- Author:
- Michael Cooling <mcoo001@UoA.auckland.ac.nz>
- Date:
- 2016-04-11 11:48:36+12:00
- Desc:
- Initial Commit
- Permanent Source URI:
- https://models.cellml.org/workspace/2c5/rawfile/e8b0e5d10f563c9a997626435bace472ab5f7f34/ExampleDevice.cellml
<?xml version="1.0" encoding="utf-8"?>
<model xmlns:xlink="http://www.w3.org/1999/xlink" name="ExampleDevice" cmeta:id="ExampleDevice"
xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cellml="http://www.cellml.org/cellml/1.1#"
xmlns:cmeta="http://www.cellml.org/metadata/1.0#">
<import xlink:href="Principled_Base/Units_Cellular_Systems.cellml">
<units name="nM" units_ref="nM"/>
<units name="nM_per_s" units_ref="nM_per_s"/>
<units name="per_nM_per_s" units_ref="per_nM_per_s"/>
</import>
<import xlink:href="Principled_Base/Time.cellml">
<component name="Time" component_ref="Time"/>
</import>
<group>
<relationship_ref relationship="encapsulation" />
<component_ref component="ExampleDevice">
<component_ref component="Chassis" />
<component_ref component="Promoter" />
<component_ref component="RNA_n" />
<component_ref component="RNA_n_delta" />
<component_ref component="RNA_Transport" />
<component_ref component="RNA_c" />
<component_ref component="RNA_c_delta" />
<component_ref component="RNA_c_Degradation" />
<component_ref component="RBS_GFP" />
<component_ref component="CDS_GFP" />
<component_ref component="GFP" />
<component_ref component="GFP_delta" />
<component_ref component="GFP_Degradation" />
</component_ref>
</group>
<import xlink:href="Principled_Base/mohr_taylor_newell_2008_subset.cellml">
<component name="codata_2006_physicochemical" component_ref="codata_2006_physicochemical_subset" />
<units name="per_mole" units_ref="per_mole" />
</import>
<connection>
<map_components component_1="ExampleDevice" component_2="codata_2006_physicochemical"/>
<map_variables variable_1="avogadrosConstant" variable_2="Avogadro_constant"/>
</connection>
<component name="ExampleDevice_Parameters">
<variable name="transcriptionFactor" units="nM" initial_value="100" public_interface="out" />
<variable name="RNA_n_init" units="nM" initial_value="0" public_interface="out" />
<variable name="J_RNA_n_External" units="nM_per_s" initial_value="0" public_interface="out" />
<variable name="RNA_c_init" units="nM" initial_value="0" public_interface="out" />
<variable name="J_RNA_c_External" units="nM_per_s" initial_value="0" public_interface="out" />
<variable name="GFP_init" units="nM" initial_value="0" public_interface="out" />
<variable name="J_GFP_External" units="nM_per_s" initial_value="0" public_interface="out" />
</component>
<import xlink:href="ExampleDevice_Promoter.cellml">
<units name="PoPs" units_ref="PoPs"/>
<component name="Promoter_Parameters" component_ref="ExampleDevice_Promoter_Parameters"/>
</import>
<import xlink:href="Chassis_CoreModelCell.cellml">
<units name="femtoliter" units_ref="femtoliter"/>
<component name="Chassis_Parameters" component_ref="Chassis_CoreModelCell_Parameters"/>
</import>
<import xlink:href="Bioenvironment_Degradation_ExampleDeviceRNA.cellml">
<component name="RNA_Degradation_Parameters" component_ref="Bioenvironment_Degradation_ExampleDeviceRNA_Parameters"/>
</import>
<import xlink:href="Bioenvironment_Transport_RNA.cellml">
<component name="RNA_Transport_Parameters" component_ref="Bioenvironment_Transport_RNA_Parameters"/>
</import>
<import xlink:href="ExampleDevice_RBS_GFP.cellml">
<component name="ExampleDevice_RBS_GFP_Parameters" component_ref="ExampleDevice_RBS_GFP_Parameters"/>
</import>
<import xlink:href="ExampleDevice_RBS_GFP.cellml">
<component name="RBS_Parameters" component_ref="ExampleDevice_RBS_GFP_Parameters"/>
</import>
<import xlink:href="Bioenvironment_Degradation_GFP.cellml">
<component name="GFP_Degradation_Parameters" component_ref="Bioenvironment_Degradation_GFP_Parameters"/>
</import>
<component name="ExampleDevice">
<variable name="time" units="second" public_interface="in" private_interface="out"/>
<variable name="k" units="PoPs" public_interface="in" private_interface="out" />
<variable name="n" units="dimensionless" public_interface="in" private_interface="out"/>
<variable name="Km" units="nM" public_interface="in" private_interface="out"/>
<variable name="transcriptionFactor" units="nM" public_interface="in" private_interface="out"/>
