Skip to content
Snippets Groups Projects
Commit 14196bba authored by herrTilda's avatar herrTilda
Browse files

SBML models

parent fb9012d9
No related branches found
No related tags found
No related merge requests found
Expand all Hide whitespace changes
Inline Side-by-side
scripts/Models/M1.txt
+ 3
− 3
View file @ 14196bba
......@@ -31,7 +31,8 @@ d/dt(GLUT4) = -v7f+v7b %%24
d/dt(S6K) = v9b1-v9f1 %%26
d/dt(S6Kp) = v9f1-v9b1 %%27
d/dt(S6) = v9b2-v9f2 %%28
d/dt(S6p) = v9f2-v9b2 %%29
d/dt(S6p) = v9f2-v9b2 %%29
d/dt(G_p) = EGP+Ra-E-U_ii-k_1*G_p+k_2*G_t
d/dt(G_t) = (-U_id)+k_1*G_p-k_2*G_t
d/dt(I_p) = (-m_2*I_p)-m_4*I_p+m_1*I_l
......@@ -196,8 +197,7 @@ aa = 5/2/(1-b)/D
cc = 5/2/d/D
EGP = k_p1-k_p2*G_p-k_p3*I_d-k_p4*I_po
V_mmax = (1-part)*(V_m0+V_mX*INS)
V_fmax = part*(V_f0+V_fX*INS)
V_lmax = (1-part)*(V_l0+V_lX*INS)
V_fmax = part*(V_f0+V_fX*INS)
Ee = k_e1*(G_p - k_e2)
S = gamma*I_po
I = I_p/V_I
......
scripts/Models/M1.xml 0 → 100644
+ 2585
− 0
View file @ 14196bba
This diff is collapsed.
scripts/Models/M4m.xml 0 → 100644
+ 438
− 0
View file @ 14196bba
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
<model name="M4m_SBML">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
<p>sub-model version of M4, with EGP, Ra, GLUT4m, and INS as input curves
</p>
<p>adipocyte = 1 {isCompartment:}
</p>
<p>liver = 1 {isCompartment:}
</p>
<p>tissue = 1 {isCompartment:}
</p>
<p>muscle = 1 {isCompartment:}
</p>
<p>plasma = 1 {isCompartment:}
</p>
<p>fat = 1 {isCompartment:}</p>
</body>
</html>
</notes>
<listOfCompartments>
<compartment id="rootCompartment" name="rootCompartment" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="G_p" name="G_p" compartment="tissue" initialAmount="178" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
<species id="G_t" name="G_t" compartment="tissue" initialAmount="130" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
<species id="Glu_in" name="Glu_in" compartment="adipocyte" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
<species id="G6P" name="G6P" compartment="adipocyte" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
<species id="INS" name="INS" compartment="tissue" initialAmount="0" hasOnlySubstanceUnits="true" boundaryCondition="true" constant="false"/>
<species id="GLUT4m" name="GLUT4m" compartment="adipocyte" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false"/>
<species id="U_idm" name="U_idm" compartment="muscle" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false"/>
<species id="U_idl" name="U_idl" compartment="liver" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false"/>
<species id="U_idf" name="U_idf" compartment="fat" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false"/>
<species id="U_id" name="U_id" compartment="tissue" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false"/>
<species id="G" name="G" compartment="plasma" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="true" constant="false"/>
</listOfSpecies>
<listOfParameters>
<parameter id="bradykinin" name="bradykinin" value="1" constant="true"/>
<parameter id="kbf" name="kbf" value="0.01" constant="true"/>
<parameter id="INS_offset" name="INS_offset" value="7" constant="true"/>
<parameter id="be" name="be" value="3" constant="true"/>
<parameter id="nC" name="nC" value="2.1e-006" constant="true"/>
<parameter id="k8" name="k8" value="724.242" constant="true"/>
<parameter id="glut1" name="glut1" value="7042.19" constant="true"/>
<parameter id="k_1" name="k_1" value="0.065" constant="true"/>
<parameter id="k_2" name="k_2" value="0.079" constant="true"/>
<parameter id="pf" name="pf" value="34" constant="true"/>
<parameter id="V_m" name="V_m" value="2553.38" constant="true"/>
<parameter id="V_mx" name="V_mx" value="2.63167" constant="true"/>
<parameter id="K_m" name="K_m" value="129.391" constant="true"/>
<parameter id="part_l" name="part_l" value="0.00249792" constant="true"/>
<parameter id="K_l" name="K_l" value="0.120151" constant="true"/>
<parameter id="p1" name="p1" value="427.534" constant="true"/>
<parameter id="p2" name="p2" value="423.661" constant="true"/>
