diff --git a/doc/core/dispEM.html b/doc/core/dispEM.html
index fd8ce41f..58f8f66c 100644
--- a/doc/core/dispEM.html
+++ b/doc/core/dispEM.html
@@ -49,7 +49,7 @@ <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^
 <li><a href="convertCharArray.html" class="code" title="function inputConverted = convertCharArray(funcInput)">convertCharArray</a>	convertCharArray</li></ul>
 This function is called by:
 <ul style="list-style-image:url(../matlabicon.gif)">
-<li><a href="addGenesRaven.html" class="code" title="function newModel=addGenesRaven(model,genesToAdd)">addGenesRaven</a>	addGenesRaven</li><li><a href="addMets.html" class="code" title="function newModel=addMets(model,metsToAdd,copyInfo,prefix)">addMets</a>	addMets</li><li><a href="addRxns.html" class="code" title="function newModel=addRxns(model,rxnsToAdd,eqnType,compartment,allowNewMets,allowNewGenes)">addRxns</a>	addRxns</li><li><a href="addRxnsGenesMets.html" class="code" title="function model=addRxnsGenesMets(model,sourceModel,rxns,addGene,rxnNote,confidence)">addRxnsGenesMets</a>	addRxnsGenesMets</li><li><a href="addTransport.html" class="code" title="function [model, addedRxns]=addTransport(model,fromComp,toComps,metNames,isRev,onlyToExisting,prefix)">addTransport</a>	addTransport</li><li><a href="analyzeSampling.html" class="code" title="function scores=analyzeSampling(Tex, df, solutionsA, solutionsB, printResults)">analyzeSampling</a>	analyzeSampling</li><li><a href="buildEquation.html" class="code" title="function equationString=buildEquation(mets,stoichCoeffs,isrev)">buildEquation</a>	buildEquation</li><li><a href="changeRxns.html" class="code" title="function model=changeRxns(model,rxns,equations,eqnType,compartment,allowNewMets)">changeRxns</a>	changeRxns</li><li><a href="checkModelStruct.html" class="code" title="function checkModelStruct(model,throwErrors,trimWarnings)">checkModelStruct</a>	checkModelStruct</li><li><a href="checkRxn.html" class="code" title="function report=checkRxn(model,rxn,cutoff,revDir,printReport)">checkRxn</a>	checkRxn</li><li><a href="checkTasks.html" class="code" title="function [taskReport, essentialRxns, taskStructure, essentialFluxes]=checkTasks(model,inputFile,printOutput,printOnlyFailed,getEssential,taskStructure)">checkTasks</a>	checkTasks</li><li><a href="compareMultipleModels.html" class="code" title="function compStruct = compareMultipleModels(models,printResults,plotResults,groupVector,funcCompare,taskFile)">compareMultipleModels</a>	compareMultipleModels</li><li><a href="compareRxnsGenesMetsComps.html" class="code" title="function compStruct=compareRxnsGenesMetsComps(models,printResults)">compareRxnsGenesMetsComps</a>	compareRxnsGenesMetsComps</li><li><a href="constructS.html" class="code" title="function [S, mets, badRxns, reversible]=constructS(equations,mets,rxns)">constructS</a>	constructS</li><li><a href="consumeSomething.html" class="code" title="function [solution, metabolite]=consumeSomething(model,ignoreMets,isNames,minNrFluxes,params,ignoreIntBounds)">consumeSomething</a>	consumeSomething</li><li><a href="contractModel.html" class="code" title="function [reducedModel, removedRxns, indexedDuplicateRxns]=contractModel(model,distReverse,mets)">contractModel</a>	contractModel</li><li><a href="fillGaps.html" class="code" title="function [newConnected, cannotConnect, addedRxns, newModel, exitFlag]=fillGaps(model,models,allowNetProduction,useModelConstraints,supressWarnings,rxnScores,params)">fillGaps</a>	fillGaps</li><li><a href="findGeneDeletions.html" class="code" title="function [genes, fluxes, originalGenes, details, grRatioMuts]=findGeneDeletions(model,testType,analysisType,refModel,oeFactor)">findGeneDeletions</a>	findGeneDeletions</li><li><a href="fitParameters.html" class="code" title="function [parameters, fitnessScore, exitFlag, newModel]=fitParameters(model,xRxns,xValues,rxnsToFit,valuesToFit,parameterPositions,fitToRatio,initialGuess,plotFitting)">fitParameters</a>	fitParameters</li><li><a href="fitTasks.html" class="code" title="function [outModel, addedRxns]=fitTasks(model,refModel,inputFile,printOutput,rxnScores,taskStructure,params)">fitTasks</a>	fitTasks</li><li><a href="getElementalBalance.html" class="code" title="function balanceStructure=getElementalBalance(model,rxns,printUnbalanced,printUnparsable)">getElementalBalance</a>	getElementalBalance</li><li><a href="getEssentialRxns.html" class="code" title="function [essentialRxns, essentialRxnsIndexes]=getEssentialRxns(model,ignoreRxns)">getEssentialRxns</a>	getEssentialRxns</li><li><a href="getExpressionStructure.html" class="code" title="function experiment=getExpressionStructure(fileName)">getExpressionStructure</a>	getExpressionStructure</li><li><a href="getFluxZ.html" class="code" title="function Z=getFluxZ(solutionsA, solutionsB)">getFluxZ</a>	getFluxZ</li><li><a href="getMetsInComp.html" class="code" title="function [I, metNames]=getMetsInComp(model,comp)">getMetsInComp</a>	getMetsInComp</li><li><a href="getMinNrFluxes.html" class="code" title="function [x,I,exitFlag]=getMinNrFluxes(model, toMinimize, params,scores)">getMinNrFluxes</a>	getMinNrFluxes</li><li><a href="getModelFromHomology.html" class="code" title="function [draftModel, hitGenes]=getModelFromHomology(models,blastStructure,getModelFor,preferredOrder,strictness,onlyGenesInModels,maxE,minLen,minIde,mapNewGenesToOld)">getModelFromHomology</a>	getModelFromHomology</li><li><a href="getRxnsInComp.html" class="code" title="function [I, rxnNames]=getRxnsInComp(model,comp,includePartial)">getRxnsInComp</a>	getRxnsInComp</li><li><a href="guessComposition.html" class="code" title="function [model, guessedFor, couldNotGuess, guessedFormula]=guessComposition(model, printResults)">guessComposition</a>	guessComposition</li><li><a href="makeSomething.html" class="code" title="function [solution, metabolite]=makeSomething(model,ignoreMets,isNames,minNrFluxes,allowExcretion,params,ignoreIntBounds)">makeSomething</a>	makeSomething</li><li><a href="mapCompartments.html" class="code" title="function geneScoreStructure=mapCompartments(geneScoreStructure,varargin)">mapCompartments</a>	mapCompartments</li><li><a href="mergeCompartments.html" class="code" title="function [model, deletedRxns, duplicateRxns]=mergeCompartments(model,keepUnconstrained,deleteRxnsWithOneMet,distReverse)">mergeCompartments</a>	mergeCompartments</li><li><a href="mergeModels.html" class="code" title="function model=mergeModels(models,metParam,supressWarnings)">mergeModels</a>	mergeModels</li><li><a href="parseTaskList.html" class="code" title="function taskStruct=parseTaskList(inputFile)">parseTaskList</a>	parseTaskList</li><li><a href="predictLocalization.html" class="code" title="function [outModel, geneLocalization, transportStruct, scores,removedRxns] = predictLocalization(model, GSS,defaultCompartment, transportCost, maxTime, plotResults)">predictLocalization</a>	predictLocalization</li><li><a href="printFluxes.html" class="code" title="function printFluxes(model, fluxes, onlyExchange, cutOffFlux, outputFile,outputString,metaboliteList)">printFluxes</a>	printFluxes</li><li><a