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Jean-ChristopheMozziconacciandVolkerEyrichh#p://www.schrodinger.com/upload/KNIME_Overview.pdf
KNIMEdesktopandSchrödingerextensionsoverview
Schrödingerextensions• 150+nodes:
– CoveringmostoftheSchrödingertoolsMostrecentaddiGons:Residuescanning,PrimeEnergy,SiteMap,PyMOL,GlidegridwriterManytakeinandoutputsdfandpdbormol2ontopofMaestroformatNewestnodesusethesameconfiguraGonpanelasMaestro(seetheResiduescanningnode)
– StructureanddatamanipulaGonnodes(egSplitbystructure,deleteatoms)– GUInodes(egRunMaestro,RunPyMOL)– ScripGngnodes:RunMaestrocommand,Chemistryexternaltool,Pythonnodes– UGlitynodes:Setupdiagnosisandworkflowlist
• 50+workflowexamples– Workflowpage:descripGonsanddownloadtheonesofinterest– WholesetcanbedownloadedwiththeSuite– ManyotherworkflowdraXsavailableondemand
Schrödingerextensions• TestedwithlatestKNIMEversionandincludetheversionavailableattheGmeof
therelease• Parameterflowvariablecapability
– UsetheopGonsnotexposedintheconfiguraGonpanels(egcommandlineonly)– ImplementedforthemainnodesegGlide,MMod(egOPLS2.1),Jaguar
• 2Drenderer– 2DcoordinategeneraGonandrenderingThedefaultrenderercanbesetforMaestrocolumns
– CanbeusedintheReportdesigner
Schrödingerextensions• Moreandsimplifiedstart-upopGons andstand-aloneinstallaGonconfiguraGoninthePreferences
– In$SCHRODINGER/knimestart-upscript– eguseastand-aloneKNIMEinstallaGon,settemporarydirectories,thememorylimit…
• KNIMEmenuinMaestro– ConnecttoKNIMEmodetoexchangestructureswithaKNIMEsessionKNIME-Maestroconnectornode(Improvedin2015-1:automaGcconnecGon/close,moremodes)
– Build,import,editandrunworkflowsfromMaestroonprojecttabledataDynamicallygeneratedGUItoaltersomeparameters.
• SimplifiedbatchexecuGon:KNIME_batch.py– BatchcommandgeneraGonbasedonworkflowannotaGonsStand-alonedynamicallygeneratedGUI
– UsefulopGonseg-stderr/out
• EasierinstallaGoncreaGonandupdate– UsingEclipsemachineryinKNIME_install.py– eglistofextensionstoinstall,fromseveral(zipped)updatesites
SchrödingerextensionsSeedetailsin:
• h#p://www.schrodinger.com/upload/KNIME_Overview.pdf
• Thenewfeaturesslides:– Parameterflowvariables(2014-1)– SimplifiedbatchexecuGon(2013,2014-1)– Chemistryexternaltoolnodeimprovements– KNIMEmenuinMaestro(2012)– Start-upscript(2012)
• Workflowexamples:– Labs>Parameterflowvariableusage– General>InstallaGon(KNIME_install.pyscenarios)– General>Workflowlist– General>Chemistryexternaltoolnodeusage– Phase>Shapescreening,docking(batchexecuGon)– 2Drendererinthereportdesigner
WhyuseKNIMEAutomation - Automate repetitive tasks (especially complex /
error prone tasks) - e.g. PDB set preparation, Ligand database
preparation
CollaboraDon- Shareworkflowswithcolleagues(alsoinMaestroand
Seurat)- Notablackbox
- e.g. Ensembledocking,HTSanalysis
Prototyping- Testparameters
- e.g. Validatedockingparameters
DocumentaDon- Easydebugging,interrupGons,dataincluded,inspect
eachstep(2D,inMaestro/PyMOL)
CombinevariousTools- Schrodingerandthirdpartytools(vendoragnosGc),
scripts(Python,Java,shell),- e.g. QMworkflows
ReporDng- NodesforreporGngresults
- e.g. Enrichmentplo#ernode,pdf,tables,etc.- KNIMEreportdesigner(free),webportal
(KNIME.com)
Inexpensive
Overview• Organizedbylevel:
– Getstarted– Intermediate– AdvancedfuncGonaliGes
• Andbytopics:– KNIMEdesktop:GUI,specificiGes,nodes– Schrödingerextensions:specificiGes,nodes
• YoucanjumpbetweenthesecGonsusinglinks(markedwith►or◄).Seetheoverviewslides.
• Therearealsolinkstouse-caseexamples(markedwith♦).