<parameter id="p3" name="p3" value="7e-005" constant="true"/>
<parameter id="p4" name="p4" value="4389.24" constant="true"/>
<parameter id="part_f" name="part_f" value="0.932088" constant="true"/>
<parameter id="k_gluin" name="k_gluin" value="0.159629" constant="true"/>
<parameter id="k_G6P" name="k_G6P" value="0.0015" constant="true"/>
<parameter id="V_G6Pmax" name="V_G6Pmax" value="11.549" constant="true"/>
<parameter id="U_ii" name="U_ii" value="1.02548" constant="true"/>
<parameter id="EGP1" name="EGP1" value="1" constant="true"/>
<parameter id="EGP2" name="EGP2" value="1" constant="true"/>
<parameter id="EGP3" name="EGP3" value="1" constant="true"/>
<parameter id="EGP4" name="EGP4" value="1" constant="true"/>
<parameter id="EGP5" name="EGP5" value="1" constant="true"/>
<parameter id="EGP6" name="EGP6" value="1" constant="true"/>
<parameter id="EGP7" name="EGP7" value="1" constant="true"/>
<parameter id="EGP8" name="EGP8" value="1" constant="true"/>
<parameter id="EGP9" name="EGP9" value="1" constant="true"/>
<parameter id="Ra1" name="Ra1" value="1" constant="true"/>
<parameter id="Ra2" name="Ra2" value="1" constant="true"/>
<parameter id="Ra3" name="Ra3" value="1" constant="true"/>
<parameter id="Ra4" name="Ra4" value="1" constant="true"/>
<parameter id="Ra5" name="Ra5" value="1" constant="true"/>
<parameter id="Ra6" name="Ra6" value="1" constant="true"/>
<parameter id="Ra7" name="Ra7" value="1" constant="true"/>
<parameter id="Ra8" name="Ra8" value="1" constant="true"/>
<parameter id="Ra9" name="Ra9" value="1" constant="true"/>
<parameter id="INS1" name="INS1" value="1" constant="true"/>
<parameter id="INS2" name="INS2" value="1" constant="true"/>
<parameter id="INS3" name="INS3" value="1" constant="true"/>
<parameter id="INS4" name="INS4" value="1" constant="true"/>
<parameter id="INS5" name="INS5" value="1" constant="true"/>
<parameter id="INS6" name="INS6" value="1" constant="true"/>
<parameter id="INS7" name="INS7" value="1" constant="true"/>
<parameter id="INS8" name="INS8" value="1" constant="true"/>
<parameter id="INS9" name="INS9" value="1" constant="true"/>
<parameter id="GLm1" name="GLm1" value="1" constant="true"/>
<parameter id="GLm2" name="GLm2" value="1" constant="true"/>
<parameter id="GLm3" name="GLm3" value="1" constant="true"/>
<parameter id="GLm4" name="GLm4" value="1" constant="true"/>
<parameter id="GLm5" name="GLm5" value="1" constant="true"/>
<parameter id="GLm6" name="GLm6" value="1" constant="true"/>
<parameter id="GLm7" name="GLm7" value="1" constant="true"/>
<parameter id="GLm8" name="GLm8" value="1" constant="true"/>
<parameter id="GLm9" name="GLm9" value="1" constant="true"/>
<parameter id="EGP" name="EGP" value="0" constant="false"/>
<parameter id="Ra" name="Ra" value="0" constant="false"/>
<parameter id="E" name="E" value="0" constant="false"/>
<parameter id="bf_f" name="bf_f" value="0" constant="false"/>
<parameter id="bfe_f" name="bfe_f" value="0" constant="false"/>
<parameter id="part_m" name="part_m" value="0" constant="false"/>
<parameter id="V_mmax" name="V_mmax" value="0" constant="false"/>
<parameter id="V_lmax" name="V_lmax" value="0" constant="false">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
(V_l+V_lx*INS)</body>
</html>
</notes>
</parameter>
<parameter id="INS_fe" name="INS_fe" value="0" constant="false"/>
<parameter id="V_in" name="V_in" value="0" constant="false"/>
<parameter id="V_out" name="V_out" value="0" constant="false"/>
<parameter id="V_G" name="V_G" value="0" constant="false"/>
<parameter id="V_G6P" name="V_G6P" value="0" constant="false"/>
<parameter id="V_met" name="V_met" value="0" constant="false"/>
</listOfParameters>
<listOfRules>
<rateRule variable="G_p">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<minus/>
<apply>
<plus/>
<ci> EGP </ci>
<ci> Ra </ci>
</apply>
<ci> E </ci>
</apply>
<ci> U_ii </ci>
</apply>
<apply>
<times/>
<ci> k_1 </ci>
<ci> G_p </ci>
</apply>
</apply>
<apply>
<times/>
<ci> k_2 </ci>
<ci> G_t </ci>
</apply>
</apply>
</math>
</rateRule>
<rateRule variable="G_t">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<apply>
