-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Added code from commit c9b87dcb5614b95c85db173afc0dfb60382b23c5 on br…
…anch CD8Parameters
Showing
205 changed files
with
26,469 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| # Compiled class file | ||
| *.class | ||
|
|
||
| # Log file | ||
| **/*.log | ||
|
|
||
| # BlueJ files | ||
| *.ctxt | ||
|
|
||
| # Mobile Tools for Java (J2ME) | ||
| .mtj.tmp/ | ||
|
|
||
| # Package Files # | ||
| **/*.jar | ||
| *.war | ||
| *.nar | ||
| *.ear | ||
| *.zip | ||
| *.tar.gz | ||
| *.rar | ||
|
|
||
| # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml | ||
| hs_err_pid* | ||
|
|
||
| # vscode files | ||
| **/.settings | ||
| **/.vscode/ | ||
|
|
||
| # file sink in repast | ||
| **/file-sink |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <projectDescription> | ||
| <name>TB-HIV-in-vitro</name> | ||
| <comment></comment> | ||
| <projects> | ||
| </projects> | ||
| <buildSpec> | ||
| </buildSpec> | ||
| <natures> | ||
| </natures> | ||
| </projectDescription> |
Large diffs are not rendered by default.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,6 @@ | ||
| # TB-in-vitro | ||
| ### Useful Links: | ||
| - For Repast Testing: https://repast.github.io/docs/RepastModelTesting.pdf | ||
| - For Repast reference: https://repast.github.io/docs/RepastReference/RepastReference.html | ||
| - For Agent Based Modelling: https://www.tandfonline.com/doi/full/10.1057/jos.2016.7 | ||
| - Quick Start Guide for Java: https://repast.github.io/docs/RepastJavaGettingStarted.pdf |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <classpath> | ||
| <classpathentry kind="src" path="src"/> | ||
| <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"> | ||
| <attributes> | ||
| <attribute name="module" value="true"/> | ||
| </attributes> | ||
| </classpathentry> | ||
| <classpathentry exported="true" kind="con" path="GROOVY_SUPPORT"/> | ||
| <classpathentry exported="true" kind="con" path="GROOVY_DSL_SUPPORT"/> | ||
| <classpathentry exported="true" kind="con" path="REPAST_SIMPHONY_SUPPORT"/> | ||
| <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/> | ||
| <classpathentry kind="output" path="bin"/> | ||
| </classpath> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| /bin/ | ||
| /Repast.settings | ||
| debug.log | ||
| velocity.log | ||
| .DS_Store | ||
| velocity.log.1 | ||
|
|
||
|
|
||
| # Created by https://www.toptal.com/developers/gitignore/api/java | ||
| # Edit at https://www.toptal.com/developers/gitignore?templates=java | ||
|
|
||
| ### Java ### | ||
| # Compiled class file | ||
| *.class | ||
|
|
||
| # Log file | ||
| *.log | ||
|
|
||
| # BlueJ files | ||
| *.ctxt | ||
|
|
||
| # Mobile Tools for Java (J2ME) | ||
| .mtj.tmp/ | ||
|
|
||
| # Package Files # | ||
| *.war | ||
| *.nar | ||
| *.ear | ||
| *.zip | ||
| *.tar.gz | ||
| *.rar | ||
|
|
||
| # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml | ||
| hs_err_pid* | ||
|
|
||
| # End of https://www.toptal.com/developers/gitignore/api/java |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <projectDescription> | ||
| <name>jtbhivinvitro</name> | ||
| <comment></comment> | ||
| <projects> | ||
| </projects> | ||
| <buildSpec> | ||
| <buildCommand> | ||
| <name>repast.simphony.statecharts.diagram.builder</name> | ||
| <arguments> | ||
| </arguments> | ||
| </buildCommand> | ||
| <buildCommand> | ||
| <name>org.eclipse.jdt.core.javabuilder</name> | ||
| <arguments> | ||
| </arguments> | ||
| </buildCommand> | ||
| </buildSpec> | ||
| <natures> | ||
| <nature>org.eclipse.jdt.groovy.core.groovyNature</nature> | ||
| <nature>org.eclipse.jdt.core.javanature</nature> | ||
| <nature>repast.simphony.eclipse.repast_simphony_nature</nature> | ||
| <nature>repast.simphony.statecharts.diagram.repast_simphony_statechart_nature</nature> | ||
| </natures> | ||
| </projectDescription> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| log4j.rootLogger = error | ||
