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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
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<html>
<head>
<title>Matlab Index</title>
<meta name="keywords" content="INIT core external external\kegg external\metacyc hpa installation io legacy\core legacy\external pathway plotting solver struct_conversion testing\manual_tests testing\unit_tests tutorial">
<meta name="description" content="INIT core external external\kegg external\metacyc hpa installation io legacy\core legacy\external pathway plotting solver struct_conversion testing\manual_tests testing\unit_tests tutorial">
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<h1>Matlab Index</h1>
<h2>Matlab Directories</h2>
<ul style="list-style-image:url(./matlabicon.gif)">
<li><a href="INIT/index.html">INIT</a></li><li><a href="core/index.html">core</a></li><li><a href="external/index.html">external</a></li><li><a href="external/kegg/index.html">external\kegg</a></li><li><a href="external/metacyc/index.html">external\metacyc</a></li><li><a href="hpa/index.html">hpa</a></li><li><a href="installation/index.html">installation</a></li><li><a href="io/index.html">io</a></li><li><a href="legacy/core/index.html">legacy\core</a></li><li><a href="legacy/external/index.html">legacy\external</a></li><li><a href="pathway/index.html">pathway</a></li><li><a href="plotting/index.html">plotting</a></li><li><a href="solver/index.html">solver</a></li><li><a href="struct_conversion/index.html">struct_conversion</a></li><li><a href="testing/manual_tests/index.html">testing\manual_tests</a></li><li><a href="testing/unit_tests/index.html">testing\unit_tests</a></li><li><a href="tutorial/index.html">tutorial</a></li></ul>
<h2>Matlab Files found in these Directories</h2>
<table width="100%">
<tr>
<td><a href="core/FSEOF.html" title="core">FSEOF</a></td> <td><a href="struct_conversion/editMiriam.html" title="struct_conversion">editMiriam</a></td> <td><a href="external/metacyc/getModelFromMetaCyc.html" title="external\metacyc">getModelFromMetaCyc</a></td> <td><a href="solver/qMOMA.html" title="solver">qMOMA</a></td> </tr> <tr>
<td><a href="INIT/INITStepDesc.html" title="INIT">INITStepDesc</a></td> <td><a href="core/expandModel.html" title="core">expandModel</a></td> <td><a href="plotting/getObjectiveString.html" title="plotting">getObjectiveString</a></td> <td><a href="core/randomSampling.html" title="core">randomSampling</a></td> </tr> <tr>
<td><a href="testing/manual_tests/ManualINITTests.html" title="testing\manual_tests">ManualINITTests</a></td> <td><a href="io/exportForGit.html" title="io">exportForGit</a></td> <td><a href="pathway/getPathwayDimensions.html" title="pathway">getPathwayDimensions</a></td> <td><a href="struct_conversion/ravenCobraWrapper.html" title="struct_conversion">ravenCobraWrapper</a></td> </tr> <tr>
<td><a href="io/SBMLFromExcel.html" title="io">SBMLFromExcel</a></td> <td><a href="io/exportModel.html" title="io">exportModel</a></td> <td><a href="external/kegg/getPhylDist.html" title="external\kegg">getPhylDist</a></td> <td><a href="io/readYAMLmodel.html" title="io">readYAMLmodel</a></td> </tr> <tr>
<td><a href="core/addExchangeRxns.html" title="core">addExchangeRxns</a></td> <td><a href="io/exportModelToSIF.html" title="io">exportModelToSIF</a></td> <td><a href="external/kegg/getRxnsFromKEGG.html" title="external\kegg">getRxnsFromKEGG</a></td> <td><a href="core/removeBadRxns.html" title="core">removeBadRxns</a></td> </tr> <tr>
<td><a href="core/addGenesRaven.html" title="core">addGenesRaven</a></td> <td><a href="io/exportToExcelFormat.html" title="io">exportToExcelFormat</a></td> <td><a href="external/metacyc/getRxnsFromMetaCyc.html" title="external\metacyc">getRxnsFromMetaCyc</a></td> <td><a href="core/removeGenes.html" title="core">removeGenes</a></td> </tr> <tr>