GetstartedKNIMEdesktop
– GUI ► – SpecificiGes ► – Nodes ►
Schrödingerextensions– SpecificiGes ► – Schrödingernodes ►
►Intermediate
KNIMEdesktopGUI ◄ • Knime.organdKnime.com• KNIMEdesktop• StartKnime• Createanewworkflowandorganizeaworkspace• Runanode• Importandexportworkflows• Tipsandtricks • DocumentaGon
KonstanzInformaDonMinerandEcosystemKNIME.org - Leading open-source ‘pipelining/workflow’ tool - Freely available to academic and industrial researchers - KNIME Desktop, based on Eclipse h#p://www.knime.org - Community contributions:
- Modeling tools - Marvin sketcher - RDKit - Indigo - CDK - R Scripting - Erlwood - Image Processing - HCS Tools - Next Generation Sequencing - Palladian (mainly GPL3)
KNIME.com Enterprise products and Services h#p://www.knime.com - Report designer (free) - KNIME team space (share workflows) and KNIME server (web portal and SOA access) - Cluster execution (scalability) - KNIME professional (support, maintenance and training) - Commercial development
KNIMEExtensions15+ Extension Providers Extensible, cross-platform, vendor neutral:
Schrödinger, CCG, Tripos, ChemAxon/Infocom, BioSolveIT, Cresset, Dotmatics, Molecular Discovery, Molegro…
Schrödinger Extensions - First released in 2007 - 150+ nodes
- Molecular mechanics - Molecular dynamics - Quantum mechanics - Cheminformatics - Pharmacophore modeling - Combinatorial libraries - Docking - Protein structure prediction - Structure and data manipulation
- Maestro integration - Workflow execution - Structure exchange
KNIMEDesktopGUI• Fullscreenmode
• ForgetaboutEclipsespecificmenuitems
Moreabout:
• Theconsole ►
StartKNIME• StartupKNIME:
– OnLinux:run$SCHRODINGER/knime– OnWindows:clickontheicon– Use-dataMyWorkspacetoopenaspecificworkspace– File>Switchworkspace,butKNIMEtakesGmetostartupagain
• Workspace,workflowsandworkflowgroups:
Createanewworkflowandorganizeaworkspace• Underthepop-upmenuofWorkflowProjectrepository:
– NewKNIMEworkflowandNewWorkflowgroup– Copy,Paste,Delete,Move,Rename
• DraganddroptheworkflowsintheWorkflowprojectrepository
Runanode
doubleclickorpop-up
• Connectors• Nodestatus
• Inputandoutputdatatables
Importandexportworkflows• File>ImportKNIMEworkflow/ExportKNIMEworkfloworunderthepop-upmenuofaWorkflowProjectgroup
• Importfromanotherworkspaceoranarchivefile(zip)• Select1orseveralworkflows>exportasazipfileExcludeornotthecacheddatafromtheexportedfile
Tipsandtricks• Saveregularlythechanges.SinceKNIME2.10thereisanautosavefuncGonalitybutitisn’tonbydefault.SavewhilerunningcalculaGons(seePreferences►)
• MulGpleundoandredoapplyonworkflowediGon(execuGondatalostthough)
• TheKNIMEdesktopisn’tbasedonaclient-serverarchitecture.IfyouclosetheKNIMEinstancewhileacalculaGonisrunningitwon’tkillitnoryouwillbeabletorecovertheresultswhenopeningtheworkflowagain.
DocumentaDon• NodedescripGons.AlsoaccessiblefromHelp>Helpcontent>Knime>NodedescripGonsTypeinsearchfieldandinspecttheconfiguraGonpanel
• Productpage h#p://www.schrodinger.com/KNIME-Extensions NewFeatures,NewFeaturesSlides,KNIMEOverview
• SchrödingerKNIMEmanual $SCHRODINGER/docs/knime/user_manual/kni13_user_manual.pdf• SchrödingerFAQs h#p://www.schrodinger.com/kb• Workflowpage(examples) h#p://www.schrodinger.com/knimeworkflows/• Schrödinger’sextensionswebex h#p://www.schrodinger.com/seminarprior/19/24/• KNIME.org