<variable name="transcriptionalVolume_init" units="femtoliter" public_interface="in" private_interface="out"/>
<variable name="translationalVolume_init" units="femtoliter" public_interface="in" private_interface="out"/>
<variable name="RNA_n_init" units="nM" public_interface="in" private_interface="out" />
<variable name="J_RNA_n_External" units="nM_per_s" public_interface="in" private_interface="out" />
<variable name="RNA_c_init" units="nM" public_interface="in" private_interface="out" />
<variable name="J_RNA_c_External" units="nM_per_s" public_interface="in" private_interface="out" />
<variable name="GFP_init" units="nM" public_interface="in" private_interface="out" />
<variable name="J_GFP_External" units="nM_per_s" public_interface="in" private_interface="out" />
<variable name="RNA_kDecay" units="per_s" public_interface="in" private_interface="out" />
<variable name="RNA_Transport_k" units="per_s" public_interface="in" private_interface="out" />
<variable name="RBS_k" units="RiPs" public_interface="in" private_interface="out" />
<variable name="GFP_kDecay" units="per_s" public_interface="in" private_interface="out" />
<variable name="avogadrosConstant" units="per_mole" public_interface="in" private_interface="out"/>
<variable name="J_RNA_n" units="nM_per_s" public_interface="out" private_interface="in" />
<variable name="RNA_n" units="nM" public_interface="out" private_interface="in"/>
<variable name="J_RNA_c" units="nM_per_s" public_interface="out" private_interface="in" />
<variable name="RNA_c" units="nM" public_interface="out" private_interface="in"/>
<variable name="transcriptionalVolume" units="femtoliter" public_interface="out" private_interface="in"/>
<variable name="translationalVolume" units="femtoliter" public_interface="out" private_interface="in"/>
<variable name="J_GFP" units="nM_per_s" public_interface="out" private_interface="in" />
<variable name="GFP" units="nM" public_interface="out" private_interface="in"/>
</component>
<connection>
<map_components component_1="Time" component_2="ExampleDevice"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="Promoter_Parameters" component_2="ExampleDevice"/>
<map_variables variable_1="k" variable_2="k"/>
<map_variables variable_1="n" variable_2="n"/>
<map_variables variable_1="Km" variable_2="Km"/>
</connection>
<connection>
<map_components component_1="ExampleDevice_Parameters" component_2="ExampleDevice"/>
<map_variables variable_1="transcriptionFactor" variable_2="transcriptionFactor"/>
<map_variables variable_1="RNA_n_init" variable_2="RNA_n_init"/>
<map_variables variable_1="J_RNA_n_External" variable_2="J_RNA_n_External"/>
<map_variables variable_1="RNA_c_init" variable_2="RNA_c_init"/>
<map_variables variable_1="J_RNA_c_External" variable_2="J_RNA_c_External"/>
<map_variables variable_1="GFP_init" variable_2="GFP_init"/>
<map_variables variable_1="J_GFP_External" variable_2="J_GFP_External"/>
</connection>
<connection>
<map_components component_1="Chassis_Parameters" component_2="ExampleDevice"/>
<map_variables variable_1="transcriptionalVolume_initialValue" variable_2="transcriptionalVolume_init"/>
<map_variables variable_1="translationalVolume_initialValue" variable_2="translationalVolume_init"/>
</connection>
<connection>
<map_components component_1="RBS_Parameters" component_2="ExampleDevice"/>
<map_variables variable_1="k" variable_2="RBS_k"/>
</connection>
<connection>
<map_components component_1="RNA_Transport_Parameters" component_2="ExampleDevice"/>
<map_variables variable_1="k" variable_2="RNA_Transport_k"/>
</connection>
<connection>
<map_components component_1="RNA_Degradation_Parameters" component_2="ExampleDevice"/>
<map_variables variable_1="kDecay" variable_2="RNA_kDecay"/>
</connection>
<connection>
<map_components component_1="GFP_Degradation_Parameters" component_2="ExampleDevice"/>
<map_variables variable_1="kDecay" variable_2="GFP_kDecay"/>
</connection>
<connection>
<map_components component_1="Chassis" component_2="ExampleDevice"/>
<map_variables variable_1="transcriptionalVolume" variable_2="transcriptionalVolume"/>
<map_variables variable_1="transcriptionalVolume_initialValue" variable_2="transcriptionalVolume_init"/>
<map_variables variable_1="translationalVolume" variable_2="translationalVolume"/>