<td><a href="struct_conversion/addIdentifierPrefix.html" title="struct_conversion">addIdentifierPrefix</a></td> <td><a href="io/exportToTabDelimited.html" title="io">exportToTabDelimited</a></td> <td><a href="core/getRxnsInComp.html" title="core">getRxnsInComp</a></td> <td><a href="struct_conversion/removeIdentifierPrefix.html" title="struct_conversion">removeIdentifierPrefix</a></td> </tr> <tr>
<td><a href="io/addJavaPaths.html" title="io">addJavaPaths</a></td> <td><a href="struct_conversion/extractMiriam.html" title="struct_conversion">extractMiriam</a></td> <td><a href="io/getToolboxVersion.html" title="io">getToolboxVersion</a></td> <td><a href="INIT/removeLowScoreGenes.html" title="INIT">removeLowScoreGenes</a></td> </tr> <tr>
<td><a href="core/addMets.html" title="core">addMets</a></td> <td><a href="core/fillGaps.html" title="core">fillGaps</a></td> <td><a href="core/getTransportRxns.html" title="core">getTransportRxns</a></td> <td><a href="core/removeMets.html" title="core">removeMets</a></td> </tr> <tr>
<td><a href="installation/addRavenToUserPath.html" title="installation">addRavenToUserPath</a></td> <td><a href="testing/unit_tests/fillGapsLargeTests.html" title="testing\unit_tests">fillGapsLargeTests</a></td> <td><a href="external/kegg/getWSLpath.html" title="external\kegg">getWSLpath</a></td> <td><a href="installation/removeRavenFromPath.html" title="installation">removeRavenFromPath</a></td> </tr> <tr>
<td><a href="core/addRxns.html" title="core">addRxns</a></td> <td><a href="testing/unit_tests/fillGapsSmallTests.html" title="testing\unit_tests">fillGapsSmallTests</a></td> <td><a href="external/getWoLFScores.html" title="external">getWoLFScores</a></td> <td><a href="core/removeReactions.html" title="core">removeReactions</a></td> </tr> <tr>
<td><a href="core/addRxnsGenesMets.html" title="core">addRxnsGenesMets</a></td> <td><a href="core/findGeneDeletions.html" title="core">findGeneDeletions</a></td> <td><a href="INIT/groupRxnScores.html" title="INIT">groupRxnScores</a></td> <td><a href="core/replaceMets.html" title="core">replaceMets</a></td> </tr> <tr>
<td><a href="external/metacyc/addSpontaneousRxns.html" title="external\metacyc">addSpontaneousRxns</a></td> <td><a href="core/findRAVENroot.html" title="core">findRAVENroot</a></td> <td><a href="core/guessComposition.html" title="core">guessComposition</a></td> <td><a href="core/reporterMetabolites.html" title="core">reporterMetabolites</a></td> </tr> <tr>
<td><a href="core/addTransport.html" title="core">addTransport</a></td> <td><a href="core/fitParameters.html" title="core">fitParameters</a></td> <td><a href="core/haveFlux.html" title="core">haveFlux</a></td> <td><a href="INIT/rescaleModelForINIT.html" title="INIT">rescaleModelForINIT</a></td> </tr> <tr>
<td><a href="core/analyzeSampling.html" title="core">analyzeSampling</a></td> <td><a href="core/fitTasks.html" title="core">fitTasks</a></td> <td><a href="testing/unit_tests/hmmerTests.html" title="testing\unit_tests">hmmerTests</a></td> <td><a href="INIT/reverseRxns.html" title="INIT">reverseRxns</a></td> </tr> <tr>
<td><a href="testing/unit_tests/blastPlusTests.html" title="testing\unit_tests">blastPlusTests</a></td> <td><a href="core/followChanged.html" title="core">followChanged</a></td> <td><a href="io/importExcelModel.html" title="io">importExcelModel</a></td> <td><a href="core/runDynamicFBA.html" title="core">runDynamicFBA</a></td> </tr> <tr>
<td><a href="core/buildEquation.html" title="core">buildEquation</a></td> <td><a href="core/followFluxes.html" title="core">followFluxes</a></td> <td><a href="testing/unit_tests/importExportTests.html" title="testing\unit_tests">importExportTests</a></td> <td><a href="INIT/runINIT.html" title="INIT">runINIT</a></td> </tr> <tr>
<td><a href="core/canConsume.html" title="core">canConsume</a></td> <td><a href="INIT/ftINIT.html" title="INIT">ftINIT</a></td> <td><a href="io/importModel.html" title="io">importModel</a></td> <td><a href="core/runPhenotypePhasePlane.html" title="core">runPhenotypePhasePlane</a></td> </tr> <tr>