– Workflowexamples (preconfiguredserveraccessinKNIMEexplorer)– Screencast h#p://www.knime.com/introducGon/screencasts– Forum h#p://www.knime.org/forum/
KNIMEdesktopGUI ► • Preferences• AdvancednodefuncGonaliGes• Errors,warningsandConsoleinformaGon• Flowvariablesandworkflowvariables• Metanodes• Memorylimit• Tipsandtricks
KNIMEdesktopspecificiDes ◄ • StepwiseexecuGon• Datatablecolumntypesandconversion
StepwiseexecuDon• OnlystepwiseexecuGon IdealtotakeadvantageofSchrödinger’sjobcontrolinfrastructure
• NopredefinedexecuGonorderfornonconnectedbranches.Usetheflowvariableports[KNIME2.3]
• Datacachedateachstep• Preferences>KNIME>Maximumworkingthreadsfarallnodes• 1:1connecGonbetweennodes(usetheconcatenatenodetocombineinputflows)
Datatablecolumntypesandconversion• KNIMEreliesonstrictdatatablecolumntyping• Converternodes:
– DoubletoInt(integer),Stringtonumber,Numbertostring – Moleculetypecast(butnoMaestroconversion)– Openbabel,CDKtomolecule,MoleculetoCDK
• IntheSchrödingerextensions:– String-to-type– Molecule-to-MAE,MAE-to-Pdb,MAE-to-SD,MAE-to-Smiles,MAE-to-mol2,SD-to-smiles
– Canvasobjectconverters
Schrödingerspecificcelltypes• Structures:Maestro,Sequence,Alignment• Severalfiles:Glidegrid,PhaseHypothesis• Desmondtrajectory• Binaryformats:CanvasfingerprintandmatrixReadersandwriters,converters
KNIMEworkbenchnodes ◄ • KNIMEworkbenchnodes• DatamanipulaGonnodes• Dataexchange
KNIMEworkbenchnodes• I/OnodesforreadingandwriGngdatafromfilesanddatabases
• DatamanipulaGonnodesformanagingtheinternaldatatablesthatareusedtopassinformaGonbetweennodes
• CharGngandplopngtools• Loopsupport,GmeSeries,Distancematrix• StaGsGcsanddataminingnodes(Mining,Weka)suchasclustering,neuralnetworks,decisiontrees,LibSVMRstaGsGcalcomputaGon
• Basicchemistry-awarenodes(CDK)verylimited,seeSchrödingerextensionnodes►
ThemostoPenusednodesfordatamanipulaDon• Rowfilter,Rowspli#erandSorter• Columnfilter,Columnresorter,ColumncombinerandRename• Joiner(seealsoSchrödingerLookupandaddcolumnnode►)andConcatenate
(only2inputs)
Andalso:• Javasnippet,RowIDandGroupBynode ►• SchrödingernodesfordatamanipulaGon ►
Dataexchange• Astextfiles:Filereaderandcsvwriternodes• InExcelformat:xlsreaderandxlswriternodes• Betweenworkflows:tablereaderandtablewriternodes
• SeealsoamongtheSchrödingernodes:
– Schrödingerreaderandwriternodes– CSVreader(readseveralfiles)– ViewCSV ►
KNIMEworkbenchnodes ► • KNIME.comLabsnodes• ScripGngandrunathirdpartytool• Javasnippet• RowID• Groupby• Miscellaneousnodes:InteracGvetable,Mathformula,CDKSketcher• PlopngfaciliGes• LoopingfuncGonaliGes-Basics• Modelbuildingnodes
SchrödingerextensionsspecificiDes ◄ • Canvas2Drenderer• Groupedstructuresinacell• OutputcolumnstructureopGons• Jobcontroltab
Canvas2Drenderer• Preferences>KNIME>Preferredrenderer
Groupedstructuresinacell• #CTs:numberofstructures• SetofconformaGons,Glideposes,Ligprepforms…• Groupandungroupnodes,matchopGon• AlsogroupedSD,mol2
OutputcolumnstructureopDons• InputplusOutput,OutputreplacesInput,Outputonly• ExtractMAEproperGes,SetMAEproperGesanddeleteMAE
properGesnodes.
