###-------------------------------------------------
### Input parameter settings file for 
###
###       BA         Bayesian 
###         N        Network Inference
###          J       with Java
###           O      Objects
###
### Banjo is licensed from Duke University.
### Copyright (c) 2005-07 by Alexander J. Hartemink.
### All rights reserved.
###
### Settings file consistent with version 2.0.0
###-------------------------------------------------

###-------------------------------------------------
### Project information
###-------------------------------------------------

project =                     GSE141593 piz ko mice suppgenes 32h
user =                            samanthagonzales
dataset =                   211-vars-10-observations
notes =            static bayesian network inference

###-------------------------------------------------
### Search component specifications
###-------------------------------------------------

searcherChoice =                           SimAnneal  
proposerChoice =                     RandomLocalMove
evaluatorChoice =                            default
deciderChoice =                              default

###-------------------------------------------------
### Input and output locations
###-------------------------------------------------

inputDirectory =   /home/samanthagonzales/piz_mice/analysis/banjo/input
observationsFile =        GSE141593_piz_ko_mice_gene_expr_suppgenes_log2fc=2.txt
outputDirectory = /home/samanthagonzales/piz_mice/analysis/banjo/output
reportFile =       	piz.ko.mice.suppgenes.32h.ma.bs.report.@TS@.txt

###-------------------------------------------------
### We require this only to validate the input
###-------------------------------------------------

variableCount =                                  211
variablesAreInRows = 				  no
variableNames = 			      inFile
observationCount = 				   10

###-------------------------------------------------
### Pre-processing options
###-------------------------------------------------

discretizationPolicy =                          none  
discretizationExceptions =  
createDiscretizationReport =                	  no

###-------------------------------------------------
### Network structure properties
###-------------------------------------------------

minMarkovLag =                                     0
maxMarkovLag =                                     0
dbnMandatoryIdentityLags =                         
equivalentSampleSize =                           1.0
maxParentCount =                                   5
defaultMaxParentCount =                           10

###-------------------------------------------------
### Network structure properties, optional
###-------------------------------------------------

initialStructureFile =           
mustBePresentEdgesFile =        
mustNotBePresentEdgesFile = 

###-------------------------------------------------
### Stopping criteria
###-------------------------------------------------

maxTime =                                       32 h
maxProposedNetworks =                    
maxRestarts =                                  200000
minNetworksBeforeChecking =                     1000

###-------------------------------------------------
### Search monitoring properties
###-------------------------------------------------

nBestNetworks =                                    1
bestNetworksAre =             
screenReportingInterval =                        4 h
fileReportingInterval =                          8 h                 

###-------------------------------------------------
### Parameters used by specific search methods
###-------------------------------------------------

### For simulated annealing:
initialTemperature =                           10000
coolingFactor =                                  0.7
reannealingTemperature =                         800
maxAcceptedNetworksBeforeCooling =              2500
maxProposedNetworksBeforeCooling =             10000
minAcceptedNetworksBeforeReannealing =           500

### For greedy:
minProposedNetworksAfterHighScore =             1000
minProposedNetworksBeforeRestart =              3000
maxProposedNetworksBeforeRestart =              5000
restartWithRandomNetwork =                       yes
maxParentCountForRestart =                         3

###-------------------------------------------------
### Command line user interface options
###-------------------------------------------------

askToVerifySettings =                             no

###-------------------------------------------------
### Post-processing options
###-------------------------------------------------

createDotOutput =                                yes
computeInfluenceScores =                         yes
computeConsensusGraph =                          yes
createConsensusGraphAsHtml =                     yes
fileNameForTopGraph =                 piz.ko.mice.suppgenes.32h.ma.top.graph.@TS@
fileNameForConsensusGraph =     piz.ko.mice.suppgenes.32h.ma.consensus.graph.@TS@
dotGraphicsFormat =                              svg
dotFileExtension =                               txt
htmlFileExtension =                             html
fullPathToDotExecutable = 		/usr/bin/dot
timeStampFormat =                yyyy.MM.dd.HH.mm.ss

###-------------------------------------------------
### Memory management and performance options
###-------------------------------------------------

precomputeLogGamma =                             yes
useCache =                                fastLevel2
cycleCheckingMethod =                            dfs  
threads = 					   7
###-------------------------------------------------
### Misc. options
###-------------------------------------------------

displayMemoryInfo =                              yes 
displayStructures =                              yes