<td><a href="core/canProduce.html" title="core">canProduce</a></td> <td><a href="INIT/ftINITFillGaps.html" title="INIT">ftINITFillGaps</a></td> <td><a href="external/metacyc/linkMetaCycKEGGRxns.html" title="external\metacyc">linkMetaCycKEGGRxns</a></td> <td><a href="core/runProductionEnvelope.html" title="core">runProductionEnvelope</a></td> </tr> <tr>
<td><a href="testing/unit_tests/cdhitTests.html" title="testing\unit_tests">cdhitTests</a></td> <td><a href="INIT/ftINITFillGapsForAllTasks.html" title="INIT">ftINITFillGapsForAllTasks</a></td> <td><a href="io/loadSheet.html" title="io">loadSheet</a></td> <td><a href="core/runRobustnessAnalysis.html" title="core">runRobustnessAnalysis</a></td> </tr> <tr>
<td><a href="legacy/core/changeGeneAssoc.html" title="legacy\core">changeGeneAssoc</a></td> <td><a href="INIT/ftINITFillGapsMILP.html" title="INIT">ftINITFillGapsMILP</a></td> <td><a href="io/loadWorkbook.html" title="io">loadWorkbook</a></td> <td><a href="core/runSimpleOptKnock.html" title="core">runSimpleOptKnock</a></td> </tr> <tr>
<td><a href="core/changeGrRules.html" title="core">changeGrRules</a></td> <td><a href="INIT/ftINITInternalAlg.html" title="INIT">ftINITInternalAlg</a></td> <td><a href="testing/unit_tests/mafftTests.html" title="testing\unit_tests">mafftTests</a></td> <td><a href="INIT/scoreComplexModel.html" title="INIT">scoreComplexModel</a></td> </tr> <tr>
<td><a href="core/changeRxns.html" title="core">changeRxns</a></td> <td><a href="core/gapReport.html" title="core">gapReport</a></td> <td><a href="external/makeFakeBlastStructure.html" title="external">makeFakeBlastStructure</a></td> <td><a href="hpa/scoreModel.html" title="hpa">scoreModel</a></td> </tr> <tr>
<td><a href="io/checkFileExistence.html" title="io">checkFileExistence</a></td> <td><a href="core/generateNewIds.html" title="core">generateNewIds</a></td> <td><a href="core/makeSomething.html" title="core">makeSomething</a></td> <td><a href="plotting/setColorToMapRxns.html" title="plotting">setColorToMapRxns</a></td> </tr> <tr>
<td><a href="installation/checkFunctionUniqueness.html" title="installation">checkFunctionUniqueness</a></td> <td><a href="core/getAllRxnsFromGenes.html" title="core">getAllRxnsFromGenes</a></td> <td><a href="core/mapCompartments.html" title="core">mapCompartments</a></td> <td><a href="core/setExchangeBounds.html" title="core">setExchangeBounds</a></td> </tr> <tr>
<td><a href="installation/checkInstallation.html" title="installation">checkInstallation</a></td> <td><a href="core/getAllSubGraphs.html" title="core">getAllSubGraphs</a></td> <td><a href="pathway/mapPathwayRxnNames.html" title="pathway">mapPathwayRxnNames</a></td> <td><a href="plotting/setOmicDataToRxns.html" title="plotting">setOmicDataToRxns</a></td> </tr> <tr>
<td><a href="core/checkModelStruct.html" title="core">checkModelStruct</a></td> <td><a href="core/getAllowedBounds.html" title="core">getAllowedBounds</a></td> <td><a href="pathway/markPathwayWithExpression.html" title="pathway">markPathwayWithExpression</a></td> <td><a href="core/setParam.html" title="core">setParam</a></td> </tr> <tr>
<td><a href="core/checkProduction.html" title="core">checkProduction</a></td> <td><a href="external/getBlast.html" title="external">getBlast</a></td> <td><a href="pathway/markPathwayWithFluxes.html" title="pathway">markPathwayWithFluxes</a></td> <td><a href="solver/setRavenSolver.html" title="solver">setRavenSolver</a></td> </tr> <tr>
<td><a href="core/checkRxn.html" title="core">checkRxn</a></td> <td><a href="external/getBlastFromExcel.html" title="external">getBlastFromExcel</a></td> <td><a href="core/mergeCompartments.html" title="core">mergeCompartments</a></td> <td><a href="plotting/setTitle.html" title="plotting">setTitle</a></td> </tr> <tr>
<td><a href="solver/checkSolution.html" title="solver">checkSolution</a></td> <td><a href="plotting/getColorCodes.html" title="plotting">getColorCodes</a></td> <td><a href="INIT/mergeLinear.html" title="INIT">mergeLinear</a></td> <td><a href="core/simplifyModel.html" title="core">simplifyModel</a></td> </tr> <tr>
