Commit c5991337 authored by SOLIMAN Sylvain's avatar SOLIMAN Sylvain
Browse files

new version

parent 5f3dc316
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"load(library:examples/cell_cycle/Tyson_1991.bc)."
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"option(time:150)."
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"parameter(k8=100)."
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
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" },\n",
" axes: {\n",
" xaxis: {\n",
" label: \"Time\",\n",
" renderer: $.jqplot.LinearAxisRenderer,\n",
" tickOptions: {\n",
" formatString: \"%.3p\"\n",
" }\n",
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" yaxis: {\n",
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" tickOptions: {\n",
" formatString: \"%.3p\"\n",
" }\n",
" }\n",
" },\n",
" legend: {\n",
" show: true,\n",
" placement: \"outside\",\n",
" labels: [\"Cdc2\", \"Cdc2~{p1}\", \"Cyclin~{p1}\", \"Cdc2-Cyclin~{p1}\", \"Cdc2-Cyclin~{p1,p2}\", \"Cyclin\", \"YT\"],\n",
" renderer: $.jqplot.EnhancedLegendRenderer,\n",
" rendererOptions: {\n",
" seriesToggle: true,\n",
" showLineStyle: true,\n",
" numberRows: 12,\n",
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" },\n",
" sortData: false,\n",
" cursor: {\n",
" show: true,\n",
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" highlighter: {\n",
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" });\n",
" $('#plot_0_25626').contextmenu(function() {\n",
" $('#plot_0_25626').jqplotSaveImage();\n",
" return false;\n",
" });\n",
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" var png = $('#plot_0_25626').jqplotToImageStr({}).substring(22);\n",
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]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"numerical_simulation.\n",
"plot."
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0.974450\r\n"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"satisfaction_degree(exists(max, exists(min, F(Cdc2-Cyclin~{p1} > max /\\ F(Cdc2-Cyclin~{p1} < min /\\ F(Cdc2-Cyclin~{p1} > max /\\ F(Cdc2-Cyclin~{p1} < min)))) /\\ max - min > amp)), [amp -> 0.19])."
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Time: 6.363 s\r\n",
"Robustness degree: 0.978333\r\n"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"seed(0).\n",
"robustness(exists(max, exists(min, F(Cdc2-Cyclin~{p1} > max /\\ F(Cdc2-Cyclin~{p1} < min /\\ F(Cdc2-Cyclin~{p1} > max /\\ F(Cdc2-Cyclin~{p1} < min)))) /\\ max - min > amp)), [k4, k6], [amp -> 0.19])."
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"parameter(k4=550, k6=2)."
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