href="randomSampling.html" class="code" title="function [solutions, goodRxns]=randomSampling(model,nSamples,replaceBoundsWithInf,supressErrors,runParallel,goodRxns,minFlux)">randomSampling</a>	randomSampling</li><li><a href="removeBadRxns.html" class="code" title="function [newModel, removedRxns]=removeBadRxns(model,rxnRules,ignoreMets,isNames,balanceElements,refModel,ignoreIntBounds,printReport)">removeBadRxns</a>	removeBadRxns</li><li><a href="reporterMetabolites.html" class="code" title="function repMets=reporterMetabolites(model,genes,genePValues,printResults,outputFile,geneFoldChanges)">reporterMetabolites</a>	reporterMetabolites</li><li><a href="setParam.html" class="code" title="function model=setParam(model, paramType, rxnList, params, var)">setParam</a>	setParam</li><li><a href="simplifyModel.html" class="code" title="function [reducedModel, deletedReactions, deletedMetabolites]=simplifyModel(model,deleteUnconstrained, deleteDuplicates, deleteZeroInterval, deleteInaccessible, deleteMinMax, groupLinear, constrainReversible, reservedRxns, suppressWarnings)">simplifyModel</a>	simplifyModel</li><li><a href="sortModel.html" class="code" title="function model=sortModel(model,sortReversible,sortMetName,sortReactionOrder)">sortModel</a>	sortModel</li></ul>
+<li><a href="addGenesRaven.html" class="code" title="function newModel=addGenesRaven(model,genesToAdd)">addGenesRaven</a>	addGenesRaven</li><li><a href="addMets.html" class="code" title="function newModel=addMets(model,metsToAdd,copyInfo,prefix)">addMets</a>	addMets</li><li><a href="addRxns.html" class="code" title="function newModel=addRxns(model,rxnsToAdd,eqnType,compartment,allowNewMets,allowNewGenes)">addRxns</a>	addRxns</li><li><a href="addRxnsGenesMets.html" class="code" title="function model=addRxnsGenesMets(model,sourceModel,rxns,addGene,rxnNote,confidence)">addRxnsGenesMets</a>	addRxnsGenesMets</li><li><a href="addTransport.html" class="code" title="function [model, addedRxns]=addTransport(model,fromComp,toComps,metNames,isRev,onlyToExisting,prefix)">addTransport</a>	addTransport</li><li><a href="analyzeSampling.html" class="code" title="function scores=analyzeSampling(Tex, df, solutionsA, solutionsB, printResults)">analyzeSampling</a>	analyzeSampling</li><li><a href="buildEquation.html" class="code" title="function equationString=buildEquation(mets,stoichCoeffs,isrev)">buildEquation</a>	buildEquation</li><li><a href="changeRxns.html" class="code" title="function model=changeRxns(model,rxns,equations,eqnType,compartment,allowNewMets)">changeRxns</a>	changeRxns</li><li><a href="checkModelStruct.html" class="code" title="function checkModelStruct(model,throwErrors,trimWarnings)">checkModelStruct</a>	checkModelStruct</li><li><a href="checkRxn.html" class="code" title="function report=checkRxn(model,rxn,cutoff,revDir,printReport)">checkRxn</a>	checkRxn</li><li><a href="checkTasks.html" class="code" title="function [taskReport, essentialRxns, taskStructure, essentialFluxes]=checkTasks(model,inputFile,printOutput,printOnlyFailed,getEssential,taskStructure)">checkTasks</a>	checkTasks</li><li><a href="compareMultipleModels.html" class="code" title="function compStruct = compareMultipleModels(models,printResults,plotResults,groupVector,funcCompare,taskFile)">compareMultipleModels</a>	compareMultipleModels</li><li><a href="compareRxnsGenesMetsComps.html" class="code" title="function compStruct=compareRxnsGenesMetsComps(models,printResults)">compareRxnsGenesMetsComps</a>	compareRxnsGenesMetsComps</li><li><a href="constructS.html" class="code" title="function [S, mets, badRxns, reversible]=constructS(equations,mets,rxns)">constructS</a>	constructS</li><li><a href="consumeSomething.html" class="code" title="function [solution, metabolite]=consumeSomething(model,ignoreMets,isNames,minNrFluxes,params,ignoreIntBounds)">consumeSomething</a>	consumeSomething</li><li><a href="contractModel.html" class="code" title="function [reducedModel, removedRxns, indexedDuplicateRxns]=contractModel(model,distReverse,mets)">contractModel</a>	contractModel</li><li><a href="fillGaps.html" class="code" title="function [newConnected, cannotConnect, addedRxns, newModel, exitFlag]=fillGaps(model,models,allowNetProduction,useModelConstraints,supressWarnings,rxnScores,params)">fillGaps</a>	fillGaps</li><li><a href="findGeneDeletions.html" class="code" title="function [genes, fluxes, originalGenes, details, grRatioMuts]=findGeneDeletions(model,testType,analysisType,refModel,oeFactor)">findGeneDeletions</a>	findGeneDeletions</li><li><a href="fitParameters.html" class="code" title="function [parameters, fitnessScore, exitFlag, newModel]=fitParameters(model,xRxns,xValues,rxnsToFit,valuesToFit,parameterPositions,fitToRatio,initialGuess,plotFitting)">fitParameters</a>	fitParameters</li><li><a href="fitTasks.html" class="code" title="function [outModel, addedRxns]=fitTasks(model,refModel,inputFile,printOutput,rxnScores,taskStructure,params)">fitTasks</a>	fitTasks</li><li><a href="getElementalBalance.html" class="code" title="function balanceStructure=getElementalBalance(model,rxns,printUnbalanced,printUnparsable)">getElementalBalance</a>	getElementalBalance</li><li><a href="getEssentialRxns.html" class="code" title="function [essentialRxns, essentialRxnsIndexes]=getEssentialRxns(model,ignoreRxns)">getEssentialRxns</a>	getEssentialRxns</li><li><a href="getExpressionStructure.html" class="code" title="function experiment=getExpressionStructure(fileName)">getExpressionStructure</a>	getExpressionStructure</li><li><a href="getFluxZ.html" class="code" title="function Z=getFluxZ(solutionsA, solutionsB)">getFluxZ</a>	getFluxZ</li><li><a href="getMetsInComp.html" class="code" title="function [I, metNames]=getMetsInComp(model,comp)">getMetsInComp</a>	getMetsInComp</li><li><a href="getMinNrFluxes.html" class="code" title="function [x,I,exitFlag]=getMinNrFluxes(model, toMinimize, params,scores)">getMinNrFluxes</a>	getMinNrFluxes</li><li><a href="getModelFromHomology.html" class="code" title="function [draftModel, hitGenes]=getModelFromHomology(models,blastStructure,getModelFor,preferredOrder,strictness,onlyGenesInModels,maxE,minLen,minIde,mapNewGenesToOld)">getModelFromHomology</a>	getModelFromHomology</li><li><a href="getRxnsInComp.html" class="code" title="function [I, rxnNames]=getRxnsInComp(model,comp,includePartial)">getRxnsInComp</a>	getRxnsInComp</li><li><a href="guessComposition.html" class="code" title="function [model, guessedFor, couldNotGuess]=guessComposition(model, printResults)">guessComposition</a>	guessComposition</li><li><a href="makeSomething.html" class="code" title="function [solution, metabolite]=makeSomething(model,ignoreMets,isNames,minNrFluxes,allowExcretion,params,ignoreIntBounds)">makeSomething</a>	makeSomething</li><li><a href="mapCompartments.html" class="code" title="function geneScoreStructure=mapCompartments(geneScoreStructure,varargin)">mapCompartments</a>	mapCompartments</li><li><a href="mergeCompartments.html" class="code" title="function [model, deletedRxns, duplicateRxns]=mergeCompartments(model,keepUnconstrained,deleteRxnsWithOneMet,distReverse)">mergeCompartments</a>	