<td><a href="core/checkTasks.html" title="core">checkTasks</a></td> <td><a href="external/getDiamond.html" title="external">getDiamond</a></td> <td><a href="core/mergeModels.html" title="core">mergeModels</a></td> <td><a href="solver/solveLP.html" title="solver">solveLP</a></td> </tr> <tr>
<td><a href="testing/unit_tests/checkTasksTests.html" title="testing\unit_tests">checkTasksTests</a></td> <td><a href="core/getElementalBalance.html" title="core">getElementalBalance</a></td> <td><a href="testing/unit_tests/miriamTests.html" title="testing\unit_tests">miriamTests</a></td> <td><a href="solver/solveQP.html" title="solver">solveQP</a></td> </tr> <tr>
<td><a href="io/cleanSheet.html" title="io">cleanSheet</a></td> <td><a href="external/metacyc/getEnzymesFromMetaCyc.html" title="external\metacyc">getEnzymesFromMetaCyc</a></td> <td><a href="testing/unit_tests/modelAbilitiesTests.html" title="testing\unit_tests">modelAbilitiesTests</a></td> <td><a href="testing/unit_tests/solverTests.html" title="testing\unit_tests">solverTests</a></td> </tr> <tr>
<td><a href="io/closeModel.html" title="io">closeModel</a></td> <td><a href="core/getEssentialRxns.html" title="core">getEssentialRxns</a></td> <td><a href="testing/unit_tests/modelConversionTests.html" title="testing\unit_tests">modelConversionTests</a></td> <td><a href="io/sortIdentifiers.html" title="io">sortIdentifiers</a></td> </tr> <tr>
<td><a href="pathway/colorPathway.html" title="pathway">colorPathway</a></td> <td><a href="core/getExchangeRxns.html" title="core">getExchangeRxns</a></td> <td><a href="testing/unit_tests/modelCurationTests.html" title="testing\unit_tests">modelCurationTests</a></td> <td><a href="core/sortModel.html" title="core">sortModel</a></td> </tr> <tr>
<td><a href="plotting/colorSubsystem.html" title="plotting">colorSubsystem</a></td> <td><a href="INIT/getExprForRxnScore.html" title="INIT">getExprForRxnScore</a></td> <td><a href="testing/unit_tests/modelSortingTests.html" title="testing\unit_tests">modelSortingTests</a></td> <td><a href="core/standardizeGrRules.html" title="core">standardizeGrRules</a></td> </tr> <tr>
<td><a href="external/combineMetaCycKEGGModels.html" title="external">combineMetaCycKEGGModels</a></td> <td><a href="core/getExpressionStructure.html" title="core">getExpressionStructure</a></td> <td><a href="solver/optimizeProb.html" title="solver">optimizeProb</a></td> <td><a href="struct_conversion/standardizeModelFieldOrder.html" title="struct_conversion">standardizeModelFieldOrder</a></td> </tr> <tr>
<td><a href="core/compareMultipleModels.html" title="core">compareMultipleModels</a></td> <td><a href="core/getFluxZ.html" title="core">getFluxZ</a></td> <td><a href="core/parallelPoolRAVEN.html" title="core">parallelPoolRAVEN</a></td> <td><a href="io/startup.html" title="io">startup</a></td> </tr> <tr>
<td><a href="core/compareRxnsGenesMetsComps.html" title="core">compareRxnsGenesMetsComps</a></td> <td><a href="io/getFullPath.html" title="io">getFullPath</a></td> <td><a href="core/parseFormulas.html" title="core">parseFormulas</a></td> <td><a href="testing/unit_tests/tinitTests.html" title="testing\unit_tests">tinitTests</a></td> </tr> <tr>
<td><a href="core/constructEquations.html" title="core">constructEquations</a></td> <td><a href="core/getGenesFromGrRules.html" title="core">getGenesFromGrRules</a></td> <td><a href="hpa/parseHPA.html" title="hpa">parseHPA</a></td> <td><a href="pathway/trimPathway.html" title="pathway">trimPathway</a></td> </tr> <tr>
<td><a href="external/kegg/constructMultiFasta.html" title="external\kegg">constructMultiFasta</a></td> <td><a href="external/kegg/getGenesFromKEGG.html" title="external\kegg">getGenesFromKEGG</a></td> <td><a href="hpa/parseHPArna.html" title="hpa">parseHPArna</a></td> <td><a href="tutorial/tutorial1.html" title="tutorial">tutorial1</a></td> </tr> <tr>