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[129.499, 0.00655524], [130.999, 0.00725796], [132.499, 0.00799344], [133.999, 0.00876706], [135.499, 0.00958752], [136.999, 0.0104672], [138.499, 0.0114236], [139.999, 0.0124827], [141.499, 0.0136852], [142.999, 0.0151025], [144.499, 0.0168774], [145.999, 0.0193713], [147.499, 0.0240188], [148.231, 0.0296759], [148.802, 0.0505069], [148.874, 0.0638579], [149.692, 0.219028], [150, 0.20938]], [[0, 0], [3.0e-6, 3.64434e-23], [1.8e-5, 4.71878e-20], [0.000193, 6.17092e-16], [0.001068, 5.47862e-13], [0.007943, 1.05159e-9], [0.16709, 3.01124e-6], [1.66709, 0.000156817], [3.16709, 0.000351009], [4.66709, 0.000544267], [6.16709, 0.000735717], [7.66709, 0.000926395], [9.16709, 0.00111738], [10.6671, 0.00130975], [12.1671, 0.0015046], [13.6671, 0.00170308], [15.1671, 0.00190648], [16.6671, 0.00211623], [18.1671, 0.00233404], [19.6671, 0.00256196], [21.1671, 0.00280255], [22.6671, 0.00305916], [24.1671, 0.00333631], [25.6671, 0.00364039], [27.1671, 0.00398102], [28.6671, 0.00437381], [30.1671, 0.00484676], [31.6671, 0.00545822], [33.1671, 0.0063616], [34.6671, 0.00817707], [36.1671, 0.0204673], [36.5354, 0.0849415], [36.6378, 0.215731], [38.0055, 0.0212291], [39.5055, 0.00136723], [41.0055, 0.000463902], [42.5055, 0.000600154], [44.0055, 0.000788325], [45.5055, 0.00097882], [47.0055, 0.00117007], [48.5055, 0.00136301], [50.0055, 0.00155874], [51.5055, 0.00175844], [53.0055, 0.00196343], [54.5055, 0.00217521], [56.0055, 0.00239558], [57.5055, 0.00262669], [59.0055, 0.00287132], [60.5055, 0.00313306], [62.0055, 0.00341687], [63.5055, 0.00372985], [65.0055, 0.0040829], [66.5055, 0.00449414], [68.0055, 0.00499723], [69.5055, 0.00566616], [71.0055, 0.0067137], [72.5055, 0.00918796], [73.2375, 0.0133874], [73.8135, 0.0361952], [74.3168, 0.174502], [75.8168, 0.0102541], [77.3168, 0.000800297], [78.8168, 0.000481889], [80.3168, 0.000647697], [81.8168, 0.000837205], [83.3168, 0.00102784], [84.8168, 0.00121942], [86.3168, 0.00141297], [87.8168, 0.0016096], [89.3168, 0.00181052], [90.8168, 0.00201711], [92.3168, 0.00223091], [93.8168, 0.00245381], [95.3168, 0.00268811], [96.8168, 0.00293674], [98.3168, 0.00320361], [99.8168, 0.00349412], [101.317, 0.00381614], [102.817, 0.004182], [104.317, 0.00461265], [105.817, 0.00514857], [107.317, 0.00588373], [108.817, 0.00711686], [110.317, 0.0107411], [111.049, 0.0216112], [111.499, 0.225962], [112.999, 0.0162564], [114.499, 0.00110332], [115.999, 0.000467658], [117.499, 0.000617486], [118.999, 0.000806281], [120.499, 0.000996825], [121.999, 0.00118819], [123.499, 0.00138134], [124.999, 0.00157739], [126.499, 0.00177753], [127.999, 0.0019831], [129.499, 0.00219561], [130.999, 0.00241689], [132.499, 0.00264915], [133.999, 0.00289522], [135.499, 0.00315881], [136.999, 0.00344502], [138.499, 0.00376124], [139.999, 0.00411886], [141.499, 0.00453696], [142.999, 0.00505153], [144.499, 0.00574319], [145.999, 0.00685194], [147.499, 0.0096625], [148.231, 0.0152746], [148.802, 0.0769393], [148.874, 0.15228], [149.692, 0.0645224], [150, 0.0361824]], [[0, 0], [3.0e-6, 2.69939e-15], [1.8e-5, 5.82413e-13], [0.000193, 7.08501e-10], [0.001068, 1.12117e-7], [0.007943, 2.55452e-5], [0.16709, 0.00235267], [1.66709, 0.0244855], [3.16709, 0.0460266], [4.66709, 0.0669863], [6.16709, 0.0873709], [7.66709, 0.107183], [9.16709, 0.126423], [10.6671, 