mergeCompartments</li><li><a href="mergeModels.html" class="code" title="function model=mergeModels(models,metParam,supressWarnings)">mergeModels</a>	mergeModels</li><li><a href="parseTaskList.html" class="code" title="function taskStruct=parseTaskList(inputFile)">parseTaskList</a>	parseTaskList</li><li><a href="predictLocalization.html" class="code" title="function [outModel, geneLocalization, transportStruct, scores,removedRxns] = predictLocalization(model, GSS,defaultCompartment, transportCost, maxTime, plotResults)">predictLocalization</a>	predictLocalization</li><li><a href="printFluxes.html" class="code" title="function printFluxes(model, fluxes, onlyExchange, cutOffFlux, outputFile,outputString,metaboliteList)">printFluxes</a>	printFluxes</li><li><a href="randomSampling.html" class="code" title="function [solutions, goodRxns]=randomSampling(model,nSamples,replaceBoundsWithInf,supressErrors,runParallel,goodRxns,minFlux)">randomSampling</a>	randomSampling</li><li><a href="removeBadRxns.html" class="code" title="function [newModel, removedRxns]=removeBadRxns(model,rxnRules,ignoreMets,isNames,balanceElements,refModel,ignoreIntBounds,printReport)">removeBadRxns</a>	removeBadRxns</li><li><a href="reporterMetabolites.html" class="code" title="function repMets=reporterMetabolites(model,genes,genePValues,printResults,outputFile,geneFoldChanges)">reporterMetabolites</a>	reporterMetabolites</li><li><a href="setParam.html" class="code" title="function model=setParam(model, paramType, rxnList, params, var)">setParam</a>	setParam</li><li><a href="simplifyModel.html" class="code" title="function [reducedModel, deletedReactions, deletedMetabolites]=simplifyModel(model,deleteUnconstrained, deleteDuplicates, deleteZeroInterval, deleteInaccessible, deleteMinMax, groupLinear, constrainReversible, reservedRxns, suppressWarnings)">simplifyModel</a>	simplifyModel</li><li><a href="sortModel.html" class="code" title="function model=sortModel(model,sortReversible,sortMetName,sortReactionOrder)">sortModel</a>	sortModel</li></ul>
 <!-- crossreference -->
 
 
diff --git a/doc/core/parseFormulas.html b/doc/core/parseFormulas.html
index 57519a72..2a99eeab 100644
--- a/doc/core/parseFormulas.html
+++ b/doc/core/parseFormulas.html
@@ -65,7 +65,7 @@ <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^
 </ul>
 This function is called by:
 <ul style="list-style-image:url(../matlabicon.gif)">
-<li><a href="checkModelStruct.html" class="code" title="function checkModelStruct(model,throwErrors,trimWarnings)">checkModelStruct</a>	checkModelStruct</li><li><a href="getElementalBalance.html" class="code" title="function balanceStructure=getElementalBalance(model,rxns,printUnbalanced,printUnparsable)">getElementalBalance</a>	getElementalBalance</li><li><a href="guessComposition.html" class="code" title="function [model, guessedFor, couldNotGuess, guessedFormula]=guessComposition(model, printResults)">guessComposition</a>	guessComposition</li></ul>
+<li><a href="checkModelStruct.html" class="code" title="function checkModelStruct(model,throwErrors,trimWarnings)">checkModelStruct</a>	checkModelStruct</li><li><a href="getElementalBalance.html" class="code" title="function balanceStructure=getElementalBalance(model,rxns,printUnbalanced,printUnparsable)">getElementalBalance</a>	getElementalBalance</li><li><a href="guessComposition.html" class="code" title="function [model, guessedFor, couldNotGuess]=guessComposition(model, printResults)">guessComposition</a>	guessComposition</li></ul>
 <!-- crossreference -->