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createCelloProductionKineticLaw modifitaction

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Modified the method to be able to assign parameters for k, n, ymax, ymin
from the Cello parameters and promoter interaction lists

pom.xml

Changed VPR version from .12 to .14

productionInteractions

added method that makes a map of promoters, if they are repressed or
activated, and by which protein

hasCelloParameters2

added new method that searches all sbol document, and creates a list
with all components and their Cello parameters, if they exist
This commit is contained in:
Pedro Fontanarrosa 2018-11-26 12:01:41 -07:00
parent aa5efc7bf3
commit 56cc0cfd61
2 changed files with 183 additions and 15 deletions
Download patch file Download diff file Expand all files Collapse all files

57
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/parser/BioModel.java
View file

@ -2020,7 +2020,7 @@ public class BioModel extends CoreObservable{
}
//TODO PEDRO createCelloSDProductionReaction
public Reaction createCelloSDProductionReactions(Species mRNA, String reactionID, String TU , HashMap<FunctionalComponent, HashMap<String, String>> celloParameters, String kSDdegrad, String n, String k_react,
public Reaction createCelloSDProductionReactions(Species mRNA, String reactionID, String TU , HashMap<String, List<String>> celloParameters, String kSDdegrad, String n, String k_react,
String ymax, String ymin, boolean onPort, String[] dimensions, BioModel targetModel) {
//This method should create a production reaction for the mRNA that is transcribed from the TU.
@ -2098,7 +2098,7 @@ public class BioModel extends CoreObservable{
}
//TODO PEDRO createCelloTFProductionReaction
public Reaction createCelloTFProductionReactions(Species mRNA, String rxnID, List<Participation> products, HashMap<FunctionalComponent, HashMap<String, String>> celloParameters, String kTFdegrad, String ko,
public Reaction createCelloTFProductionReactions(Species mRNA, String rxnID, List<Participation> products, HashMap<String, List<String>> celloParameters, String kTFdegrad, String ko,
String kb, String KoStr, String KaoStr, boolean onPort, String[] dimensions) {
//This method should create a production reaction for all Protein or Products the TU produces.
@ -2227,7 +2227,7 @@ public class BioModel extends CoreObservable{
}
//TODO PEDRO createCelloProductionKineticLaw
public static String createCelloProductionKineticLaw(Reaction reaction, HashMap<FunctionalComponent, HashMap<String, String>> celloParameters, HashMap<String, HashMap <String, String>> promoterInteractions, Set<String> promoters) {
public static String createCelloProductionKineticLaw(Reaction reaction, HashMap<String, List<String>> celloParameters, HashMap<String, HashMap <String, String>> promoterInteractions, Set<String> promoters) {
String kineticLaw = "";
//boolean activated = false;
String promoter = "";
@ -2259,13 +2259,30 @@ public class BioModel extends CoreObservable{
String temp = "("+ K +"/" + activator + ")^" + n;
denominator += temp;
LocalParameter K_para = reaction.getKineticLaw().createLocalParameter();
K_para.setId(K);
//K_para.setValue(kdegrad);
LocalParameter n_para = reaction.getKineticLaw().createLocalParameter();
n_para.setId(n);
//n_para.setValue(kdegrad);
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);
}
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);
}
} else if (interaction.equals("repression")) {
String repressor = promInter.get(entry).toString();
String K = "K_" + repressor;
@ -2274,12 +2291,30 @@ public class BioModel extends CoreObservable{
String temp = "(" + repressor + "/"+ K + ")^" + n;
denominator += temp;
LocalParameter K_para = reaction.getKineticLaw().createLocalParameter();
K_para.setId(K);
//K_para.setValue(kdegrad);
LocalParameter n_para = reaction.getKineticLaw().createLocalParameter();
n_para.setId(n);
//n_para.setValue(kdegrad);
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) != null) {
double ymin_value = Double.parseDouble(celloParameters.get(repressor).get(3));
ymin_p.setValue(ymin_value);
}
}
}
kineticLaw += "+" + "kdegrad" + "*(" + numerator + "/(" + denominator + ")+" + ymin + ")";