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ElsjePienaarGroup · Jan 24, 2022 · 7488105 · 7488105
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commit 7488105
Showing 1 changed file with 18 additions and 18 deletions.
diff --git a/N803_model_2.m b/N803_model_2.m
@@ -1,14 +1,14 @@
 %% N803_model_2.m - solves ODE model for N-803 treatment of SIV
 %
 %     /--------------------------------------------------------------\
-%     | Date:         10/28/2021                                     |
+%     | Date:         10/31/2021                                     |
 %     | Author:       Jonathan Cody                                  |
 %     | Affiliation:  Purdue University                              |
 %     |               Weldon School of Biomedical Engineering        |
 %     |               Pienaar Computational Systems Pharmacology Lab |
 %     \--------------------------------------------------------------/
 %
-% Version 2D+
+% Version 2D+ (also allowing regulation calibration)
 %
 % Nomenclature: V  = SIV virions [#/無]
 %               E0 = resting SIV-specific CD8+ T cells [#/無]
@@ -54,6 +54,7 @@
 %
 % Y_OUT(:,1) = V at points in 'SoluTimes' [log fold change]
 % Y_OUT(:,2) = E at points in 'SoluTimes' [fold change]
+% Y_OUT(:,3) = R at points in 'SoluTimes' [fold change]
 %
 % If 'fullOut' is non-empty, more columns are included (see code)
 %
@@ -190,9 +191,9 @@
 
 Y = abs(Y) ;% removing negatives resulting from numerical error
 
-% V,E,K [fold change]
 Y_OUT = [ log10(Y(:,1)/Vi)     ... V [log fold change]
-        , sum(Y(:,2:13),2)/EBi ];% E [fold change]
+        , sum(Y(:,2:13),2)/EBi ... E [fold change]
+        , Y(:,15+nR)/Y(1,15+nR) ];% R [fold change]
 
 %% ------------------------------------------------------------------------
 % Add columns to 'Y_OUT' (if requested) -----------------------------------
@@ -208,19 +209,18 @@
 R  = Y(:,15+nR)          ;% immune regulation []
 [F,T] = terms(Y) ;% modifiers for 'gE0','gB0','p0','aE0','aB0'
 
-Y_OUT(:,03) = (E0+Ea) / (E0(1)+Ea(1)) ;% E [fold change]
-Y_OUT(:,04) = (B0+Ba) / (B0(1)+Ba(1)) ;% B [fold change]
-Y_OUT(:,05) = E0 / E0(1) ;% E0 [fold change]
-Y_OUT(:,06) = B0 / B0(1) ;% B0 [fold change]
-Y_OUT(:,07) = Ea / Ea(1) ;% Ea [fold change]
-Y_OUT(:,08) = Ba / Ba(1) ;% Ba [fold change]
-Y_OUT(:,09) = (E0+Ea)./(E0+B0+Ea+Ba) ;% E frequency in (E+B)
-Y_OUT(:,10) = (Ea+Ba)./(E0+B0+Ea+Ba) ;% activated frequency in (E+B)
-Y_OUT(:,11) = (Ea)./(E0+Ea) ;% activated frequency in E
-Y_OUT(:,12) = (Ba)./(B0+Ba) ;% activated frequency in B
-Y_OUT(:,13) = Y(:,14) ;% X [pmol/kg]
-Y_OUT(:,14) = Y(:,15) ;% C [pM]
-Y_OUT(:,15) = R / R(1) ;% R [fold change]
+Y_OUT(:,04) = (E0+Ea) / (E0(1)+Ea(1)) ;% E [fold change]
+Y_OUT(:,05) = (B0+Ba) / (B0(1)+Ba(1)) ;% B [fold change]
+Y_OUT(:,06) = E0 / E0(1) ;% E0 [fold change]
+Y_OUT(:,07) = B0 / B0(1) ;% B0 [fold change]
+Y_OUT(:,08) = Ea / Ea(1) ;% Ea [fold change]
+Y_OUT(:,09) = Ba / Ba(1) ;% Ba [fold change]
+Y_OUT(:,10) = (E0+Ea)./(E0+B0+Ea+Ba) ;% E frequency in (E+B)
+Y_OUT(:,11) = (Ea+Ba)./(E0+B0+Ea+Ba) ;% activated frequency in (E+B)
+Y_OUT(:,12) = (Ea)./(E0+Ea) ;% activated frequency in E
+Y_OUT(:,13) = (Ba)./(B0+Ba) ;% activated frequency in B
+Y_OUT(:,14) = Y(:,14) ;% X [pmol/kg]
+Y_OUT(:,15) = Y(:,15) ;% C [pM]
 Y_OUT(:,16) = T ;% T []
 
 Y_OUT(:,17) = F(:,01) ;% N803 effect []
@@ -305,7 +305,7 @@
     dY(4:9)= 2*pE*Ea(1:6) - dA*Ea(2:7) - pE*Ea(2:7) ;% dE2-7/dt
     dY(10) = 2*pE*Ea(7)   - dA*Ea(8)   - mE*Ea(8)   ;% dE8/dt
     dY(11) = p*B0 - aB*B0 - d*B0       + mB*Ba(2)   ;% dB0/dt
-    dY(12) =      + aB*B0 - dA*Ba(2)   - pB*Ba(1)   ;% dB1/dt
+    dY(12) =      + aB*B0 - dA*Ba(2)   - pB*Ba(1)   ;% dB1/dt               !!!!! dA*Ba(1) !!!!!
     dY(13) = 2*pB*Ba(1)   - dA*Ba(2)   - mB*Ba(2)   ;% dB2/dt
     dY(14) =         - ka*X ;% dX/dt
     dY(15) = ka*X/vd - ke*C ;% dC/dt