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Team:Paris Saclay/Modeling/Simulator/hsimexemple
From 2013.igem.org
(Difference between revisions)
(Created page with "title = "FNR simulator"; //declare the molecules and metabolite molecule fnr_on, fnr_off, fnr_on_pair; molecule prom_fnr, prom_fnr_binded; molecule protein; metabolite o2; //decl...") |
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| - | title = "FNR simulator"; | + | <blockquote> |
| - | + | title = "FNR simulator";<br> | |
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| + | //declare the molecules and metabolite<br> | ||
| + | molecule fnr_on, fnr_off, fnr_on_pair;<br> | ||
| + | molecule prom_fnr, prom_fnr_binded;<br> | ||
| + | molecule protein;<br> | ||
| + | metabolite o2;<br> | ||
| + | |||
| + | //declare the size of molecule<br> | ||
| + | |||
| + | size (fnr_on) = 0.1; | ||
| + | size (fnr_on_pair) = 0.2; | ||
| + | size (fnr_off) = 0.1;<br> | ||
| + | speed (fnr_on) = 0.1; | ||
| + | speed (fnr_on_pair) = 0.05; | ||
| + | speed (fnr_off) = 0.1;<br> | ||
| + | size (prom_fnr) = 2.0; | ||
| + | speed (prom_fnr) = 0.05; | ||
| + | size (prom_fnr_binded) = 2.0;<br> | ||
| + | speed (prom_fnr_binded) = 0.05; | ||
| + | size (protein) = 0.2; | ||
| + | speed (protein) = 0.1;<br> | ||
| + | |||
| + | //syntax of reaction rules <br> | ||
| + | |||
| + | fnr_on + o2 -> fnr_off + o2 [0.7];// probability for this rule take place is 0.7<br> | ||
| + | fnr_off -> fnr_on [0.001]; <br> | ||
| + | fnr_on + fnr_on -> fnr_on_pair [0.5]; <br> | ||
| + | fnr_on_pair -> fnr_on + fnr_on [0.001]; <br> | ||
| + | |||
| + | prom_fnr + fnr_on_pair -> prom_fnr_binded [0.6];<br> | ||
| + | prom_fnr_binded -> prom_fnr + fnr_on_pair [0.03]; <br> | ||
| + | prom_fnr_binded -> prom_fnr_binded + protein [0.01]; <br> | ||
| + | |||
| + | |||
| + | |||
| + | //Initial concentrations<br> | ||
| + | init (10000, fnr_on);<br> | ||
| + | init (3, prom_fnr);<br> | ||
| + | init (2, o2); //oxy<br> | ||
| + | </blockquote> | ||
[https://2013.igem.org/Team:Paris_Saclay/Modeling/Simulator Back] | [https://2013.igem.org/Team:Paris_Saclay/Modeling/Simulator Back] | ||
Latest revision as of 21:25, 4 October 2013
title = "FNR simulator";
//declare the molecules and metabolite
molecule fnr_on, fnr_off, fnr_on_pair;
molecule prom_fnr, prom_fnr_binded;
molecule protein;
metabolite o2;
//declare the size of molecule
size (fnr_on) = 0.1; size (fnr_on_pair) = 0.2; size (fnr_off) = 0.1;
speed (fnr_on) = 0.1; speed (fnr_on_pair) = 0.05; speed (fnr_off) = 0.1;
size (prom_fnr) = 2.0; speed (prom_fnr) = 0.05; size (prom_fnr_binded) = 2.0;
speed (prom_fnr_binded) = 0.05; size (protein) = 0.2; speed (protein) = 0.1;
//syntax of reaction rules
fnr_on + o2 -> fnr_off + o2 [0.7];// probability for this rule take place is 0.7
fnr_off -> fnr_on [0.001];
fnr_on + fnr_on -> fnr_on_pair [0.5];
fnr_on_pair -> fnr_on + fnr_on [0.001];
prom_fnr + fnr_on_pair -> prom_fnr_binded [0.6];
prom_fnr_binded -> prom_fnr + fnr_on_pair [0.03];
prom_fnr_binded -> prom_fnr_binded + protein [0.01];
//Initial concentrations
init (10000, fnr_on);
init (3, prom_fnr);
init (2, o2); //oxy
