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Merge pull request #592 from MyersResearchGroup/Default_Parameters

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Default parameters
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Fontanapink 2019-12-12 10:24:51 -03:00 • committed by GitHub
commit e6b9a2e17e
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2 changed files with 71 additions and 36 deletions
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94
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/parser/BioModel.java
View file

@ -2344,26 +2344,42 @@ public class BioModel extends CoreObservable{
LocalParameter n_para = reaction.getKineticLaw().createLocalParameter();
n_para.setId(n);
if (celloParameters.get(activator).get(0) != null) {
double n_value = Double.parseDouble(celloParameters.get(activator).get(0));
n_para.setValue(n_value);
}
LocalParameter K_para = reaction.getKineticLaw().createLocalParameter();
K_para.setId(K);
if (celloParameters.get(activator) != null) {
double K_value = Double.parseDouble(celloParameters.get(activator).get(1));
K_para.setValue(K_value);
}
//set parameters to the model, use a default value if there is no parameter found
if (celloParameters.get(activator) != null) {
double ymax_value = Double.parseDouble(celloParameters.get(activator).get(2));
ymax_p.setValue(ymax_value);
}
if (celloParameters.get(activator) != null) {
double ymin_value = Double.parseDouble(celloParameters.get(activator).get(3));
ymin_p.setValue(ymin_value);
if (celloParameters.get(activator).get(0) != null) {
double n_value = Double.parseDouble(celloParameters.get(activator).get(0));
n_para.setValue(n_value);
}
else {
n_para.setValue(GlobalConstants.CELLO_PARAMETER_N);
}
if (celloParameters.get(activator).get(1) != null) {
double K_value = Double.parseDouble(celloParameters.get(activator).get(1));
K_para.setValue(K_value);
}
else {
K_para.setValue(GlobalConstants.CELLO_PARAMETER_K);
}
if (celloParameters.get(activator).get(2) != null) {
double ymax_value = Double.parseDouble(celloParameters.get(activator).get(2));
ymax_p.setValue(ymax_value);
}
else {
ymax_p.setValue(GlobalConstants.CELLO_PARAMETER_YMAX);
}
if (celloParameters.get(activator).get(3) != null) {
double ymin_value = Double.parseDouble(celloParameters.get(activator).get(3));
ymin_p.setValue(ymin_value);
}
else {
ymin_p.setValue(GlobalConstants.CELLO_PARAMETER_YMIN);
}
}
in_parentesis = "(" + numerator + "/(" + denominator + ") +" + ymin + ")";
@ -2387,27 +2403,43 @@ public class BioModel extends CoreObservable{
LocalParameter n_para = reaction.getKineticLaw().createLocalParameter();
n_para.setId(n);
if (celloParameters.get(repressor) != null) {
double n_value = Double.parseDouble(celloParameters.get(repressor).get(0));
n_para.setValue(n_value);
}
LocalParameter K_para = reaction.getKineticLaw().createLocalParameter();
K_para.setId(K);
if (celloParameters.get(repressor) != null) {
double K_value = Double.parseDouble(celloParameters.get(repressor).get(1));
K_para.setValue(K_value);
}
if (celloParameters.get(repressor) != null) {
double ymax_value = Double.parseDouble(celloParameters.get(repressor).get(2));
ymax_p.setValue(ymax_value);
if (celloParameters.get(repressor).get(0) != null) {
double n_value = Double.parseDouble(celloParameters.get(repressor).get(0));
n_para.setValue(n_value);
}
else {
n_para.setValue(GlobalConstants.CELLO_PARAMETER_N);
}
if (celloParameters.get(repressor).get(1) != null) {
double K_value = Double.parseDouble(celloParameters.get(repressor).get(1));
K_para.setValue(K_value);
}
else {
K_para.setValue(GlobalConstants.CELLO_PARAMETER_K);
}
if (celloParameters.get(repressor).get(2) != null) {
double ymax_value = Double.parseDouble(celloParameters.get(repressor).get(2));
ymax_p.setValue(ymax_value);
}
else {
ymax_p.setValue(GlobalConstants.CELLO_PARAMETER_YMAX);
}
if (celloParameters.get(repressor).get(3) != null) {
double ymin_value = Double.parseDouble(celloParameters.get(repressor).get(3));
ymin_p.setValue(ymin_value);
}
else {
ymin_p.setValue(GlobalConstants.CELLO_PARAMETER_YMIN);
}
}
if (celloParameters.get(repressor) != null) {
double ymin_value = Double.parseDouble(celloParameters.get(repressor).get(3));
ymin_p.setValue(ymin_value);
}
in_parentesis = "(" + numerator + "/(" + denominator + ") +" + ymin + ")";
} else if (interaction.equals("sensor")) {

13
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/util/GlobalConstants.java
View file

@ -369,11 +369,14 @@ public class GlobalConstants {
return path.substring(0, path.lastIndexOf(File.separator));
}
//Cello Parameters
//Cello Parameters used for dynamical modeling. These parameters are obtained from the Cello paper
// and from https://synbiohub.programmingbiology.org/public/Eco1C1G1T1/Eco1C1G1T1_collection/1
public static final double k_SD_DIM_S = 1.0/300;
public static final double k_TF_DIM_S = 1.0/3600;
public static final double CELLO_PARAMETER_N = 2.56;
public static final double CELLO_PARAMETER_K = 0.122;
public static final double CELLO_PARAMETER_YMAX = 7.54;
public static final double CELLO_PARAMETER_YMIN = 0.012;
public static final double CELLO_PARAMETER_K = 0.1295;
public static final double CELLO_PARAMETER_N = 2.65;
public static final double CELLO_PARAMETER_YMAX = 2.829583333;
public static final double CELLO_PARAMETER_YMIN = 0.0464125;
public static final double CELLO_PARAMETER_ALPHA = 0.408417245;
public static final double CELLO_PARAMETER_BETA = 0.432373669;
}