<?xml version="1.0" encoding="utf-8"?>
<sedML xmlns:math="http://www.w3.org/1998/Math/MathML" xmlns="http://sed-ml.org/"  level="1" version="1">
		<notes>
		<p xmlns="http://www.w3.org/1999/xhtml">
		Showing the oscillating behaviour of the Repressilator model
		using deterministic and stochastic simulators
		</p>
		</notes>
		
	
	<listOfSimulations>
		<uniformTimeCourse id="simulation1" initialTime="0"
			outputStartTime="0" outputEndTime="1000" numberOfPoints="1000">
			<algorithm kisaoID="KISAO:0000088" />
		</uniformTimeCourse>
		<uniformTimeCourse id="simulation2" initialTime="0"
			outputStartTime="0" outputEndTime="1000" numberOfPoints="1000">
			<algorithm kisaoID="KISAO:0000027" />
		</uniformTimeCourse>
	</listOfSimulations>
	<listOfModels>
	
		<model id="model1" name="Repressilator-regular oscillations"
			language="urn:sedml:language:sbml.level-2.version-3" source="urn:miriam:biomodels.db:BIOMD0000000012" >
			<notes>
		<p xmlns="http://www.w3.org/1999/xhtml">
		This is the unmodified model.
		</p>
		</notes>
		</model>
		<model id="model2" name="Damped oscillations"
			language="urn:sedml:language:sbml.level-2.version-3" source="model1">
				<notes>
		<p xmlns="http://www.w3.org/1999/xhtml">
		This variant produces damped oscillations.
		</p>
		</notes>
			<listOfChanges>
				<changeAttribute
					target="/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@name='tps_repr']/@value"
					newValue="1.3e-5"></changeAttribute>
				<changeAttribute
					target="/sbml:sbml/sbml:model/sbml:listOfParameters/sbml:parameter[@name='tps_active']/@value"
					newValue="0.013"></changeAttribute>

			</listOfChanges>
		</model>
	</listOfModels>
	<listOfTasks>
		<task id="task1" name="Oscillation using a deterministic simulator"
			modelReference="model1" simulationReference="simulation1" />
		<task id="task2" name="Damped oscillations using a deterministic simulator"
			modelReference="model2" simulationReference="simulation1" />
	</listOfTasks>
	<listOfDataGenerators>
		<dataGenerator id="timeDG" name="Time">
			<listOfVariables>
				<variable id="Time" taskReference="task1" symbol="urn:sedml:symbol:time" />
			</listOfVariables>
			<math:math xmlns="http://www.w3.org/1998/Math/MathML">
				<math:ci> Time </math:ci>
			</math:math>
		</dataGenerator>
		<dataGenerator id="LaCI" name="LaCI repressor">
			<listOfVariables>
				<variable id="v1" taskReference="task1"
					target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PX']" />
			</listOfVariables>
			<math:math>
				<math:ci>v1</math:ci>
			</math:math>
		</dataGenerator>
		<dataGenerator id="TetR" name="TetR repressor">
			<listOfVariables>
				<variable id="v2" taskReference="task1"
					target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PY']" />
			</listOfVariables>
			<math:math>
				<math:ci>v2</math:ci>
			</math:math>
		</dataGenerator>
		<dataGenerator id="CI" name="CI repressor">
			<listOfVariables>
				<variable id="v3" taskReference="task1"
					target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PZ']" />
			</listOfVariables>
			<math:math>
				<math:ci>v3</math:ci>
			</math:math>
		</dataGenerator>
		<dataGenerator id="timeDG2" name="Time">
			<listOfVariables>
				<variable id="time" taskReference="task2" symbol="urn:sedml:symbol:time" />
			</listOfVariables>
			<math:math>
				<math:ci> time </math:ci>
			</math:math>
		</dataGenerator>
		<dataGenerator id="LaCIb" name="LaCI repressor">
			<listOfVariables>
				<variable id="v1b" taskReference="task2"
					target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PX']" />
			</listOfVariables>
			<math:math>
				<math:ci>v1b</math:ci>
			</math:math>
		</dataGenerator>
		<dataGenerator id="LacIbNormalizedDG" name=" NormalizedLaCI repressor">
			<listOfVariables>
				<variable id="LacIbNormalized" taskReference="task1"
					target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PX']" />
			</listOfVariables>
			<math xmlns="http://www.w3.org/1998/Math/MathML">
				<apply>
					<divide />
					<ci>LacIbNormalized</ci>
					<apply>
						<csymbol definitionURL="http://sed-ml.org/#max" encoding="text">max
						</csymbol>
						<ci>LacIbNormalized</ci>
					</apply>
				</apply>
			</math>
		</dataGenerator>
		<dataGenerator id="TetRb" name="TetR repressor">
			<listOfVariables>
				<variable id="v2b" taskReference="task2"
					target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PY']" />
			</listOfVariables>
			<math:math>
				<math:ci>v2b</math:ci>
			</math:math>
		</dataGenerator>
		<dataGenerator id="TetRNormalizedDG" name=" Normalized TetR repressor">
			<listOfVariables>
				<variable id="TetRNormalized" taskReference="task1"
					target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PY']" />
			</listOfVariables>
			<math xmlns="http://www.w3.org/1998/Math/MathML">
				<apply>
					<divide />
					<ci>TetRNormalized</ci>
					<apply>
						<csymbol definitionURL="http://sed-ml.org/#max" encoding="text">max
						</csymbol>
						<ci>TetRNormalized</ci>
					</apply>
				</apply>
			</math>
		</dataGenerator>
		<dataGenerator id="CIb" name="CI repressor">
			<listOfVariables>
				<variable id="v3b" taskReference="task2"
					target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PZ']" />
			</listOfVariables>
			<math:math>
				<math:ci>v3b</math:ci>
			</math:math>
		</dataGenerator>
		<dataGenerator id="CIb_normalizedDG" name="Normalized CI repressor">
			<listOfVariables>
				<variable id="CIb_normalized" taskReference="task1"
					target="/sbml:sbml/sbml:model/sbml:listOfSpecies/sbml:species[@id='PZ']" />
			</listOfVariables>
			<math xmlns="http://www.w3.org/1998/Math/MathML">
				<apply>
					<divide />
					<ci>CIb_normalized</ci>
					<apply>
						<csymbol definitionURL="http://sed-ml.org/#max" encoding="text">max
						</csymbol>
						<ci>CIb_normalized</ci>
					</apply>
				</apply>
			</math>
		</dataGenerator>