|
|
||
| log4j.logger.org.java.plugin = warn, stdout | ||
| log4j.logger.org.apache.commons= warn, stdout | ||
| log4j.logger.repast.simphony.plugin = warn, stdout | ||
|
|
||
| log4j.logger.MessageCenter.INTERNAL.repast = info, stdout, R | ||
| log4j.logger.MessageCenter.INTERNAL.saf = info, stdout, R | ||
|
|
||
| log4j.logger.repast.simphony.batch = info, stdout, R | ||
| log4j.logger.repast.simphony.batch.ssh.SSHSessionFactory = warn, stdout, R | ||
|
|
||
| log4j.appender.stdout = org.apache.log4j.ConsoleAppender | ||
| log4j.appender.stdout.layout = simphony.util.messages.MessageCenterLayout | ||
| log4j.appender.stdout.layout.conversionPattern =%-5p [%t] %d{HH:mm:ss,SSS} %c - %m%n | ||
| #log4j.appender.stdout.Threshold=debug | ||
|
|
||
| log4j.appender.R=org.apache.log4j.RollingFileAppender | ||
| log4j.appender.R.File=debug.log | ||
| log4j.appender.R.MaxFileSize=100KB | ||
| log4j.appender.R.MaxBackupIndex=1 | ||
| #log4j.appender.R.Threshold=info | ||
| log4j.appender.R.layout=simphony.util.messages.MessageCenterLayout | ||
| log4j.appender.R.layout.ConversionPattern=%-5p [%t] %d{ISO8601} %c - %m%n |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| Place your Repast Simphony batch run files in this directory. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| # | ||
| #Tue Apr 23 10:44:29 EDT 2019 | ||
| output.directory=/Users/mjis1052user/eclipse-workspace/TB-HIV-in-vitro/jtbhivinvitro/output | ||
| host.0.type=LOCAL | ||
| batch.param.file=/Users/mjis1052user/eclipse-workspace/TB-HIV-in-vitro/jtbhivinvitro/batch/batch_params.xml | ||
| key.directory=/Users/mjis1052user/.ssh | ||
| model.directory=/Users/mjis1052user/eclipse-workspace/TB-HIV-in-vitro/jtbhivinvitro | ||
| vm.arguments=-Xmx512M | ||
| param.file=/Users/mjis1052user/eclipse-workspace/TB-HIV-in-vitro/jtbhivinvitro/jtbhivinvitro.rs/parameters.xml | ||
| host.0.instances=2 | ||
| poll.frequency=1.0 | ||
| scenario.directory=/Users/mjis1052user/eclipse-workspace/TB-HIV-in-vitro/jtbhivinvitro/jtbhivinvitro.rs |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| <?xml version="1.0" ?><sweep runs="1"><parameter name="virusDiffusionCoefficient" type="constant" constant_type="double" value="0"></parameter><parameter name="CD8Fraction" type="constant" constant_type="double" value="0"></parameter><parameter name="isBatchRun" type="constant" constant_type="double" value="1.0"></parameter><parameter name="cellsNeededToBeAddedToGran" type="constant" constant_type="double" value="5.0"></parameter><parameter name="percentHIVInfected" type="constant" constant_type="double" value="0"></parameter><parameter name="maximumCD8Generations" type="constant" constant_type="double" value="0"></parameter><parameter name="TNFDiffusionCoefficient" type="constant" constant_type="double" value="0.4"></parameter><parameter name="MinBurstLimit" type="constant" constant_type="double" value="20.0"></parameter><parameter name="cd4DoublingTimeVariance" type="constant" constant_type="double" value="0.25"></parameter><parameter name="isPlainColors" type="constant" constant_type="double" value="6.0"></parameter><parameter name="daysToRun" type="constant" constant_type="double" value="8"></parameter><parameter name="stat1Span" type="constant" constant_type="double" value="71.6"></parameter><parameter name="cd8PopulationDoublingTime" type="constant" constant_type="double" value="9.0"></parameter><parameter name="activatedMovementProbabilityMacro" type="constant" constant_type="double" value="1.0"></parameter><parameter name="cd4Population_ActivatedLifespan" type="constant" constant_type="double" value="3.0"></parameter><parameter name="mtbInternalDoublingTime" type="constant" constant_type="double" value="24.0"></parameter><parameter name="granQualificationImmuneCellCount" type="constant" constant_type="double" value="12"></parameter><parameter