Wholecell Toy Model

Model version: 11

BOUNDS submodel

Submodel for dynamically calculating the flux bounds. The dynamically changing flux bounds are the input to the FBA model.

Description

This is a toy model for coupling models with different modeling frameworks via comp.

This file has been produced by Matthias Koenig.

Terms of use

Redistribution and use of any part of this model, with or without modification, are permitted provided that the following conditions are met:

Redistributions of this SBML file must retain the above copyright notice, this list of conditions and the following disclaimer.
Redistributions in a different form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

This model is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Model : toy_wholecell_bounds

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-06-19 10:53
Modified: 2017-06-19 10:53

id	toy_wholecell_bounds `meta_toy_wholecell_bounds`
name	toy_wholecell (BOUNDS)
time	s
substance	item
extent	item
volume	m3
area	m2
length	m

L3V1 comp-V1

SBO:0000293

type	Ports [9]	referenced element	id ref	sbo
Port	dt_port dt_port <comp:port sboTerm="SBO:0000599" comp:idRef="dt" comp:id="dt_port"/>	`Parameter: dt`	dt	SBO:0000599
Port	extern_port extern_port <comp:port sboTerm="SBO:0000599" comp:idRef="extern" comp:id="extern_port"/>	`Compartment: extern`	extern	SBO:0000599
Port	A_port A_port <comp:port sboTerm="SBO:0000599" comp:idRef="A" comp:id="A_port"/>	`Species: A`	A	SBO:0000599
Port	C_port C_port <comp:port sboTerm="SBO:0000599" comp:idRef="C" comp:id="C_port"/>	`Species: C`	C	SBO:0000599
Port	lb_EX_A_port lb_EX_A_port <comp:port sboTerm="SBO:0000599" comp:idRef="lb_EX_A" comp:id="lb_EX_A_port"/>	`Parameter: lb_EX_A`	lb_EX_A	SBO:0000599
Port	ub_EX_A_port ub_EX_A_port <comp:port sboTerm="SBO:0000599" comp:idRef="ub_EX_A" comp:id="ub_EX_A_port"/>	`Parameter: ub_EX_A`	ub_EX_A	SBO:0000599
Port	lb_EX_C_port lb_EX_C_port <comp:port sboTerm="SBO:0000599" comp:idRef="lb_EX_C" comp:id="lb_EX_C_port"/>	`Parameter: lb_EX_C`	lb_EX_C	SBO:0000599
Port	ub_EX_C_port ub_EX_C_port <comp:port sboTerm="SBO:0000599" comp:idRef="ub_EX_C" comp:id="ub_EX_C_port"/>	`Parameter: ub_EX_C`	ub_EX_C	SBO:0000599
Port	ub_R1_port ub_R1_port <comp:port sboTerm="SBO:0000599" comp:idRef="ub_R1" comp:id="ub_R1_port"/>	`Parameter: ub_R1`	ub_R1	SBO:0000599

type	FunctionDefinitions [2]	name	math	sbo	cvterm
FunctionDefinition	max max <functionDefinition id="max" name="min"> <math xmlns="http://www.w3.org/1998/Math/MathML"> <lambda> <bvar> <ci> x </ci> </bvar> <bvar> <ci> y </ci> </bvar> <piecewise> <piece> <ci> x </ci> <apply> <gt/> <ci> x </ci> <ci> y </ci> </apply> </piece> <otherwise> <ci> y </ci> </otherwise> </piecewise> </lambda> </math> </functionDefinition>	min	$x y x x y y$
FunctionDefinition	min min <functionDefinition id="min" name="max"> <math xmlns="http://www.w3.org/1998/Math/MathML"> <lambda> <bvar> <ci> x </ci> </bvar> <bvar> <ci> y </ci> </bvar> <piecewise> <piece> <ci> x </ci> <apply> <lt/> <ci> x </ci> <ci> y </ci> </apply> </piece> <otherwise> <ci> y </ci> </otherwise> </piecewise> </lambda> </math> </functionDefinition>	max	$x y x x y y$

type	UnitDefinitions [9]	name	units	cvterm
UnitDefinition	s `meta_s` s <unitDefinition metaid="meta_s" id="s" name="second"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_s"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/uo/UO:0000010"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfUnits> <unit kind="second" exponent="1" scale="0" multiplier="1"/> </listOfUnits> </unitDefinition>	second	$s$	BQB_IS UO:0000010
UnitDefinition	kg `meta_kg` kg <unitDefinition metaid="meta_kg" id="kg" name="kilogram"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_kg"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/uo/UO:0000009"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfUnits> <unit kind="kilogram" exponent="1" scale="0" multiplier="1"/> </listOfUnits> </unitDefinition>	kilogram	$kg$	BQB_IS UO:0000009
UnitDefinition	m `meta_m` m <unitDefinition metaid="meta_m" id="m" name="meter"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_m"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/uo/UO:0000008"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfUnits> <unit kind="metre" exponent="1" scale="0" multiplier="1"/> </listOfUnits> </unitDefinition>	meter	$m$	BQB_IS UO:0000008
UnitDefinition	m2 `meta_m2` m2 <unitDefinition metaid="meta_m2" id="m2" name="square meter"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_m2"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/uo/UO:0000080"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfUnits> <unit kind="metre" exponent="2" scale="0" multiplier="1"/> </listOfUnits> </unitDefinition>	square meter	$m 2$	BQB_IS UO:0000080
UnitDefinition	m3 `meta_m3` m3 <unitDefinition metaid="meta_m3" id="m3" name="cubic meter"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_m3"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/uo/UO:0000096"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfUnits> <unit kind="metre" exponent="3" scale="0" multiplier="1"/> </listOfUnits> </unitDefinition>	cubic meter	$m 3$	BQB_IS UO:0000096
UnitDefinition	mM `meta_mM` mM <unitDefinition metaid="meta_mM" id="mM" name="millimolar"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_mM"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/uo/UO:0000063"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> <listOfUnits> <unit kind="mole" exponent="1" scale="0" multiplier="1"/> <unit kind="metre" exponent="-3" scale="0" multiplier="1"/> </listOfUnits> </unitDefinition>	millimolar	$mole m 3$	BQB_IS UO:0000063
UnitDefinition	per_s per_s <unitDefinition id="per_s"> <listOfUnits> <unit kind="second" exponent="-1" scale="0" multiplier="1"/> </listOfUnits> </unitDefinition>		$1 s$
UnitDefinition	item_per_s item_per_s <unitDefinition id="item_per_s"> <listOfUnits> <unit kind="item" exponent="1" scale="0" multiplier="1"/> <unit kind="second" exponent="-1" scale="0" multiplier="1"/> </listOfUnits> </unitDefinition>		$item s$
UnitDefinition	item_per_m3 item_per_m3 <unitDefinition id="item_per_m3"> <listOfUnits> <unit kind="item" exponent="1" scale="0" multiplier="1"/> <unit kind="metre" exponent="-3" scale="0" multiplier="1"/> </listOfUnits> </unitDefinition>		$item m 3$