0.145087], [12.1671, 0.163167], [13.6671, 0.180654], [15.1671, 0.197534], [16.6671, 0.213788], [18.1671, 0.229393], [19.6671, 0.24432], [21.1671, 0.258533], [22.6671, 0.271984], [24.1671, 0.284616], [25.6671, 0.296351], [27.1671, 0.307085], [28.6671, 0.316673], [30.1671, 0.324891], [31.6671, 0.331367], [33.1671, 0.335341], [34.6671, 0.334638], [36.1671, 0.310297], [36.5354, 0.223655], [36.6378, 0.0650702], [38.0055, 0.00935146], [39.5055, 0.0304777], [41.0055, 0.0518458], [42.5055, 0.0726461], [44.0055, 0.0928733], [45.5055, 0.112528], [47.0055, 0.13161], [48.5055, 0.150115], [50.0055, 0.168033], [51.5055, 0.185355], [53.0055, 0.202065], [54.5055, 0.218143], [56.0055, 0.233565], [57.5055, 0.248299], [59.0055, 0.262308], [60.5055, 0.27554], [62.0055, 0.287934], [63.5055, 0.299406], [65.0055, 0.309842], [66.5055, 0.31908], [68.0055, 0.326867], [69.5055, 0.332757], [71.0055, 0.335787], [72.5055, 0.332683], [73.2375, 0.323586], [73.8135, 0.286161], [74.3168, 0.00084586], [75.8168, 0.0144815], [77.3168, 0.0360174], [78.8168, 0.0572429], [80.3168, 0.0778958], [81.8168, 0.097976], [83.3168, 0.117484], [84.8168, 0.136418], [86.3168, 0.154773], [87.8168, 0.17254], [89.3168, 0.189706], [90.8168, 0.206255], [92.3168, 0.222168], [93.8168, 0.237416], [95.3168, 0.251968], [96.8168, 0.265783], [98.3168, 0.278807], [99.8168, 0.290973], [101.317, 0.302191], [102.817, 0.312337], [104.317, 0.321232], [105.817, 0.328585], [107.317, 0.33387], [108.817, 0.33584], [110.317, 0.329287], [111.049, 0.308355], [111.499, 0.0509016], [112.999, 0.0111726], [114.499, 0.0325168], [115.999, 0.0538334], [117.499, 0.0745795], [118.999, 0.0947526], [120.499, 0.114354], [121.999, 0.133381], [123.499, 0.151831], [124.999, 0.169694], [126.499, 0.186958], [127.999, 0.203609], [129.499, 0.219627], [130.999, 0.234985], [132.499, 0.249653], [133.999, 0.263591], [135.499, 0.276747], [136.999, 0.289058], [138.499, 0.300437], [139.999, 0.310768], [141.499, 0.319882], [142.999, 0.327513], [144.499, 0.333189], [145.999, 0.335852], [147.499, 0.331666], [148.231, 0.319783], [148.802, 0.233424], [148.874, 0.143371], [149.692, 0.00326497], [150, 0.0060585]], [[0, 0], [3.0e-6, 4.5e-8], [1.8e-5, 2.69999e-7], [0.000193, 2.89429e-6], [0.001068, 1.59079e-5], [0.007943, 9.35988e-5], [0.16709, 0.000150343], [1.66709, 0.000153778], [3.16709, 0.000157283], [4.66709, 0.000160851], [6.16709, 0.000164481], [7.66709, 0.00016817], [9.16709, 0.000171916], [10.6671, 0.000175714], [12.1671, 0.000179559], [13.6671, 0.000183443], [15.1671, 0.000187358], [16.6671, 0.000191293], [18.1671, 0.000195234], [19.6671, 0.000199164], [21.1671, 0.000203062], [22.6671, 0.000206904], [24.1671, 0.000210657], [25.6671, 0.000214283], [27.1671, 0.000217732], [28.6671, 0.000220937], [30.1671, 0.000223808], [31.6671, 0.000226208], [33.1671, 0.000227896], [34.6671, 0.000228308], [36.1671, 0.000224353], [36.5354, 0.000217835], [36.6378, 0.000210694], [38.0055, 0.000154825], [39.5055, 0.000154928], [41.0055, 0.000158268], [42.5055, 0.000161843], [44.0055, 