<plus/>
<apply>
<minus/>
<ci> U_id </ci>
</apply>
<apply>
<times/>
<ci> k_1 </ci>
<ci> G_p </ci>
</apply>
</apply>
<apply>
<times/>
<ci> k_2 </ci>
<ci> G_t </ci>
</apply>
</apply>
</math>
</rateRule>
<rateRule variable="Glu_in">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<apply>
<times/>
<ci> p1 </ci>
<apply>
<minus/>
<ci> V_in </ci>
<ci> V_out </ci>
</apply>
</apply>
<ci> V_G6P </ci>
</apply>
</math>
</rateRule>
<rateRule variable="G6P">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<ci> V_G6P </ci>
<ci> V_met </ci>
</apply>
</math>
</rateRule>
<assignmentRule variable="INS"/>
<assignmentRule variable="EGP"/>
<assignmentRule variable="Ra"/>
<assignmentRule variable="GLUT4m"/>
<assignmentRule variable="E">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<cn type="integer"> 0 </cn>
</math>
</assignmentRule>
<assignmentRule variable="bf_f">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> bradykinin </ci>
<apply>
<plus/>
<ci> be </ci>
<apply>
<times/>
<ci> kbf </ci>
<apply>
<plus/>
<ci> INS </ci>
<ci> INS_offset </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="bfe_f">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> bf_f </ci>
</math>
</assignmentRule>
<assignmentRule variable="part_m">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<minus/>
<cn type="integer"> 1 </cn>
<ci> part_l </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="V_mmax">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> part_m </ci>
<apply>
<plus/>
<ci> V_m </ci>
<apply>
<times/>
<ci> V_mx </ci>
<ci> INS </ci>
</apply>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="V_lmax">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<body>
(V_l+V_lx*INS)</body>
</html>
</notes>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> part_l </ci>
<ci> V_mmax </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="INS_fe">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> nC </ci>
<apply>
<plus/>
<apply>
<divide/>
<apply>
<times/>
<ci> k8 </ci>
<ci> GLUT4m </ci>
</apply>
<ci> pf </ci>
</apply>
<apply>
<divide/>
<ci> glut1 </ci>
<ci> pf </ci>
</apply>
<ci> bfe_f </ci>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="V_in">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> p4 </ci>
<ci> G_t </ci>
<ci> INS_fe </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="V_out">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> p3 </ci>
<ci> Glu_in </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="U_idm">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> V_mmax </ci>
<ci> G_t </ci>
</apply>
<apply>
<plus/>
<ci> K_m </ci>
<ci> G_t </ci>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="U_idl">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<ci> V_lmax </ci>
<ci> G_t </ci>
</apply>
<apply>
<plus/>
<ci> K_l </ci>
<ci> G_t </ci>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="U_idf">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> part_f </ci>
<apply>
<minus/>
<ci> V_in </ci>
<ci> V_out </ci>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="U_id">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> U_idf </ci>
<ci> U_idm </ci>
<ci> U_idl </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="V_G">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<cn> 1.88 </cn>
</math>
</assignmentRule>
<assignmentRule variable="G">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<ci> G_p </ci>
<ci> V_G </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="V_G6P">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<times/>
<apply>
<divide/>
<apply>
<times/>
<ci> V_G6Pmax </ci>
<ci> Glu_in </ci>
</apply>
<apply>
<plus/>
<ci> k_gluin </ci>
<ci> Glu_in </ci>
</apply>
</apply>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<plus/>
<ci> k_G6P </ci>
<ci> G6P </ci>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="V_met">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> p2 </ci>
<ci> G6P </ci>
</apply>
</math>
</assignmentRule>
</listOfRules>
</model>
</sbml>
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment