New figures for E. coli (definitive)

For maintenance, the final figure is the one in previous post.

Summary of results:

 

D=0.05

D=0.1

D=0.2

D=0.3

D=0.4

Delta for main plots

1.5

1.99

2.54

4.22

5.31

p_growth (main plots)

0.01

0.0058

2.0000e-004

4.8000e-004

6.2000e-004

p_ATP (main plots)

NaN

0.1739

0.2399

0.0854

0.1211

max(p_growth) (all Deltas)

0.0187

0.0383

0.0517

0.0024

0.0011

min(p_ATP) (all Deltas)

NaN

0.0920

0.0302

0.0280

0.0245

 

Growth 0.05 (maybe not final, maybe will not be included):

>> fig_pap_coli_13(1,0,.05)

Growth 0.1:
>> fig_pap_coli_13(1,0,.1)

>> fig_pap_coli_13(1,0,.2)

>> fig_pap_coli_13(1,0,.3)

>> fig_pap_coli_13(1,0,.4)

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New figures for E. coli (not definitive)

Maintenance:

>> fig_pap_coli_mantenimiento_02(1)

Figures for growth 0.1, 0.2, 0.3 and 0.4, respectively:

>> fig_pap_coli_13(1,0,.1)

>> fig_pap_coli_13(1,0,.2)

>> fig_pap_coli_13(1,0,.3)

>> fig_pap_coli_13(1,0,.4)

Calibration of the metric for E. coli: Preliminary results

I use the model for growth that is used in Figure 4.

fig_pap_coli_11(1,0)

(and use internal variables from now on)

New metric:

p=calibrametrica(model_growth,flujosexp_finales,1000,100,Delta);
K>> hist(p)

K>> hist(log10(p))

K>> sum(p<.05)
ans =
2

Looks good, but I will repeat it with more repetitions.

Now I test the old metric:

p2=calibrametrica(model_growth,flujosexp_finales,1000,100,Delta,2);
K>> hist(p2)

K>> hist(log10(p2))


K>> sum(p2<.05)
ans =
0

K>> sum(p2<.1)

ans =
3

It seems there was a bias. I will also repeat it with more repetitions.

New Figure 4

Growth 0.1. New maintenance. Old data. New metric.

>> fig_pap_coli_11(1,1)

 

Growth 0.4:

>> fig_pap_coli_11(1,1)

New Figure 4 after revision

>> fig_pap_coli_10(1,zeros(100))

Main questions:

– Are the labels OK? In particular, this style with the description, comma, the symbol. And the description of Delta.
– Are the words ATP, BIOMASS where they should be? In boxes A, B they might be inside the box.
– Colorbar: It is modified to show dark red in the top. Enough?

Figure of the metabolic network

Only the core metabolism (no oxygen). Only colors for reactions that involve ATP and metabolites that contribute to biomass.