	</listOfDataGenerators>
	<listOfOutputs>
		<notes>
		<p xmlns="http://www.w3.org/1999/xhtml">
		This is the basic time-series of the unmodified model described in section 1.1.1 of the L1V1 specification document.
		</p>
		</notes>
		<plot2D id="plot1_Basic" name="protein numbers per time point">
			<listOfCurves>
				<curve id="c1" logX="false" logY="false" xDataReference="timeDG"
					yDataReference="LaCI" />
				<curve id="c2" logX="false" logY="false" xDataReference="timeDG"
					yDataReference="TetR" />
				<curve id="c3" logX="false" logY="false" xDataReference="timeDG"
					yDataReference="CI" />
			</listOfCurves>
		</plot2D>
	
		<plot2D id="plot2_damped_oscillations"
			name="protein numbers per time point - damped oscillations">
				<notes>
		<p xmlns="http://www.w3.org/1999/xhtml">
		This is the damped oscillation plot described in section 1.1.2 of the L1V1 specification document.
		</p>
		</notes>
			<listOfCurves>
				<curve id="c4" logX="false" logY="false" xDataReference="timeDG2"
					yDataReference="LaCIb" />
				<curve id="c5" logX="false" logY="false" xDataReference="timeDG2"
					yDataReference="TetRb" />
				<curve id="c6" logX="false" logY="false" xDataReference="timeDG2"
					yDataReference="CIb" />
			</listOfCurves>
		</plot2D>
		
		<plot2D id="plot3_normalized_protein_levels" name="Normalized Plot">
		<notes>
		<p xmlns="http://www.w3.org/1999/xhtml">
		This is the plot of normalized protein levels described in section 1.1.3 of the L1V1 specification document.
		</p>
		</notes>
			<listOfCurves>
				<curve id="c7" logX="false" logY="false" xDataReference="LacIbNormalizedDG"
					yDataReference="TetRNormalizedDG" />
				<curve id="c8" logX="false" logY="false" xDataReference="TetRNormalizedDG"
					yDataReference="CIb_normalizedDG" />
				<curve id="c9" logX="false" logY="false" xDataReference="CIb_normalizedDG"
					yDataReference="LacIbNormalizedDG" />
			</listOfCurves>
		</plot2D>
	</listOfOutputs>
</sedML>

