Commit 9d776d68 authored by Antonio Politi's avatar Antonio Politi

final changes of revised manuscript + TPR dataset

parent 6bbc4c54
time int_avg int_sd mat_avg mat_sd
19.2000 3.7066 1.1912 4.3051 2.9756
24.4000 2.5548 1.8080 3.2638 3.0584
28.4000 2.8685 1.9448 0.7257 0.8852
36.3000 1.6465 1.2804 3.8867 3.1354
42.0000 5.3638 3.5139 4.5204 2.8718
53.2000 2.7601 1.0185 3.7098 1.5762
60.8000 0.3114 0.6229 9.3678 2.5641
65.6000 0.6860 1.0028 5.9860 1.9396
73.6000 1.2769 1.4383 6.6834 0.7126
82.9000 0.8490 0.5670 11.0643 1.8468
100.2000 0.4336 0.5956 11.5611 1.2783
time int_avg int_sd mat_avg mat_sd
19.2000 3.7066 1.1912 4.3051 2.9756
24.4000 2.5548 1.8080 3.2638 3.0584
28.4000 2.8685 1.9448 0.7257 0.8852
36.3000 1.6465 1.2804 3.8867 3.1354
42.0000 5.3638 3.5139 4.5204 2.8718
53.2000 2.7601 1.0185 3.7098 1.5762
60.8000 0.3114 0.6229 9.3678 2.5641
65.6000 0.6860 1.0028 5.9860 1.9396
73.6000 1.2769 1.4383 6.6834 0.7126
82.9000 0.8490 0.5670 11.0643 1.8468
100.2000 0.4336 0.5956 11.5611 1.2783
116.4000 1.1289 1.2736 9.2309 0.7013
\ No newline at end of file
time int_avg int_sd mat_avg mat_sd
19.2 5.4398 4.0326 7.0806 2.3042
24.4 2.368 0.869 9.7306 1.4395
28.4 4.9731 2.2017 7.0488 2.3073
36.3 3.5654 1.3458 6.7678 2.8673
42 2.7424 2.1469 9.2873 1.8365
53.2 2.877 1.1693 7.9687 1.9991
60.8 0.2252 0.4504 10.5707 1.5535
65.6 1.068 0.8514 7.5591 2.0611
73.6 0.398 0.6893 11.1441 2.5738
82.9 1.1013 1.1236 12.6691 2.933
100.2 1.8179 0.6596 9.3471 4.0471
116.4 0.388 0.6721 10.4042 2.9619
time int_avg int_sd mat_avg mat_sd
19.2 5.4398 4.0326 7.0806 2.3042
24.4 2.368 0.869 9.7306 1.4395
28.4 4.9731 2.2017 7.0488 2.3073
36.3 3.5654 1.3458 6.7678 2.8673
42 2.7424 2.1469 9.2873 1.8365
53.2 2.877 1.1693 7.9687 1.9991
60.8 0.2252 0.4504 10.5707 1.5535
65.6 1.068 0.8514 7.5591 2.0611
73.6 0.398 0.6893 11.1441 2.5738
82.9 1.1013 1.1236 12.6691 2.933
100.2 1.8179 0.6596 9.3471 4.0471
116.4 0.388 0.6721 10.4042 2.9619
%surface area nucleus fitted to a0 + a1*(1-exp(-kg1*(t-ts)) + kg2*(t-ts). Time is time after anaphase (in min)
%a0(um2) a1(um2) kg1/min kg2/min ts min
4.240e+02 1.613e+02 7.219e-02 3.969e-01 1.0e+01
%surface area nucleus fitted to a0 + a1*(1-exp(-kg1*(t-ts)) + kg2*(t-ts). Time is time after anaphase (in min)
%a0(um2) a1(um2) kg1/min kg2/min ts min
4.240e+02 1.613e+02 7.219e-02 3.969e-01 1.0e+01
%surface area nucleus fitted to a0 + a1*(1-exp(-kg1*(t-ts)) + kg2*(t-ts). Time is time after anaphase (in min)
%a0(um2) a1(um2) kg1/min kg2/min ts min
4.240e+02 1.613e+02 7.219e-02 3.969e-01 1.0e+01
%surface area nucleus fitted to a0 + a1*(1-exp(-kg1*(t-ts)) + kg2*(t-ts). Time is time after anaphase (in min)
%a0(um2) a1(um2) kg1/min kg2/min ts min
4.240e+02 1.613e+02 7.219e-02 3.969e-01 1.0e+01
%surface area nucleus fitted to a0 + a1*(1-exp(-kg1*(t-ts)) + kg2*(t-ts). Time is time after anaphase (in min)
%a0(um2) a1(um2) kg1/min kg2/min ts min
3.175e+02 1.916e+02 1.647e-01 5.122e-01 8
%surface area nucleus fitted to a0 + a1*(1-exp(-kg1*(t-ts)) + kg2*(t-ts). Time is time after anaphase (in min)
%a0(um2) a1(um2) kg1/min kg2/min ts min
3.175e+02 1.916e+02 1.647e-01 5.122e-01 8
%time_postAO(min) surface(um2) std(um2)
6 324.8838339 18.15142832
7 315.8900239 19.53950786
8 321.0277787 23.81656551
9 337.1243338 34.84300125
10 363.6998202 38.4406309
11 392.7566558 38.67294496
12 415.8168124 35.7484849
13 429.9164754 31.18123245
14 444.017039 32.44525028
15 457.1619369 31.79038923
16 466.7431851 33.60232131
17 471.733251 30.41374791
18 476.1295178 31.14088926
19 482.731503 31.93595667
20 489.1776554 37.36734493
21 491.5282724 32.97423953
22 497.0544242 35.93057587
23 494.2970468 33.62245759
24 502.8318599 34.43697764
25 505.2158906 36.13638465
26 506.9994813 36.30619571
27 506.2619541 36.84512951
28 509.5164614 39.77100388
29 510.1100672 36.2627043
30 511.9498016 37.95221268
31 514.7284827 35.97185517
32 514.2483254 36.95299492
33 517.860587 38.83293821
34 517.0401314 36.15027388
35 518.8191212 36.58525751
36 520.1365832 37.18478761
37 521.2651901 37.59631804
38 521.3830181 36.34211381
39 521.9237606 37.10399573
40 523.2215716 37.71325899
41 525.4984825 37.04248188
42 526.3112009 36.75790231
43 527.2027436 37.31180504
44 528.9424158 37.29834561
45 527.7604905 35.37487771
46 528.7967054 35.46626823
47 528.4522008 35.58633286
48 528.7950116 34.79139585
49 532.7137128 35.26097401
50 532.3228134 34.59742598
51 530.9802146 35.57327822
52 533.9783856 33.2691179
53 532.550759 34.52739285
54 532.7183134 35.93523315
55 534.7627231 34.52522721
56 534.7088233 36.45408496
57 536.1463516 34.16878695
58 535.9168799 35.14782676
59 539.1551386 34.05547923
60 537.4627865 33.45413272
61 536.4576801 34.79876509
62 537.2966621 34.38098229
63 537.8086312 34.83063725
64 539.3583948 33.80635446
65 538.2687594 32.85181268
66 539.1354378 34.39405602
67 539.1853132 36.03639469
68 541.4035922 35.10060046
69 539.3561702 36.72485241
70 541.0621873 35.17019146
71 542.0360931 35.82328798
72 540.9000071 36.58290588
73 539.6277763 37.32767447
74 541.3406091 33.8364112
75 541.3476057 34.02110702
76 543.5948244 35.8409171
77 544.3611041 34.29895627
78 542.9601491 34.34901517
79 546.1955792 31.99471812
80 546.3065139 33.99844594
81 548.1659007 32.79144322
82 548.4622188 32.7139039
83 548.3596439 32.02631316
84 549.0740163 33.84159465
85 550.9338666 32.19715598
86 549.3801059 32.97028006
87 551.7064804 32.97169913
88 553.1256013 33.2484377
89 552.6513749 30.80272358
90 551.6983572 29.26123246
91 553.0578423 30.76932326
92 553.5905258 30.57991802
93 556.5435613 32.05590728
94 555.8980209 29.98958888
95 556.067013 30.71423652
96 554.9590536 29.38072374
97 555.196635 30.61302625
98 556.0598404 31.41465538
99 556.1567784 31.50242146
100 556.6184394 30.20141837
101 556.3938785 29.92546717
102 557.5592695 30.52307581
103 558.4815422 30.82579651
104 557.6330132 30.83395494
105 558.8908575 33.05439821
106 559.2341971 30.567685
107 559.4096466 33.14209208
108 559.6938521 33.46733186
109 557.4060738 31.70818345
110 558.5523162 32.46489652
111 560.1902346 34.960441
112 559.960764 32.36046612
113 560.4568526 32.29818862
114 562.4055175 32.84270214
115 562.9503778 34.74568538
116 562.7557437 32.80025536
117 563.0570623 32.07146234
118 561.5993974 32.66755066
119 563.6139791 32.74035027
120 565.339107 34.72703474
%time_postAO(min) surface(um2) std(um2)
6 324.8838339 18.15142832
7 315.8900239 19.53950786
8 321.0277787 23.81656551
9 337.1243338 34.84300125
10 363.6998202 38.4406309
11 392.7566558 38.67294496
12 415.8168124 35.7484849
13 429.9164754 31.18123245
14 444.017039 32.44525028
15 457.1619369 31.79038923
16 466.7431851 33.60232131
17 471.733251 30.41374791
18 476.1295178 31.14088926
19 482.731503 31.93595667
20 489.1776554 37.36734493
21 491.5282724 32.97423953
22 497.0544242 35.93057587
23 494.2970468 33.62245759
24 502.8318599 34.43697764
25 505.2158906 36.13638465
26 506.9994813 36.30619571
27 506.2619541 36.84512951
28 509.5164614 39.77100388
29 510.1100672 36.2627043
30 511.9498016 37.95221268
31 514.7284827 35.97185517
32 514.2483254 36.95299492
33 517.860587 38.83293821
34 517.0401314 36.15027388
35 518.8191212 36.58525751
36 520.1365832 37.18478761
37 521.2651901 37.59631804
38 521.3830181 36.34211381
39 521.9237606 37.10399573
40 523.2215716 37.71325899
41 525.4984825 37.04248188
42 526.3112009 36.75790231
43 527.2027436 37.31180504
44 528.9424158 37.29834561
45 527.7604905 35.37487771
46 528.7967054 35.46626823
47 528.4522008 35.58633286
48 528.7950116 34.79139585
49 532.7137128 35.26097401
50 532.3228134 34.59742598
51 530.9802146 35.57327822
52 533.9783856 33.2691179
53 532.550759 34.52739285
54 532.7183134 35.93523315
55 534.7627231 34.52522721
56 534.7088233 36.45408496
57 536.1463516 34.16878695
58 535.9168799 35.14782676
59 539.1551386 34.05547923
60 537.4627865 33.45413272
61 536.4576801 34.79876509
62 537.2966621 34.38098229
63 537.8086312 34.83063725
64 539.3583948 33.80635446
65 538.2687594 32.85181268
66 539.1354378 34.39405602
67 539.1853132 36.03639469
68 541.4035922 35.10060046
69 539.3561702 36.72485241
70 541.0621873 35.17019146
71 542.0360931 35.82328798
72 540.9000071 36.58290588
73 539.6277763 37.32767447
74 541.3406091 33.8364112
75 541.3476057 34.02110702
76 543.5948244 35.8409171
77 544.3611041 34.29895627
78 542.9601491 34.34901517
79 546.1955792 31.99471812
80 546.3065139 33.99844594
81 548.1659007 32.79144322
82 548.4622188 32.7139039
83 548.3596439 32.02631316
84 549.0740163 33.84159465
85 550.9338666 32.19715598
86 549.3801059 32.97028006
87 551.7064804 32.97169913
88 553.1256013 33.2484377
89 552.6513749 30.80272358
90 551.6983572 29.26123246
91 553.0578423 30.76932326
92 553.5905258 30.57991802
93 556.5435613 32.05590728
94 555.8980209 29.98958888
95 556.067013 30.71423652
96 554.9590536 29.38072374
97 555.196635 30.61302625
98 556.0598404 31.41465538
99 556.1567784 31.50242146
100 556.6184394 30.20141837
101 556.3938785 29.92546717
102 557.5592695 30.52307581
103 558.4815422 30.82579651
104 557.6330132 30.83395494
105 558.8908575 33.05439821
106 559.2341971 30.567685
107 559.4096466 33.14209208
108 559.6938521 33.46733186
109 557.4060738 31.70818345
110 558.5523162 32.46489652
111 560.1902346 34.960441
112 559.960764 32.36046612
113 560.4568526 32.29818862
114 562.4055175 32.84270214
115 562.9503778 34.74568538
116 562.7557437 32.80025536
117 563.0570623 32.07146234
118 561.5993974 32.66755066
119 563.6139791 32.74035027
120 565.339107 34.72703474
This diff is collapsed.
function [dist, distI, distM] = afitround(MO, par, ifit, nrfits, parfile)
denfile = fullfile(MO.outdir,[parfile '_den.txt']);
prodratefile = fullfile(MO.outdir, [parfile '_prodrate.txt']);
fractionMaturefile = fullfile(MO.outdir, [parfile '_fracM.txt']);
parfile = [parfile '.txt'];
MO.runFit(par, ifit, nrfits, 0.5, parfile)
MO.plotBestfit(fullfile(MO.outdir, parfile), 1, 1);
parf = MO.getBestfit(fullfile(MO.outdir, parfile));
[dist, distI, distM] = MO.distMO(parf(ifit), ifit, parf);
dist = sum(dist.^2);
distI = sum(distI.^2);
distM = [sum(distM.^2) sum(distM(1:12).^2) sum(distM(13:24).^2)];
MO.writeDensities(parf,denfile);
MO.writeProdRate(parf, prodratefile);
MO.writeFractionMatureIP(parf, fractionMaturefile);
%%
[soli, solo] = MO.solve(parf, [parf(1) 1200]);
timPM = [180:1:1200];
yi = deval(soli, timPM);
yo = deval(solo, timPM);
A = MO.getSurf(timPM);
mean(yi(3,:)./A*0.68 + yo(3,:)./A*0.32)
std(yi(3,:)./A*0.68 + yo(3,:)./A*0.32)
mean((yi(1,:)+yi(2,:))./A*0.68 + (yi(1,:)+yi(2,:))./A*0.32)
std((yi(1,:)+yi(2,:))./A*0.68 + (yi(1,:)+yi(2,:))./A*0.32)
function [dist, distI, distM] = afitround(MO, par, ifit, nrfits, parfile)
denfile = fullfile(MO.outdir,[parfile '_den.txt']);
prodratefile = fullfile(MO.outdir, [parfile '_prodrate.txt']);
fractionMaturefile = fullfile(MO.outdir, [parfile '_fracM.txt']);
parfile = [parfile '.txt'];
MO.runFit(par, ifit, nrfits, 0.5, parfile)
MO.plotBestfit(fullfile(MO.outdir, parfile), 1, 1);
parf = MO.getBestfit(fullfile(MO.outdir, parfile));
[dist, distI, distM] = MO.distMO(parf(ifit), ifit, parf);
dist = sum(dist.^2);
distI = sum(distI.^2);
distM = [sum(distM.^2) sum(distM(1:12).^2) sum(distM(13:24).^2)];
MO.writeDensities(parf,denfile);
MO.writeProdRate(parf, prodratefile);
MO.writeFractionMatureIP(parf, fractionMaturefile);
%%
[soli, solo] = MO.solve(parf, [parf(1) 1200]);
timPM = [180:1:1200];
yi = deval(soli, timPM);
yo = deval(solo, timPM);
A = MO.getSurf(timPM);
mean(yi(3,:)./A*0.68 + yo(3,:)./A*0.32)
std(yi(3,:)./A*0.68 + yo(3,:)./A*0.32)
mean((yi(1,:)+yi(2,:))./A*0.68 + (yi(1,:)+yi(2,:))./A*0.32)
std((yi(1,:)+yi(2,:))./A*0.68 + (yi(1,:)+yi(2,:))./A*0.32)
end
\ No newline at end of file
%%
% dealyedMaturation model with production proportional to free area
% V = v*A
% par(1): ts, start of interphase assembly
% par(2): v, maximal rate of interphase assembly
% par(3): kM, initiation of maturation
% par(4): tauM, maturation time
% par(5): kd, decay of Mature pore
% par(6): number of minipores at ts inner core
% par(7): number of mature pores at ts inner core
% par(7): number of minipores at ts outer core
% par(8): number of mature pores at ts outer core
