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Basic usage of code generation tool limpet_fe.py

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\nAuthor: Edward\ \ Vigmond edward.vigmond@ubordeaux-1.fr\n

This tutorial explains the basics\ \ of using the code generation tool limpet_fe.py for generating ODE\ \ solver code for models of cellular dynamics. A more detailed explanation of the\ \ background is found in the section on code generation in the CME manual.

\n\ <h2 id=\"limpet-fe-tutorial\">Usage of limpet_fe.py\n

limpet_fe.py\ \ is the EasyML to C translator for writing ionic models. The easiest way to see\ \ how to write a model is to examine a simpler example. To work on this tutorial\ \ do

\n<div class=\"sourceCode\" id=\"cb1\"><pre class=\"sourceCode bash\"><code\ \ class=\"sourceCode bash\"><span id=\"cb1-1\"><a href=\"#cb1-1\" aria-hidden=\"\ true\"><span class=\"bu\">cd <span class=\"va\">${TUTORIALS}/01_EP_single_cell/04_limpet_fe\n\ <h2 id=\"input-.model-file\">Input .model file\n

Let's look at the <code\ \ class=\"interpreted-text\" role=\"download\">Beeler-Reuter model </downloads/my_MBRDR.model>\ \ as modified by Drouhard and Roberge:

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Iion; .nodal(); .external();\n\
V; .nodal(); .external(Vm); \n\nV; .lookup(-800, 800, 0.05);\nCa_i; .lookup(0.001,\
\ 30, 0.001); .units(uM);\n\nV_init = -86.926861;\n\n# sodium current\nGNa = 15;\n\
ENa  = 40.0;\nI_Na = GNammmh(V-ENa);\nI_Na  = sv->j;\n\na_m = ((V <\
\ 100)\n       ? 0.9(V+42.65)/(1.-exp(-0.22(V+42.65)))\n       : 890.94379exp(.0486479163(V-100.))/\n\
\            (1.+5.93962526exp(.0486479163(V-100.)))\n       );\nb_m = ((V <\
\ -85)\n       ? 1.437exp(-.085(V+39.75))\n       : 100./(1.+.48640816exp(.2597503577(V+85.)))\n\
\       );\na_h = ((V>-90.)\n       ? 0.1exp(-.193(V+79.65))\n       : .737097507-.1422598189(V+90.)\n\
\       );\nb_h = 1.7/(1.+exp(-.095(V+20.5)));\n\na_d = APDshorten(0.095exp(-0.01(V-5.)))/\n\
\  (exp(-0.072(V-5.))+1.);\nb_d = APDshorten(0.07exp(-0.017(V+44.)))/\n  (exp(0.05(V+44.))+1.)\
\ ;\n\na_f = APDshorten(0.012exp(-0.008(V+28.)))/\n  (exp(0.15(V+28.))+1.);\n\
b_f = APDshorten(0.0065exp(-0.02(V+30.)))/\n  (exp(-0.2(V+30.))+1.);\n\na_X\
\ = ((V<400.)\n       ? (0.0005exp(0.083(V+50.)))/\n       (exp(0.057(V+50.))+1.)\
\ \n       : 151.7994692exp(.06546786198(V-400.))/\n       (1.+1.517994692exp(.06546786198(V-400.)))\n\
\       );\n\nb_X   = (0.0013exp(-0.06(V+20.)))/(exp(-0.04(V+20.))+1.);\n\nxti\
\   = 0.8(exp(0.04(V+77.))-1.)/exp(0.04(V+35.));\n\nI_K = (( V != -23. )\n  \
\     ? 0.35(4.(exp(0.04(V+85.))-1.)/(exp(0.08(V+53.))+\n                  \
\                            exp(0.04(V+53.)))-\n               0.2(V+23.)/expm1(-0.04(V+23.)))\n\
\       : \n       0.35(4.(exp(0.04(V+85.))-1.)/(exp(0.08(V+53.))+\n       \
\                                     exp(0.04(V+53.))) + 0.2/0.04 )\n       );\n\
\n# slow inward\nGsi = 0.09;\nEsi = -82.3-13.0287log(Ca_i/1.e6);\nI_si = Gsidf(V-Esi);\n\
I_X  = Xxti;\n\nIion= I_Na+I_si+I_X+I_K;\n\nCa_i_init = 3.e-1;\ndiff_Ca_i = ((V<200.)\n\
\             ? (-1.e-1I_si+0.071.e6*(1.e-7-Ca_i/1.e6))\n             : 0\n  \
\           );\n\ngroup {\n  GNa;\n  Gsi;\n  APDshorten = 1;\n} .param();\n\ngroup\
\ {\n  I_Na;\n  I_si;\n  I_X;\n  I_K;\n} .trace();

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Generally, it\ \ looks like C code with a few extra commands. Let's break it down a bit:

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Iion; .nodal(); .external();\nV; .nodal(); .external(Vm); 

03A_voltage_clamp 05_EasyML