0.000165489], [45.5055, 0.000169194], [47.0055, 0.000172955], [48.5055, 0.000176766], [50.0055, 0.000180623], [51.5055, 0.000184517], [53.0055, 0.000188438], [54.5055, 0.000192376], [56.0055, 0.000196316], [57.5055, 0.00020024], [59.0055, 0.000204125], [60.5055, 0.000207946], [62.0055, 0.000211669], [63.5055, 0.000215251], [65.0055, 0.00021864], [66.5055, 0.000221764], [68.0055, 0.000224522], [69.5055, 0.000226757], [71.0055, 0.000228178], [72.5055, 0.000227994], [73.2375, 0.000226365], [73.8135, 0.00022175], [74.3168, 0.000183247], [75.8168, 0.000153843], [77.3168, 0.000155725], [78.8168, 0.000159177], [80.3168, 0.000162774], [81.8168, 0.000166435], [83.3168, 0.000170155], [84.8168, 0.000173929], [86.3168, 0.000177753], [87.8168, 0.00018162], [89.3168, 0.000185522], [90.8168, 0.000189449], [92.3168, 0.000193389], [93.8168, 0.000197326], [95.3168, 0.000201242], [96.8168, 0.000205114], [98.3168, 0.000208913], [99.8168, 0.000212604], [101.317, 0.000216143], [102.817, 0.000219471], [104.317, 0.000222512], [105.817, 0.000225154], [107.317, 0.000227217], [108.817, 0.000228342], [110.317, 0.000227378], [111.049, 0.000224099], [111.499, 0.000209671], [112.999, 0.000154298], [114.499, 0.000155211], [115.999, 0.000158601], [117.499, 0.000162185], [118.999, 0.000165836], [120.499, 0.000169547], [121.999, 0.000173312], [123.499, 0.000177128], [124.999, 0.000180989], [126.499, 0.000184886], [127.999, 0.00018881], [129.499, 0.000192748], [130.999, 0.000196687], [132.499, 0.000200608], [133.999, 0.000204489], [135.499, 0.000208302], [136.999, 0.000212013], [138.499, 0.00021558], [139.999, 0.000218948], [141.499, 0.000222042], [142.999, 0.000224758], [144.499, 0.000226933], [145.999, 0.00022825], [147.499, 0.000227812], [148.231, 0.000225737], [148.802, 0.000218314], [148.874, 0.000214469], [149.692, 0.000161253], [150, 0.00015679]], [[0, 0], [3.0e-6, 4.5e-8], [1.8e-5, 2.7e-7], [0.000193, 2.895e-6], [0.001068, 1.602e-5], [0.007943, 0.000119145], [0.16709, 0.00250634], [1.66709, 0.0249582], [3.16709, 0.0471312], [4.66709, 0.068848], [6.16709, 0.0900356], [7.66709, 0.110667], [9.16709, 0.130733], [10.6671, 0.150229], [12.1671, 0.16915], [13.6671, 0.187489], [15.1671, 0.205239], [16.6671, 0.222385], [18.1671, 0.238912], [19.6671, 0.254797], [21.1671, 0.270014], [22.6671, 0.284528], [24.1671, 0.298297], [25.6671, 0.311266], [27.1671, 0.323362], [28.6671, 0.334488], [30.1671, 0.344509], [31.6671, 0.353217], [33.1671, 0.360254], [34.6671, 0.364858], [36.1671, 0.364153], [36.5354, 0.360898], [36.6378, 0.358586], [38.0055, 0.221863], [39.5055, 0.121231], [41.0055, 0.0899793], [42.5055, 0.0897089], [44.0055, 0.101854], [45.5055, 0.118716], [47.0055, 0.137155], [48.5055, 0.155896], [50.0055, 0.174415], [51.5055, 0.192495], [53.0055, 0.21004], [54.5055, 0.227001], [56.0055, 0.243347], [57.5055, 0.259049], [59.0055, 0.274075], [60.5055, 0.288389], [62.0055, 0.301944], [63.5055, 0.314681], [65.0055, 0.326521], [66.5055, 0.33736], [68.0055, 0.347045], [69.5055, 0.355338], [71.0055, 