TNF_TNFR_TRADD__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='TNF_TNFR_TRADD']" taskReference="task1"/>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TNFRC1__x </ci>
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<variable id="auto_dg_for_task1_TNFRC1__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='TNFRC1']" taskReference="task1"/>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TNFRCint1__x </ci>
</math>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TNFRCint2__x </ci>
</math>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TNFRCint3__x </ci>
</math>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TNFRC2__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_TNFRC2__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='TNFRC2']" taskReference="task1"/>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_FLIP__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_FLIP__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='FLIP']" taskReference="task1"/>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TNFRC2_FLIP__x </ci>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TNFRC2_pCasp8__x </ci>
</math>
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<variable id="auto_dg_for_task1_TNFRC2_pCasp8__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='TNFRC2_pCasp8']" taskReference="task1"/>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TNFRC2_FLIP_FLIP__x </ci>
</math>
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<variable id="auto_dg_for_task1_TNFRC2_FLIP_FLIP__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='TNFRC2_FLIP_FLIP']" taskReference="task1"/>
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<dataGenerator id="auto_dg_for_task1_TNFRC2_pCasp8_pCasp8">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TNFRC2_pCasp8_pCasp8__x </ci>
</math>
<listOfVariables>
<variable id="auto_dg_for_task1_TNFRC2_pCasp8_pCasp8__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='TNFRC2_pCasp8_pCasp8']" taskReference="task1"/>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TNFRC2_FLIP_pCasp8__x </ci>
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<dataGenerator id="auto_dg_for_task1_TNFRC2_FLIP_pCasp8_RIP_TRAF2">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_TNFRC2_FLIP_pCasp8_RIP_TRAF2__x </ci>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_IKK__x </ci>
</math>
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</dataGenerator>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_IKKa__x </ci>
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<dataGenerator id="auto_dg_for_task1_A20">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_A20__x </ci>
</math>
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</dataGenerator>
<dataGenerator id="auto_dg_for_task1_NFkB">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_NFkB__x </ci>
</math>
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<variable id="auto_dg_for_task1_NFkB__x" target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='NFkB']" taskReference="task1"/>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_IkBa__x </ci>
</math>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_IkBa_NFkB__x </ci>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_PIkBa__x </ci>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_NFkB_N__x </ci>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_IkBa_N__x </ci>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_IkBa_NFkB_N__x </ci>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_A20_mRNA__x </ci>
</math>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_IkBa_mRNA__x </ci>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_XIAP_mRNA__x </ci>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_FLIP_mRNA__x </ci>
</math>
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<ci> auto_dg_for_task1_BAR__x </ci>
</math>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_XIAP__x </ci>
</math>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_pCasp8__x </ci>
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<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> auto_dg_for_task1_pCasp3__x </ci>
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<ci> auto_dg_for_task1_pCasp6__x </ci>
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<dataSet id="autogen_task1_TNF_E" label="TNF_E" dataReference="auto_dg_for_task1_TNF_E"/>
<dataSet id="autogen_task1_TNF_TNFR_E" label="TNF_TNFR_E" dataReference="auto_dg_for_task1_TNF_TNFR_E"/>
<dataSet id="autogen_task1_TNFR" label="TNFR" dataReference="auto_dg_for_task1_TNFR"/>
<dataSet id="autogen_task1_RIP" label="RIP" dataReference="auto_dg_for_task1_RIP"/>
<dataSet id="autogen_task1_TRADD" label="TRADD" dataReference="auto_dg_for_task1_TRADD"/>
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<dataSet id="autogen_task1_FADD" label="FADD" dataReference="auto_dg_for_task1_FADD"/>