<td><a href="legacy/external/constructPathwayFromCelldesigner.html" title="legacy\external">constructPathwayFromCelldesigner</a></td> <td><a href="INIT/getINITModel.html" title="INIT">getINITModel</a></td> <td><a href="core/parseRxnEqu.html" title="core">parseRxnEqu</a></td> <td><a href="tutorial/tutorial2.html" title="tutorial">tutorial2</a></td> </tr> <tr>
<td><a href="core/constructS.html" title="core">constructS</a></td> <td><a href="INIT/getINITSteps.html" title="INIT">getINITSteps</a></td> <td><a href="external/parseScores.html" title="external">parseScores</a></td> <td><a href="tutorial/tutorial2_solutions.html" title="tutorial">tutorial2_solutions</a></td> </tr> <tr>
<td><a href="core/consumeSomething.html" title="core">consumeSomething</a></td> <td><a href="core/getIndexes.html" title="core">getIndexes</a></td> <td><a href="core/parseTaskList.html" title="core">parseTaskList</a></td> <td><a href="tutorial/tutorial3.html" title="tutorial">tutorial3</a></td> </tr> <tr>
<td><a href="core/contractModel.html" title="core">contractModel</a></td> <td><a href="external/kegg/getKEGGModelForOrganism.html" title="external\kegg">getKEGGModelForOrganism</a></td> <td><a href="core/permuteModel.html" title="core">permuteModel</a></td> <td><a href="tutorial/tutorial3_solutions.html" title="tutorial">tutorial3_solutions</a></td> </tr> <tr>
<td><a href="core/convertCharArray.html" title="core">convertCharArray</a></td> <td><a href="io/getMD5Hash.html" title="io">getMD5Hash</a></td> <td><a href="plotting/plotAdditionalInfo.html" title="plotting">plotAdditionalInfo</a></td> <td><a href="tutorial/tutorial4.html" title="tutorial">tutorial4</a></td> </tr> <tr>
<td><a href="core/convertToIrrev.html" title="core">convertToIrrev</a></td> <td><a href="external/metacyc/getMetaCycModelForOrganism.html" title="external\metacyc">getMetaCycModelForOrganism</a></td> <td><a href="plotting/plotLabels.html" title="plotting">plotLabels</a></td> <td><a href="tutorial/tutorial4_solutions.html" title="tutorial">tutorial4_solutions</a></td> </tr> <tr>
<td><a href="core/copyToComps.html" title="core">copyToComps</a></td> <td><a href="external/kegg/getMetsFromKEGG.html" title="external\kegg">getMetsFromKEGG</a></td> <td><a href="core/predictLocalization.html" title="core">predictLocalization</a></td> <td><a href="tutorial/tutorial5.html" title="tutorial">tutorial5</a></td> </tr> <tr>
<td><a href="core/deleteUnusedGenes.html" title="core">deleteUnusedGenes</a></td> <td><a href="external/metacyc/getMetsFromMetaCyc.html" title="external\metacyc">getMetsFromMetaCyc</a></td> <td><a href="INIT/prepINITModel.html" title="INIT">prepINITModel</a></td> <td><a href="tutorial/tutorial6.html" title="tutorial">tutorial6</a></td> </tr> <tr>
<td><a href="testing/unit_tests/diamondTests.html" title="testing\unit_tests">diamondTests</a></td> <td><a href="core/getMetsInComp.html" title="core">getMetsInComp</a></td> <td><a href="core/printFluxes.html" title="core">printFluxes</a></td> <td><a href="external/updateDocumentation.html" title="external">updateDocumentation</a></td> </tr> <tr>
<td><a href="core/dispEM.html" title="core">dispEM</a></td> <td><a href="core/getMinNrFluxes.html" title="core">getMinNrFluxes</a></td> <td><a href="core/printModel.html" title="core">printModel</a></td> <td><a href="io/writeSheet.html" title="io">writeSheet</a></td> </tr> <tr>
<td><a href="plotting/drawMap.html" title="plotting">drawMap</a></td> <td><a href="core/getModelFromHomology.html" title="core">getModelFromHomology</a></td> <td><a href="core/printModelStats.html" title="core">printModelStats</a></td> <td><a href="io/writeYAMLmodel.html" title="io">writeYAMLmodel</a></td> </tr> <tr>
<td><a href="plotting/drawPathway.html" title="plotting">drawPathway</a></td> <td><a href="external/kegg/getModelFromKEGG.html" title="external\kegg">getModelFromKEGG</a></td> <td><a href="core/printOrange.html" title="core">printOrange</a></td> <td><a href="" title=""></a></td> </tr></table>
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