name="divisionBiomassThreshold" type="constant" constant_type="double" value="2.0"></parameter><parameter name="newMtbPlacementRange" type="constant" constant_type="double" value="0.2"></parameter><parameter name="activePhagocytosisProbability" type="constant" constant_type="double" value="0.8"></parameter><parameter name="IFNthresholdForStat1Activation" type="constant" constant_type="double" value="2.0"></parameter><parameter name="timeStep" type="constant" constant_type="double" value="6.0"></parameter><parameter name="fractionCD3" type="constant" constant_type="double" value="0.5"></parameter><parameter name="gridDim_X_Y" type="constant" constant_type="int" value="100"></parameter><parameter name="fractionCD4" type="constant" constant_type="double" value="0.4"></parameter><parameter name="nfkbVariance" type="constant" constant_type="double" value="0.1"></parameter><parameter name="basePhagocytosisProbability" type="constant" constant_type="double" value="0.99"></parameter><parameter name="mtbExternalDoublingTime" type="constant" constant_type="double" value="24.0"></parameter><parameter name="DiffusionTimeStepMultiplier" type="constant" constant_type="double" value="4.0"></parameter><parameter name="fractionTBSpecific" type="constant" constant_type="double" value="0.05"></parameter><parameter name="activatedTBSpecificCD4Fraction" type="constant" constant_type="double" value="0"></parameter><parameter name="ActivatedMacrophageTNFSecretion" type="constant" constant_type="double" value="5.0"></parameter><parameter name="ActivatedCD4IFNSecretion" type="constant" constant_type="double" value="5.0"></parameter><parameter name="mtbGrowthRateVariance" type="constant" constant_type="double" value="0.1"></parameter><parameter name="mtbInitialNumber" type="constant" constant_type="double" value="160"></parameter><parameter name="macrophagePopulation_MaxLifespan" type="constant" constant_type="double" value="100.0"></parameter><parameter name="cd8LifeSpanVariance" type="constant" constant_type="double" value="0"></parameter><parameter name="isSpheroid" type="constant" constant_type="double" value="0"></parameter><parameter name="CD8KillProbability" type="constant" constant_type="double" value="0"></parameter><parameter name="stat1Variance" type="constant" constant_type="double" value="0.1"></parameter><parameter name="divisionBiomassVariance" type="constant" constant_type="double" value="0.2"></parameter><parameter name="InfectedMacrophageTNFSecretion" type="constant" constant_type="double" value="5.0"></parameter><parameter name="activatedTBSpecificCD8Fraction" type="constant" constant_type="double" value="0.0"></parameter><parameter name="randomSeed" type="constant" constant_type="int" value="22222"></parameter><parameter name="viralConcentrationForInfection" type="constant" constant_type="double" value="0"></parameter><parameter name="granulomaFractionOfDiffusion" type="constant" constant_type="double" value="0.25"></parameter><parameter name="ActivatedCD8IFNSecretion" type="constant" constant_type="double" value="5.0"></parameter><parameter name="TNFthresholdForImmuneCellMovement" type="constant" constant_type="double" value="2.0"></parameter><parameter name="mutationProbability" type="constant" constant_type="double" value="0.0"></parameter><parameter name="cellularDysfunctionThreshold" type="constant" constant_type="double" value="12.0"></parameter><parameter name="timeTouchingToMerge" type="constant" constant_type="double" value="0"></parameter><parameter name="InitialPBMCs" type="constant" constant_type="double" value="1600"></parameter><parameter name="baseMovementProbabilityCD4" type="constant" constant_type="double" value="1"></parameter><parameter name="CD4ActivationProbability" type="constant" constant_type="double" value="0.5"></parameter><parameter name="macrophageLifeSpanVariance" type="constant" constant_type="double" value="0.1"></parameter><parameter name="activatedMovementProbabilityCD4" type="constant" constant_type="double" value="1"></parameter><parameter name="agentLimit" type="constant" constant_type="double" value="60000000"></parameter><parameter name="ActivatedCD4TNFSecretion" type="constant" constant_type="double" value="5.0"></parameter><parameter name="ActivatedCD8TNFSecretion" type="constant" constant_type="double" value="5.0"></parameter><parameter name="CD4DeactivationProbability" type="constant" constant_type="double" value="0.01"></parameter><parameter name="cellsNeededToRemainInGran" type="constant" constant_type="double" value="5.0"></parameter><parameter name="maximumCD4Generations" type="constant" constant_type="double" value="6"></parameter><parameter name="fractionMonocyte" type="constant" constant_type="double" value="0.1"></parameter><parameter name="CD8DeactivationProbability" type="constant" constant_type="double" value="0.1"></parameter><parameter name="baseKillingProbability" type="constant" constant_type="double" value="0.002"></parameter><parameter name="timeToAddInfectedTcells" type="constant" constant_type="double" value="1"></parameter><parameter name="cd4PopulationDoublingTime" type="constant" constant_type="double" value="9.0"></parameter><parameter name="sphereEfficiency" type="constant" constant_type="double" value="0.7"></parameter><parameter name="CaseNumber" type="constant" constant_type="double" value="6.0"></parameter><parameter name="activatedMacrophageProportion" type="constant" constant_type="double" value="0"></parameter><parameter name="virusDegradationRate" type="constant" constant_type="double" value="0.99"></parameter><parameter name="activeKillingProbability" type="constant" constant_type="double" value="0.01"></parameter><parameter name="cd4Population_MaxLifespan" type="constant" constant_type="double" value="100.0"></parameter><parameter name="TNFthresholdForNFkBActivation" type="constant" constant_type="double" value="5.0"></parameter><parameter name="baseMovementProbabilityMacro" type="constant" constant_type="double" value="1.0"></parameter><parameter name="TNFDegradationRatePerSecond" type="constant" constant_type="double" value="0.0"></parameter><parameter name="nfkbSpan" type="constant" constant_type="double" value="2.5"></parameter><parameter name="hivInfectionProbability" type="constant" constant_type="double" value="0"></parameter><parameter name="viralProductionRatePerDay" type="constant" constant_type="double" value="5.0"></parameter><parameter name="isVirus" type="constant" constant_type="double" value="0"></parameter><parameter name="CD8ActivationProbability" type="constant" constant_type="double" value="0"></parameter><parameter name="gridDim_Z" type="constant" constant_type="int" value="10"></parameter><parameter name="macrophagePopulation_MaxActivatedLifespan" type="constant" constant_type="double" value="10.0"></parameter><parameter name="IFNDiffusionCoefficient" type="constant" constant_type="double" value="0.4"></parameter><parameter name="totalHIVInfectedCD4Count" type="constant" constant_type="double" value="100.0"></parameter><parameter name="fractionLymphocyte" type="constant" constant_type="double" value="0.9"></parameter><parameter name="bacThresholdForNFkBActivation" type="constant" constant_type="double" value="20"></parameter><parameter name="IFNDegradationRatePerSecond" type="constant" constant_type="double" value="0.0"></parameter><parameter name="timeToAddTcells" type="constant" constant_type="double" value="48.0"></parameter><parameter name="cd4LifeSpanVariance" type="constant" constant_type="double" value="0.1"></parameter><parameter name="tbSpecificCD8Fraction" type="constant" constant_type="double" value="0.05"></parameter><parameter name="MaxBurstLimit" type="constant" constant_type="double" value="40.0"></parameter><parameter name="phagocytosisThreshold" type="constant" constant_type="double" value="5.0"></parameter></sweep> |
Oops, something went wrong.