0.361813], [72.5055, 0.365463], [73.2375, 0.365286], [73.8135, 0.362679], [74.3168, 0.343157], [75.8168, 0.186807], [77.3168, 0.1085], [78.8168, 0.0879779], [80.3168, 0.0920726], [81.8168, 0.10591], [83.3168, 0.123372], [84.8168, 0.141969], [86.3168, 0.160685], [87.8168, 0.179106], [89.3168, 0.197054], [90.8168, 0.214453], [92.3168, 0.231259], [93.8168, 0.247443], [95.3168, 0.262974], [96.8168, 0.277821], [98.3168, 0.291945], [99.8168, 0.305296], [101.317, 0.317811], [102.817, 0.329406], [104.317, 0.339965], [105.817, 0.34932], [107.317, 0.357199], [108.817, 0.363088], [110.317, 0.365624], [111.049, 0.364003], [111.499, 0.358285], [112.999, 0.208196], [114.499, 0.116073], [115.999, 0.0890428], [117.499, 0.0904978], [118.999, 0.103315], [120.499, 0.120417], [121.999, 0.138923], [123.499, 0.157658], [124.999, 0.176142], [126.499, 0.194174], [127.999, 0.211666], [129.499, 0.228571], [130.999, 0.244857], [132.499, 0.260496], [133.999, 0.275457], [135.499, 0.289702], [136.999, 0.303182], [138.499, 0.315838], [139.999, 0.327589], [141.499, 0.338326], [142.999, 0.347892], [144.499, 0.356036], [145.999, 0.362304], [147.499, 0.365575], [148.231, 0.364959], [148.802, 0.361088], [148.874, 0.359723], [149.692, 0.286977], [150, 0.251778]]], {\n",
" seriesDefaults: {\n",
" showMarker: false\n",
" },\n",
" axes: {\n",
" xaxis: {\n",
" label: \"Time\",\n",
" renderer: $.jqplot.LinearAxisRenderer,\n",
" tickOptions: {\n",
" formatString: \"%.3p\"\n",
" }\n",
" },\n",
" yaxis: {\n",
" renderer: $.jqplot.LinearAxisRenderer,\n",
" tickOptions: {\n",
" formatString: \"%.3p\"\n",
" }\n",
" }\n",
" },\n",
" legend: {\n",
" show: true,\n",
" placement: \"outside\",\n",
" labels: [\"Cdc2\", \"Cdc2~{p1}\", \"Cyclin~{p1}\", \"Cdc2-Cyclin~{p1}\", \"Cdc2-Cyclin~{p1,p2}\", \"Cyclin\", \"YT\"],\n",
" renderer: $.jqplot.EnhancedLegendRenderer,\n",
" rendererOptions: {\n",
" seriesToggle: true,\n",
" showLineStyle: true,\n",
" numberRows: 12,\n",
" }\n",
" },\n",
" sortData: false,\n",
" cursor: {\n",
" show: true,\n",
" zoom: true,\n",
" tooltipFormatString: \"%.3p, %.3p\",\n",
" cursorLegendFormatString: \"%.3p, %.3p\"\n",
" },\n",
" highlighter: {\n",
" formatString: \"%.3p\"\n",
" }\n",
" });\n",
" $('#plot_1_25626').contextmenu(function() {\n",
" $('#plot_1_25626').jqplotSaveImage();\n",
" return false;\n",
" });\n",
" // dirty way to insert image as secondary data in current\n",
" // output area\n",
" window.setTimeout(\n",
" function () {\n",
" var png = $('#plot_1_25626').jqplotToImageStr({}).substring(22);\n",
" var div = $('<div/>').addClass('output_subarea');\n",
" var img = $('<img/>');\n",
" img[0].src = 'data:image/png;base64,'+ png;\n",
" div.append(img);\n",
" $('#plot_1_25626').parent().append(div);\n",
" div.hide();\n",
" }, 1000\n",
" );\n",
" } else { window.setTimeout(waitForJQplot_1_25626, 250);}\n",
" }\n",
" $(document).ready(waitForJQplot_1_25626);\n",
" </script>\n",
" "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"numerical_simulation. plot."
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"1.009960\r\n"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"satisfaction_degree(exists(max, exists(min, F(Cdc2-Cyclin~{p1} > max /\\ F(Cdc2-Cyclin~{p1} < min /\\ F(Cdc2-Cyclin~{p1} > max /\\ F(Cdc2-Cyclin~{p1} < min)))) /\\ max - min > amp)), [amp -> 0.19])."
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Time: 8.757 s\r\n",
"Robustness degree: 0.996442\r\n"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"seed(0).\n",
"robustness(exists(max, exists(min, F(Cdc2-Cyclin~{p1} > max /\\ F(Cdc2-Cyclin~{p1} < min /\\ F(Cdc2-Cyclin~{p1} > max /\\ F(Cdc2-Cyclin~{p1} < min)))) /\\ max - min > amp)), [k4, k6], [amp -> 0.19], robustness_coeff_var: 0.1)."
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Biocham",
"language": "",
"name": "biocham"
},
"language_info": {
"codemirror_mode": "biocham",
"file_extension": ".bc",
"mimetype": "text/plain",
"name": "biocham",
"pygments_lexer": "prolog"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
%% Cell type:code id: tags:
```
load(library:examples/cell_cycle/Tyson_1991.bc).
```
%% Cell type:code id: tags:
```
option(time:150).
```
%% Cell type:code id: tags:
```
parameter(k8=100).
```
%% Cell type:code id: tags:
```
numerical_simulation.
plot.
```
%%%% Output: display_data
%% Cell type:code id: tags:
```
satisfaction_degree(exists(max, exists(min, F(Cdc2-Cyclin~{p1} > max /\ F(Cdc2-Cyclin~{p1} < min /\ F(Cdc2-Cyclin~{p1} > max /\ F(Cdc2-Cyclin~{p1} < min)))) /\ max - min > amp)), [amp -> 0.19]).
```
%%%% Output: execute_result
0.974450
%% Cell type:code id: tags:
```
seed(0).
robustness(exists(max, exists(min, F(Cdc2-Cyclin~{p1} > max /\ F(Cdc2-Cyclin~{p1} < min /\ F(Cdc2-Cyclin~{p1} > max /\ F(Cdc2-Cyclin~{p1} < min)))) /\ max - min > amp)), [k4, k6], [amp -> 0.19]).
```
%%%% Output: execute_result
Time: 6.363 s
Robustness degree: 0.978333
%% Cell type:code id: tags:
```
parameter(k4=550, k6=2).
```
%% Cell type:code id: tags:
```
numerical_simulation. plot.
```
%%%% Output: display_data
%% Cell type:code id: tags:
```
satisfaction_degree(exists(max, exists(min, F(Cdc2-Cyclin~{p1} > max /\ F(Cdc2-Cyclin~{p1} < min /\ F(Cdc2-Cyclin~{p1} > max /\ F(Cdc2-Cyclin~{p1} < min)))) /\ max - min > amp)), [amp -> 0.19]).
```
%%%% Output: execute_result
1.009960
%% Cell type:code id: tags:
```
seed(0).
robustness(exists(max, exists(min, F(Cdc2-Cyclin~{p1} > max /\ F(Cdc2-Cyclin~{p1} < min /\ F(Cdc2-Cyclin~{p1} > max /\ F(Cdc2-Cyclin~{p1} < min)))) /\ max - min > amp)), [k4, k6], [amp -> 0.19], robustness_coeff_var: 0.1).
```
%%%% Output: execute_result
Time: 8.757 s
Robustness degree: 0.996442
%% Cell type:code id: tags:
```
```
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