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Updated createCelloProductionKineticLaw

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This update adds roadblocking effects to when creating the kinetic model of the genetic circuit. This is only added if there are 2 tandem promoters.
This commit is contained in:
Pedro Fontanarrosa 2020-01-11 10:03:20 -03:00
parent 4f86b52eee
commit 97d125c54f
1 changed files with 74 additions and 15 deletions
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61
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/parser/BioModel.java
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@ -2311,9 +2311,11 @@ public class BioModel extends CoreObservable{
String kineticLaw = ""; String kineticLaw = "";
//boolean activated = false; //boolean activated = false;
String promoter = ""; String promoter = "";
int promoterCnt = 0;
for (Object it : promoters.toArray()) { for (Object it : promoters.toArray()) {
promoter = it.toString(); promoter = it.toString();
promoterCnt++;
String numerator = ""; String numerator = "";
String denominator = ""; String denominator = "";
@ -2403,6 +2405,16 @@ public class BioModel extends CoreObservable{
} }
in_parentesis = "(" + numerator + "/(" + denominator + ") +" + ymin + ")"; in_parentesis = "(" + numerator + "/(" + denominator + ") +" + ymin + ")";
if(promoters.toArray().length == 2 && promoterCnt == 2) {
String top = "";
String bottom = "";
top = "(" + K + "^" + n + "+ " + beta + "*" + activator + "^" + n + ")";
bottom = "(" + K + "^" + n + "+ " + activator + "^" + n + ")";
kineticLaw += "*" + alpha + "*(" + top + "/" + bottom + ")";
}
} else if (interaction.equals("repression")) { } else if (interaction.equals("repression")) {
String repressor = promInter.get(entry).toString(); String repressor = promInter.get(entry).toString();
String K = "K_" + repressor; String K = "K_" + repressor;
@ -2432,6 +2444,7 @@ public class BioModel extends CoreObservable{
LocalParameter beta_para = reaction.getKineticLaw().createLocalParameter(); LocalParameter beta_para = reaction.getKineticLaw().createLocalParameter();
beta_para.setId(beta); beta_para.setId(beta);
if (celloParameters.get(repressor) != null) { if (celloParameters.get(repressor) != null) {
if (celloParameters.get(repressor).get(0) != null && !celloParameters.get(repressor).get(0).equals("")) { if (celloParameters.get(repressor).get(0) != null && !celloParameters.get(repressor).get(0).equals("")) {
double n_value = Double.parseDouble(celloParameters.get(repressor).get(0)); double n_value = Double.parseDouble(celloParameters.get(repressor).get(0));
@ -2482,20 +2495,37 @@ public class BioModel extends CoreObservable{
in_parentesis = "(" + numerator + "/(" + denominator + ") +" + ymin + ")"; in_parentesis = "(" + numerator + "/(" + denominator + ") +" + ymin + ")";
if(promoters.toArray().length == 2 && promoterCnt == 2) {
String top = "";
String bottom = "";
top = "(" + K + "^" + n + "+ " + beta + "*" + repressor + "^" + n + ")";
bottom = "(" + K + "^" + n + "+ " + repressor + "^" + n + ")";
kineticLaw += "*" + alpha + "*(" + top + "/" + bottom + ")";
}
} else if (interaction.equals("sensor")) { } else if (interaction.equals("sensor")) {
String sensor = promInter.get(entry).toString(); String sensor = promInter.get(entry).toString();
String ymax = "ymax_" + promoter; String ymax = "ymax_" + promoter;
String ymin = "ymin_" + promoter; String ymin = "ymin_" + promoter;
String alpha = "alpha_" + promoter;
String beta = "beta_" + promoter;
LocalParameter ymax_p = reaction.getKineticLaw().createLocalParameter(); LocalParameter ymax_p = reaction.getKineticLaw().createLocalParameter();
ymax_p.setId(ymax); ymax_p.setId(ymax);
LocalParameter ymin_p = reaction.getKineticLaw().createLocalParameter(); LocalParameter ymin_p = reaction.getKineticLaw().createLocalParameter();
ymin_p.setId(ymin); ymin_p.setId(ymin);
LocalParameter alpha_para = reaction.getKineticLaw().createLocalParameter();
alpha_para.setId(alpha);
LocalParameter beta_para = reaction.getKineticLaw().createLocalParameter();
beta_para.setId(beta);
//numerator = "piecewise(piece(" + ymin_p + " ," + sensor + " == 0.0), otherwise(" + ymax_p + "))"; //numerator = "piecewise(piece(" + ymin_p + " ," + sensor + " == 0.0), otherwise(" + ymax_p + "))";
numerator = "piecewise(" + ymin + ", (" + sensor + " == 0), " + ymax + ")"; numerator = "piecewise(" + ymin + ", (" + sensor + " == 0), " + ymax + ")";
if (celloParameters.get(sensor) != null) { if (celloParameters.get(sensor) != null) {
if (celloParameters.get(sensor).get(0) != null && !celloParameters.get(sensor).get(0).equals("")) {
double ymax_value = Double.parseDouble(celloParameters.get(sensor).get(0)); double ymax_value = Double.parseDouble(celloParameters.get(sensor).get(0));
ymax_p.setValue(ymax_value); ymax_p.setValue(ymax_value);
} }
@ -2503,17 +2533,46 @@ public class BioModel extends CoreObservable{
ymax_p.setValue(GlobalConstants.CELLO_PARAMETER_YMAX); ymax_p.setValue(GlobalConstants.CELLO_PARAMETER_YMAX);
} }
if (celloParameters.get(sensor) != null) { if (celloParameters.get(sensor).get(1) != null && !celloParameters.get(sensor).get(1).equals("")) {
double ymin_value = Double.parseDouble(celloParameters.get(sensor).get(1)); double ymin_value = Double.parseDouble(celloParameters.get(sensor).get(1));
ymin_p.setValue(ymin_value); ymin_p.setValue(ymin_value);
} }
else { else {
ymin_p.setValue(GlobalConstants.CELLO_PARAMETER_YMIN); ymin_p.setValue(GlobalConstants.CELLO_PARAMETER_YMIN);
} }
if (celloParameters.get(sensor).get(2) != null && !celloParameters.get(sensor).get(2).equals("")) {
double alpha_value = Double.parseDouble(celloParameters.get(sensor).get(2));
alpha_para.setValue(alpha_value);
}
else {
alpha_para.setValue(GlobalConstants.CELLO_PARAMETER_ALPHA);
}
if (celloParameters.get(sensor).get(3) != null && !celloParameters.get(sensor).get(3).equals("")) {
double beta_value = Double.parseDouble(celloParameters.get(sensor).get(3));
beta_para.setValue(beta_value);
}
else {
beta_para.setValue(GlobalConstants.CELLO_PARAMETER_BETA);
}
}
in_parentesis = "(" + numerator + ")"; in_parentesis = "(" + numerator + ")";
// if(promoters.toArray().length == 2 && promoterCnt == 2) {
//
// String top = "";
// String bottom = "";
//
// top = "(" + K + "^" + n + "+ " + beta + "*" + sensor + "^" + n + ")";
// bottom = "(" + K + "^" + n + "+ " + sensor + "^" + n + ")";
// kineticLaw += "*" + alpha + "*(" + top + "/" + bottom + ")";
// }
} }
} }
// if(promoters.toArray().length == 2 && promoterCnt == 2) {
// kineticLaw += "*" + alpha + "*(" + ")";
// }
kineticLaw += " + " + "kdegrad" + "*" + in_parentesis; kineticLaw += " + " + "kdegrad" + "*" + in_parentesis;
} }
return kineticLaw; return kineticLaw;