CTs: Structures + properties
CTs, columns new CTs and/or new columns KNIME
Schrödinger tools New CTs
Extract mae properties
Set mae properties
Reader Writer, Maestro
Delete mae properties
OutputcolumnstructureopDons
Jobcontrol
SchrödingerextensionsspecificiDes ► • Schrödinger preferences • Start-up script options • Access to flow variables
Schrödingernodes ◄ • Schrödinger node repository
• Configuration panel visual coherence
• Nodes of general use: – Readers and converters – Run Maestro and Run Maestro command – Structure manipulation – Data manipulation and viewers – Scripting
• KNIME workflow webpage
AccesstoSchrödingertoolsviaKNIME• RunonLinux,MacandWindows
32and64bit• AddourextensionstoanexisGngKNIME
installaGonusingtheupdatesite• 150+nodescoveringthewholeSchrödinger
Suite
CheminformaDcsFingerprintBasedTools
-FingerprintGeneraGon-GeneratePairwiseMatrix-GeneratePairwiseMatrix(2Inputs)-SimilarityMatrix(fromMolecules)-DissimilaritySelecGon(fromMatrix)-BuildReportforClustering(fromMatrix)-HierarchicalClustering(fromMatrix)
FiltersandMiningTools-MaximumCommonSubstructureSearch-SubstructureSearch-REOSFilter-StructureFilter
UDliDesandConverters-PrincipalComponents-MulG-dimensionalScaling-CombineFingerprints-ConcatenateBitvectors-ConvertFingerprinttoBitvector-ConvertFingerprinttoTable-ConvertMatrixtoTable-ConvertTabletoFingerPrint-ConvertTabletoMatrix-ConvertBitvectortoFingerPrint
Modeling-BayesClassificaGonModelBuilding
MolecularMechanics-MacroModelSinglePointEnergy-MacroModelMinimizaGon-MacroModelCoordinateScan-ConfGenStandard-ConfGen-ConformaGonalSearch-ConformaGonalSearchandCluster-Premin-Impref-UffminQuantumMechanics-JaguarSinglePointEnergy-JaguarMinimizaGon-NMRShieldingConstants-JaguarCharges
PharmacophoreModeling-PhaseShape-PhaseDBQuery-PhaseFileQuery-PhaseDBCreaGon-PhaseHypothesisIdenGficaGonDockingandScoring-GlideGridGeneraGon-GlideLigandDocking-GlideMulGpleLigandDocking-XPVisualizer
Post-processing-PrimeMM-GBSA-EmbraceMinimizaGon-StrainRescore-PoseEntropy-PoseFilter-GlideEnsembleMerge-GlideMerge-GlideSortResults
ProteinStructurePredicDon-BLAST-PrimeBuildHomologyModel-PrimeSideChainSampling-PrimeMinimizaGon
SchrödingernodesWorkflowsProteinPreparaGon-ProteinPreparaGonWizard-ProteinAssignmentInduced-fitdocking-IFDandindividualstepsLigandPreparaDon-LigPrep-Ligprepindividualtools(Ionizer,
Desalter,Neutralizer…)-EpikPropertyGeneraDon-QikProp-MolecularDescriptors-CalculateproperGesFiltering-Ligfilter-Ligparse-PropertyFilter(Propfilter)
Readers/Writers-CSVReader-MoleculeReader-SD,PDB,Mol2Readernodes-SequenceReader-AlignmentReader-FingerprintReader-HypothesisReader-GlideGridReader-GlideMulGpleGridReader-VariableBasedGlideGridReader-MoleculeWriter-SequenceWriter-AlignmentWriter-HypothesisWriter-FingerprintWriterConverters-Molecule-to-MAE-MAE-to-Pdb,to-SD,to-Smilesandto-Mol2-SD-to-Smiles-PoseViewer-to-Complexes-Complexes-to-PoseViewers-String-to-Type-Hartree-to-kcal/molConverter-kJ-to-kcalConverter
Desmond-Systembuilder-MolecularDynamics-TrajectoryextractframesandmanipulaGon-Trajectoryreader,CMSreaderReporDng-RunMaestro-RunCanvas-ViewCSV(openxls/ooffice)-TextViewerToolsCombinatorialLibraries-CombiGlideLibraryEnumeraGon-CombiGlideReagentPreparaGonFragments-FragmentJoiner-FragmentsfromMoleculesDataManipulaDon-CompareLigands-LookupandAddColumns-GroupMAE-UngroupMAE
StructureManipulaDon-AddHydrogens-DeleteAtoms-SplitbyStructure-MAEParser-ExtractMAEProperGes-DeleteMAEProperGes-SetMAEProperGes-SetMoleculeTitle-SetMAEIndexUDliDes-GetPDB-AlignBindingSites-ProteinStructureAlignment-PrimeFix-RMSD-AssignBondOrders-UniqueTitleCheck-PDBName-SDFormatChecker-GenerateSmarts-UniqueSmiles-EntropyCalculaGon-RRHOEntropy-BoltzmannPopulaGon-VolumeOverlapMatrix
ScripDng-RunMaestroCommand-ChemistryExternalTool0:1,1:0,1:1,
1:2,2:1and2:2nodes-PythonScript0:1,1:0,1:1,1:2,2:1and
2:2nodes
VisualCoherence–Maestrovs.KNIME
Read in Ligands
Ligand Preparation
Filtering
Read in Grid
Docking
View Results
Nodesofgeneraluse-Readersandconverters• Moleculereader,SDreader...Glidegridreader...• Converters(Maestro,mae.gz,SD,sd.gz,mol2,PDB,smiles)includingMoleculeto
MAE,stringtotype.Canvasconverters(Matrix,Fingerprint,Bitvectorfromandtotable).SDformatchecker
• PoseviewertocomplexesandComplexestoPoseViewer
RunmaestrocommandandRunMaestro
Nodesofgeneraluse-StructuremanipulaDon• SetMAEproperGes
• ExtractMAEproperGes
Nodesofgeneraluse-StructuremanipulaDon• ExtractandSetMAEproperGes• GroupandUngroup,SetMAEindex• MAEparser• Splitbystructure,Deleteatoms• Compareligands• