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Sensor Promoter Roadblock effect

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Added alpha and beta roadblocking effect for when sensor promoter is the downstream promoter
This commit is contained in:
Pedro Fontanarrosa 2020-01-17 15:46:50 -03:00
parent 62a2411a49
commit e0b7c2a22f
2 changed files with 15 additions and 14 deletions
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4
conversion/src/main/java/edu/utah/ece/async/ibiosim/conversion/SBML2SBOL.java
View file

@ -119,9 +119,9 @@ public class SBML2SBOL {
* @throws SBOLValidationException - SBOL Exception occurred when loading referenced SBOL files
* @throws XMLStreamException - Invalid XML file.
* @throws IOException - Input Exception occurred.
* @throws SBOLConversionException - SBOL conversion exception occurred when reading in the referenced SBOL files.
* @throws SBOLConversionException - SBOL conversion exception occurred when reading in the referenced SBOL files.
* @return returning the URI of the SBOL object created
*/
public static URI convert_SBML2SBOL(SBOLDocument sbolDoc, String externalSBMLPath,
SBMLDocument sbmlDoc, String fileName, HashSet<String> sbolFiles, String sbolURIPrefix)

25
dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/biomodel/parser/BioModel.java
View file

@ -2405,8 +2405,8 @@ public class BioModel extends CoreObservable{
}
in_parentesis = "(" + numerator + "/(" + denominator + ") +" + ymin + ")";
// This adds roadblocking effects if this promoter is the downstream one of tandem promoters.
if(promoters.toArray().length == 2 && promoterCnt == 2) {
String top = "";
String bottom = "";
@ -2495,8 +2495,8 @@ public class BioModel extends CoreObservable{
in_parentesis = "(" + numerator + "/(" + denominator + ") +" + ymin + ")";
if(promoters.toArray().length == 2 && promoterCnt == 2) {
// This adds roadblocking effects if this promoter is the downstream one of tandem promoters.
if(promoters.toArray().length == 2 && promoterCnt == 2) {
String top = "";
String bottom = "";
@ -2558,15 +2558,16 @@ public class BioModel extends CoreObservable{
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 + ")";
// }
// This adds roadblocking effects if this promoter is the downstream one of tandem promoters.
if(promoters.toArray().length == 2 && promoterCnt == 2) {
String roadblock = "";
String delta_function = "";
delta_function = "piecewise( 0 , (" + sensor + " == 0), 1 )";
roadblock = "(" + alpha + "*" + beta + ")^" + delta_function ;
kineticLaw += "*(" + roadblock + ")";
}
}
}