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<dataSet id="autogen_task1_TNFRC1" label="TNFRC1" dataReference="auto_dg_for_task1_TNFRC1"/>
<dataSet id="autogen_task1_TNFRCint1" label="TNFRCint1" dataReference="auto_dg_for_task1_TNFRCint1"/>
<dataSet id="autogen_task1_TNFRCint2" label="TNFRCint2" dataReference="auto_dg_for_task1_TNFRCint2"/>
<dataSet id="autogen_task1_TNFRCint3" label="TNFRCint3" dataReference="auto_dg_for_task1_TNFRCint3"/>
<dataSet id="autogen_task1_TNFRC2" label="TNFRC2" dataReference="auto_dg_for_task1_TNFRC2"/>
<dataSet id="autogen_task1_FLIP" label="FLIP" dataReference="auto_dg_for_task1_FLIP"/>
<dataSet id="autogen_task1_TNFRC2_FLIP" label="TNFRC2_FLIP" dataReference="auto_dg_for_task1_TNFRC2_FLIP"/>
<dataSet id="autogen_task1_TNFRC2_pCasp8" label="TNFRC2_pCasp8" dataReference="auto_dg_for_task1_TNFRC2_pCasp8"/>
<dataSet id="autogen_task1_TNFRC2_FLIP_FLIP" label="TNFRC2_FLIP_FLIP" dataReference="auto_dg_for_task1_TNFRC2_FLIP_FLIP"/>
<dataSet id="autogen_task1_TNFRC2_pCasp8_pCasp8" label="TNFRC2_pCasp8_pCasp8" dataReference="auto_dg_for_task1_TNFRC2_pCasp8_pCasp8"/>
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<dataSet id="autogen_task1_IKK" label="IKK" dataReference="auto_dg_for_task1_IKK"/>
<dataSet id="autogen_task1_IKKa" label="IKKa" dataReference="auto_dg_for_task1_IKKa"/>
<dataSet id="autogen_task1_A20" label="A20" dataReference="auto_dg_for_task1_A20"/>
<dataSet id="autogen_task1_NFkB" label="NFkB" dataReference="auto_dg_for_task1_NFkB"/>
<dataSet id="autogen_task1_IkBa" label="IkBa" dataReference="auto_dg_for_task1_IkBa"/>
<dataSet id="autogen_task1_IkBa_NFkB" label="IkBa_NFkB" dataReference="auto_dg_for_task1_IkBa_NFkB"/>
<dataSet id="autogen_task1_PIkBa" label="PIkBa" dataReference="auto_dg_for_task1_PIkBa"/>
<dataSet id="autogen_task1_NFkB_N" label="NFkB_N" dataReference="auto_dg_for_task1_NFkB_N"/>
<dataSet id="autogen_task1_IkBa_N" label="IkBa_N" dataReference="auto_dg_for_task1_IkBa_N"/>
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<dataSet id="autogen_task1_A20_mRNA" label="A20_mRNA" dataReference="auto_dg_for_task1_A20_mRNA"/>
<dataSet id="autogen_task1_IkBa_mRNA" label="IkBa_mRNA" dataReference="auto_dg_for_task1_IkBa_mRNA"/>
<dataSet id="autogen_task1_XIAP_mRNA" label="XIAP_mRNA" dataReference="auto_dg_for_task1_XIAP_mRNA"/>
<dataSet id="autogen_task1_FLIP_mRNA" label="FLIP_mRNA" dataReference="auto_dg_for_task1_FLIP_mRNA"/>
<dataSet id="autogen_task1_BAR" label="BAR" dataReference="auto_dg_for_task1_BAR"/>
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<dataSet id="autogen_task1_Casp6" label="Casp6" dataReference="auto_dg_for_task1_Casp6"/>
<dataSet id="autogen_task1_BAR_Casp8" label="BAR_Casp8" dataReference="auto_dg_for_task1_BAR_Casp8"/>
<dataSet id="autogen_task1_XIAP_Casp3" label="XIAP_Casp3" dataReference="auto_dg_for_task1_XIAP_Casp3"/>
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<dataSet id="autogen_task1_extracellular" label="extracellular" dataReference="auto_dg_for_task1_extracellular"/>
<dataSet id="autogen_task1_nucleus" label="nucleus" dataReference="auto_dg_for_task1_nucleus"/>
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<dataSet id="autogen_task1_J11" label="J11" dataReference="auto_dg_for_task1_J11"/>
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</report>
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<xAxis name="Time" type="linear"/>
<yAxis name="Species" type="linear"/>
<listOfCurves>
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</listOfCurves>
</plot2D>
</listOfOutputs>
</sedML>
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End of preview. Expand
in Data Studio
SciGym: Measuring Scientific Capabilities of Language Models with a Systems Biology Dry Lab
Dataset Description
SciGym is a benchmark dataset for evaluating the scientific discovery capabilities of language models through iterative experiment design in a simulated biological environment. It challenges models to uncover biological mechanisms by designing and interpreting simulated experiments.
Dataset Structure
The dataset is organized into two splits:
- small: The tasks used in the paper evaluation
- large: Additional instances with more complex biological systems
Each instance contains the following files:
- truth.xml: The reference SBML model that the agent is tasked with discovering
- partial.xml: The starting SBML model provided to the agent (truth.xml with reactions removed)
- truth.sedml: The SED-ML file containing simulation configuration for the experiment
Dataset Creation
This dataset was created using expert-curated biological models from the BioModels repository. Models were selected and modified to create appropriate scientific discovery challenges, with reactions removed from the truth models to create the partial models that agents begin with.
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