type	Compartments [1]	name	size	constant	spatial dimensions	units	derived units	sbo	cvterm
Compartment	extern `meta_extern` extern <compartment metaid="meta_extern" sboTerm="SBO:0000290" id="extern" name="extern" spatialDimensions="3" size="1" units="m3" constant="true"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_extern"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/sbo/SBO:0000290"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </compartment>	extern	1.0	T	3	m3	$m 3$	SBO:0000290	BQB_IS SBO:0000290

type	Species [2]	name	compartment	boundary condition	constant	initial amount	initial concentration	substance units	derived units	sbo	cvterm
Species	A `meta_A` A <species metaid="meta_A" sboTerm="SBO:0000247" id="A" name="A" compartment="extern" initialAmount="1" substanceUnits="item" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_A"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/sbo/SBO:0000247"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species>	A	extern	F	F	1.0		item	$item$	SBO:0000247	BQB_IS SBO:0000247
Species	C `meta_C` C <species metaid="meta_C" sboTerm="SBO:0000247" id="C" name="C" compartment="extern" initialAmount="1" substanceUnits="item" hasOnlySubstanceUnits="true" boundaryCondition="false" constant="false"> <annotation> <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"> <rdf:Description rdf:about="#meta_C"> <bqbiol:is> <rdf:Bag> <rdf:li rdf:resource="http://identifiers.org/sbo/SBO:0000247"/> </rdf:Bag> </bqbiol:is> </rdf:Description> </rdf:RDF> </annotation> </species>	C	extern	F	F	1.0		item	$item$	SBO:0000247	BQB_IS SBO:0000247

type	Parameters [8]	name	constant	value	unit	derived unit	sbo
Parameter	dt dt <parameter sboTerm="SBO:0000346" id="dt" value="0.1" units="s" constant="true"/>		T	0.1	s	$s$	SBO:0000346
Parameter	lb_EX_A lb_EX_A <parameter sboTerm="SBO:0000625" id="lb_EX_A" value="-1000" units="item_per_s" constant="false"/>		F	-1000.0	item_per_s	$item s$	SBO:0000625
Parameter	ub_EX_A ub_EX_A <parameter sboTerm="SBO:0000625" id="ub_EX_A" value="1000" units="item_per_s" constant="false"/>		F	1000.0	item_per_s	$item s$	SBO:0000625
Parameter	lb_EX_C lb_EX_C <parameter sboTerm="SBO:0000625" id="lb_EX_C" value="-1000" units="item_per_s" constant="false"/>		F	-1000.0	item_per_s	$item s$	SBO:0000625
Parameter	ub_EX_C ub_EX_C <parameter sboTerm="SBO:0000625" id="ub_EX_C" value="1000" units="item_per_s" constant="false"/>		F	1000.0	item_per_s	$item s$	SBO:0000625
Parameter	lb_default lb_default <parameter id="lb_default" value="-1000" units="item_per_s" constant="true"/>		T	-1000.0	item_per_s	$item s$
Parameter	ub_R1 ub_R1 <parameter sboTerm="SBO:0000625" id="ub_R1" value="1" units="item_per_s" constant="false"/>		F	1.0	item_per_s	$item s$	SBO:0000625
Parameter	k1 k1 <parameter id="k1" name="k1" value="-0.2" units="per_s" constant="false"/>	k1	F	-0.2	per_s	$1 s$

type	Rules [3]		assignment	derived units
Rule	d ub_R1/dt ub_R1 <rateRule variable="ub_R1"> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <times/> <ci> k1 </ci> <ci> ub_R1 </ci> </apply> </math> </rateRule>	=	$k1 ub_R1$	$item s 2$
Rule	lb_EX_A lb_EX_A <assignmentRule variable="lb_EX_A"> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <ci> max </ci> <ci> lb_default </ci> <apply> <divide/> <apply> <minus/> <ci> A </ci> </apply> <ci> dt </ci> </apply> </apply> </math> </assignmentRule>	=	$max lb_default A dt$	$item s$
Rule	lb_EX_C lb_EX_C <assignmentRule variable="lb_EX_C"> <math xmlns="http://www.w3.org/1998/Math/MathML"> <apply> <ci> max </ci> <ci> lb_default </ci> <apply> <divide/> <apply> <minus/> <ci> C </ci> </apply> <ci> dt </ci> </apply> </apply> </math> </assignmentRule>	=	$max lb_default C dt$	$item s$