classdef delayedMaturation < absDelayedMaturation
methods
function MO = delayedMaturation(surf, useSpline, force)
MO@absDelayedMaturation(surf, useSpline, force)
MO.dataF = MO.dataA;
for i =1:2
MO.dataF(i).noncore = MO.dataF(i).d_noncore;
MO.dataF(i).core_i = MO.dataF(i).d_core_i;
MO.dataF(i).core_o = MO.dataF(i).d_core_o;
end
MO.parnames = 'ts v kM tauM kd P01 M01 P02 M02';
MO.LB = [0, 0, 0.001, 0, 0, 0, 0,0,0]; %Low boundary values
MO.HB = [15, 1, 10, 70, 1, 10000, 10000, 10000, 10000]; %High boundary values
MO.name = mfilename('class')
MO.N = 3;
end
%%
% solve equations for one set of parameters and provide the
function [soli, solo] = solve(MO, par, timeint)
soli = dde23(@MO.dde,[par(4)],@MO.ddehist1, timeint, ddeset, par);
solo = dde23(@MO.dde,[par(4)],@MO.ddehist2, timeint, ddeset, par);
end
%%
% get production rate of minipores and mature pores coming from PM
% only
function [prodRate, maturePM] = getProdRate(MO, par, timeint)
A = MO.getSurf(timeint);
prodRate = [par(2)*(timeint>=par(1)) par(2)*(timeint>=par(1))];
maturePM = [par(7)*exp(-par(5)*(timeint - par(1)))./A par(9)*exp(-par(5)*(timeint - par(1)))./A];
end
function obs = getObservable(MO,sol)
obs(:,1) = sol(1,:)'+ sol(2,:)';
obs(:,2) = sol(3,:)';
end
function s = ddehist1(MO,t,par)
% Constant history function for DDEX1.
s = [0, 0, par(7)];
if t == par(1)
s = [par(6), 0, par(7)];
end
end
function s = ddehist2(MO,t,par)
% Constant history function for DDEX1.
s = [0, 0, par(9)];
if t == par(1)
s = [par(8), 0, par(9)];
end
end
function dydt = dde(MO, t, y, Z, par)
% par(1): ts, start of interphase assembly
% par(2): v, maximal rate of interphase assembly
% par(3): kM, initiation of maturation
% par(4): tauM, maturation time
% par(5): kd, decay of Mature pore
% par(6): number of minipores at ts
% par(7): number of mature pores at 0
% Delay Differential equations function for DDEX1.
ylag = Z(:,1);
if t > par(1)
v = par(2);
else
v = 0;
end
A = MO.getSurf(t);
dydt = [ v*A - par(3)*y(1)
par(3)*y(1) - par(3)*ylag(1)
par(3)*ylag(1) - par(5)*y(3)];
end
function [par, norm] = testFit(MO)
ts = 10;
At0 = MO.getSurf(ts);
P01 = 4.493*At0;
M01 = 4.79*At0;
P02 = 3.935*At0;
M02 = 9.048*At0;
if nargin < 2
par = [ts, 0.014, 1.136, 40, 4.2e-04, P01, M01, P02, M02];
end
ifit = [2:4 6:9];
[parf, norm] = MO.fitModel(ifit, par)
par(ifit) = parf;
MO.plotResult(par)
end
end
%%
% dealyedMaturation model with production proportional to free area
% V = v*A
% par(1): ts, start of interphase assembly
% par(2): v, maximal rate of interphase assembly
% par(3): kM, initiation of maturation
% par(4): tauM, maturation time