<map_variables variable_1="translationalVolume_initialValue" variable_2="translationalVolume_init"/>
</connection>
<import xlink:href="Chassis_CoreModelCell.cellml">
<component name="Chassis" component_ref="Chassis_CoreModelCell"/>
</import>
<import xlink:href="ExampleDevice_Promoter.cellml">
<component name="Promoter" component_ref="ExampleDevice_Promoter"/>
</import>
<connection>
<map_components component_1="Promoter" component_2="ExampleDevice"/>
<map_variables variable_1="k" variable_2="k"/>
<map_variables variable_1="n" variable_2="n"/>
<map_variables variable_1="Km" variable_2="Km"/>
<map_variables variable_1="tFactor" variable_2="transcriptionFactor"/>
<map_variables variable_1="avogadrosConstant" variable_2="avogadrosConstant"/>
</connection>
<connection>
<map_components component_1="Chassis" component_2="Promoter"/>
<map_variables variable_1="transcriptionalVolume" variable_2="localVolume"/>
</connection>
<import xlink:href="Principled_Base/Template_Species_uM.cellml">
<component name="RNA_n" component_ref="Template_Species_uM"/>
</import>
<connection>
<map_components component_1="RNA_n" component_2="ExampleDevice"/>
<map_variables variable_1="concentrationInitialValue" variable_2="RNA_n_init"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="concentration" variable_2="RNA_n"/>
</connection>
<connection>
<map_components component_1="RNA_n" component_2="RNA_n_delta"/>
<map_variables variable_1="JGain" variable_2="JNet"/>
</connection>
<connection>
<map_components component_1="ExampleDevice" component_2="RNA_n_delta"/>
<map_variables variable_1="J_RNA_n_External" variable_2="JPlusExternal"/>
<map_variables variable_1="J_RNA_n" variable_2="JNet"/>
</connection>
<connection>
<map_components component_1="Promoter" component_2="RNA_n_delta"/>
<map_variables variable_1="JRNA" variable_2="JPlusPromoter"/>
</connection>
<component name="RNA_n_delta">
<variable name="JNet" units="nM_per_s" public_interface="out" />
<variable name="JPlusPromoter" units="nM_per_s" public_interface="in" />
<variable name="JPlusExternal" units="nM_per_s" public_interface="in" />
<variable name="JMinusTransport" units="nM_per_s" public_interface="in" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>JNet</ci>
<apply>
<minus/>
<apply>
<plus/>
<ci>JPlusExternal</ci>
<ci>JPlusPromoter</ci>
</apply>
<ci>JMinusTransport</ci>
</apply>
</apply>
</math>
</component>
<import xlink:href="Bioenvironment_Transport_RNA.cellml">
<component name="RNA_Transport" component_ref="Bioenvironment_Transport_RNA"/>
</import>
<connection>
<map_components component_1="RNA_Transport" component_2="ExampleDevice"/>
<map_variables variable_1="k" variable_2="RNA_Transport_k"/>
</connection>
<connection>
<map_components component_1="RNA_Transport" component_2="Chassis"/>
<map_variables variable_1="fromVolume" variable_2="transcriptionalVolume"/>
<map_variables variable_1="toVolume" variable_2="translationalVolume"/>
</connection>
<connection>
<map_components component_1="RNA_Transport" component_2="RNA_n"/>
<map_variables variable_1="concentration" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="RNA_Transport" component_2="RNA_c_delta"/>
<map_variables variable_1="J_toVolume" variable_2="JPlusTransport"/>
</connection>
<connection>
<map_components component_1="RNA_Transport" component_2="RNA_n_delta"/>
<map_variables variable_1="J_fromVolume" variable_2="JMinusTransport"/>
</connection>
<import xlink:href="Principled_Base/Template_Species_uM.cellml">
<component name="RNA_c" component_ref="Template_Species_uM"/>
</import>
<connection>
<map_components component_1="RNA_c" component_2="ExampleDevice"/>
<map_variables variable_1="concentrationInitialValue" variable_2="RNA_c_init"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="concentration" variable_2="RNA_c"/>
</connection>
<connection>
<map_components component_1="RNA_c" component_2="RNA_c_delta"/>
<map_variables variable_1="JGain" variable_2="JNet"/>
</connection>
<connection>
<map_components component_1="ExampleDevice" component_2="RNA_c_delta"/>
<map_variables variable_1="J_RNA_c_External" variable_2="JPlusExternal"/>
<map_variables variable_1="J_RNA_c" variable_2="JNet"/>
</connection>
<component name="RNA_c_delta">
<variable name="JNet" units="nM_per_s" public_interface="out" />
<variable name="JPlusTransport" units="nM_per_s" public_interface="in" />
<variable name="JPlusExternal" units="nM_per_s" public_interface="in" />
<variable name="JMinusDegradation" units="nM_per_s" public_interface="in" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>JNet</ci>
<apply>
<minus/>
<apply>
<plus/>
<ci>JPlusExternal</ci>
<ci>JPlusTransport</ci>
</apply>
<ci>JMinusDegradation</ci>
</apply>
</apply>
</math>
</component>
<import xlink:href="Bioenvironment_Degradation_ExampleDeviceRNA.cellml">
<units name="per_s" units_ref="per_s"/>
<component name="RNA_c_Degradation" component_ref="Bioenvironment_Degradation_ExampleDeviceRNA"/>
</import>
<connection>
<map_components component_1="RNA_c_Degradation" component_2="ExampleDevice"/>
<map_variables variable_1="kDecay" variable_2="RNA_kDecay"/>
</connection>
<connection>
<map_components component_1="RNA_c_Degradation" component_2="RNA_c"/>
<map_variables variable_1="concentration" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="RNA_c_Degradation" component_2="RNA_c_delta"/>
<map_variables variable_1="J" variable_2="JMinusDegradation"/>
</connection>
<import xlink:href="ExampleDevice_RBS_GFP.cellml">
<units name="RiPs" units_ref="RiPs"/>
<component name="RBS_GFP" component_ref="ExampleDevice_RBS_GFP"/>
</import>
<connection>
<map_components component_1="RBS_GFP" component_2="ExampleDevice"/>
<map_variables variable_1="k" variable_2="RBS_k"/>
</connection>
<connection>
<map_components component_1="RBS_GFP" component_2="Chassis"/>
<map_variables variable_1="localVolume" variable_2="translationalVolume"/>
</connection>
<connection>
<map_components component_1="RBS_GFP" component_2="RNA_c"/>
<map_variables variable_1="RNA" variable_2="concentration"/>
</connection>
<import xlink:href="ExampleDevice_ProteinCDS_GFP.cellml">
<component name="CDS_GFP" component_ref="ExampleDevice_ProteinCDS_GFP"/>
</import>
<connection>
<map_components component_1="CDS_GFP" component_2="Chassis"/>
<map_variables variable_1="localVolume" variable_2="translationalVolume"/>
</connection>
<connection>
<map_components component_1="CDS_GFP" component_2="RBS_GFP"/>
<map_variables variable_1="hostRNARiPs" variable_2="RNARiPs"/>
</connection>
<import xlink:href="Principled_Base/Template_Species_uM.cellml">
<component name="GFP" component_ref="Template_Species_uM"/>
</import>
<connection>
<map_components component_1="GFP" component_2="ExampleDevice"/>
<map_variables variable_1="concentrationInitialValue" variable_2="GFP_init"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="concentration" variable_2="GFP"/>
</connection>
<connection>
<map_components component_1="GFP" component_2="GFP_delta"/>
<map_variables variable_1="JGain" variable_2="JNet"/>
</connection>
<connection>
<map_components component_1="ExampleDevice" component_2="GFP_delta"/>
<map_variables variable_1="J_GFP_External" variable_2="JPlusExternal"/>
<map_variables variable_1="J_GFP" variable_2="JNet"/>
</connection>
<connection>
<map_components component_1="CDS_GFP" component_2="GFP_delta"/>
<map_variables variable_1="J" variable_2="JPlusCDS"/>
</connection>
<component name="GFP_delta">
<variable name="JNet" units="nM_per_s" public_interface="out" />
<variable name="JPlusCDS" units="nM_per_s" public_interface="in" />
<variable name="JPlusExternal" units="nM_per_s" public_interface="in" />
<variable name="JMinusDegradation" units="nM_per_s" public_interface="in" />
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci>JNet</ci>
<apply>
<minus/>
<apply>
<plus/>
<ci>JPlusExternal</ci>
<ci>JPlusCDS</ci>
</apply>
<ci>JMinusDegradation</ci>
</apply>
</apply>
</math>
</component>
<import xlink:href="Bioenvironment_Degradation_GFP.cellml">
<component name="GFP_Degradation" component_ref="Bioenvironment_Degradation_GFP"/>
</import>
<connection>
<map_components component_1="GFP_Degradation" component_2="GFP"/>
<map_variables variable_1="concentration" variable_2="concentration"/>
</connection>
<connection>
<map_components component_1="GFP_Degradation" component_2="ExampleDevice"/>
<map_variables variable_1="kDecay" variable_2="GFP_kDecay"/>
</connection>
<connection>
<map_components component_1="GFP_Degradation" component_2="GFP_delta"/>
<map_variables variable_1="J" variable_2="JMinusDegradation"/>
</connection>
</model>
