| Calcium Calculator Simulation Script Files | ||||
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V. Matveev,
R.S. Zucker,
A. Sherman (2004) Facilitation through Buffer Saturation: Constraints on Endogenous Buffering Properties Biophysical Journal, 86:2691-2709 [ Abstract ] [ Full Text ] [ PDF (545 KB) ] |
| ♦ FCT_main.par |
script containing the main definitions. Place it in the
same directory with the scripts below before running any of the simulations. Under Windows, file operations do not
default to current directory (a nuisance!), so make sure that the parameter path defined in scripts below
points to the directory where "FCT_main.par" is residing. |
| ♦ FCT_Fig4.par |
reproduces Figs. 2 and 4 of the manuscript. This script requires
a command line parameter specifying the total buffer concentration. Execute calc FCT_Fig4.par 500 to
reproduce Figs. 2 and 4B.
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| ♦ FCT_Fig7.par |
reproduces Figs. 6B and 7. Accepts a command-line string parameter,
control or fura, specifying whether Fura-2 should be included in the simulation.
Execute calc FCT_Fig7.par control to reproduce data in Figs. 6B and 7 (control curve).
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| ♦ FCT_Fig11.par |
reproduces Figs. 9B and 11. Accepts a command-line string parameter,
control or fura, specifying whether Fura-2 should be included in the simulation.
Execute calc FCT_Fig11.par control to reproduce data in Figs. 6B and 11 (control curve).
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| ♦ FCT_Fig10.par |
produces the distance-dependent concentration plots in Fig. 10,
as a sequence of files ("Fig10.Ca.0ms through Fig.Ca.10ms", and "Fig10.B.0ms" through "Fig10.B.10ms") corresponding
to different times after the channel closing. You can use gnuplot to view these files, i.e.
gnuplot 'Fig10.Ca.1ms' w lines.
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| ♦ FCT_decay.par |
reproduces the decay time course of facilitation shown in Fig. 12. It requires two command-line parameters: 1. The first argument accepts values of A and B, corresponding to the mobile and the fixed buffer cases,
respectively. 2. The second argument accepts values of control and fura, and specifies whether Fura-2 is to be included
in the simulation.To reproduce, for example, the Fura-2 data in Fig. 12 B, execute calc FCT_decay.par B fura .
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| ♦ FCT_Fig3.par |
produces the data for the parameter-sweep plots in Fig. 3; requires a command-line parameter
specifying the unbinding rate, koff. For instance, execute
calc FCT_Fig3.par 0.4. The resulting file will be called
FCT_vs_Btotal_and_KD_koff0.4, and will contain four columns, in the format:
Btotal KD P1 P5.
One can use gnuplot to visualize the results: at the gnuplot prompt, type
splot 'FCT_vs_Btotal_and_KD_koff0.4' u 1:2:($4/$3) w lines. This will make a surface
plot of the ratio of the 4th and 1st columns, equal to the P5/P1 value.
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| ♦ FCT_Fig5.par |
produces the data for the parameter-sweep plots in Figs. 5 and 6A; requires a command-line parameter
specifying the buffering capacity, κ0. For instance, execute
calc FCT_Fig5.par 500. The resulting file will be called
FCT_vs_Btotal_and_kon_kappa500, and will contain eight columns, in the format:
Btotal kon P11 P51
P12 P52 P13 P53
where P1i P5i are respectively the 1st and 5th
Ca2+ transients at the i-th site (see Fig. 1).
One can use gnuplot to visualize the results: at the gnuplot prompt, type
splot 'FCT_vs_Btotal_and_kon_kappa500' u 1:2:($6/$5) w lines. This will make a surface
plot of the ratio of the 4th and 1st columns, equal to the
P12/P52 value.
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| ♦ FCT_Fig13.par |
produces the data for the parameter-sweep plots in Fig. 13. Same as
FCT_Fig5.par script above, but with a low-affinity buffer added. Requires a
command-line parameter specifying the buffering capacity, κ0.
For instance, execute calc FCT_Fig13.par 500. The resulting file will be called
FCT_vs_Btotal_and_kon_2buffer_kappa500
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| ♦ FCT_Fig9.par |
produces the data for the parameter-sweep plots in Fig. 9. Same as
FCT_Fig5.par script above, but with a fixed buffer, and different parameter ranges.
Requires a
command-line parameter specifying the buffering capacity, κ0.
Execute calc FCT_Fig9.par 500. The resulting file will be called
FCT_vs_Btotal_and_kon_fixed500 |
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♦ FCT_Fig8.par |
produces the data for the parameter-sweep plot of Fig. 8B.
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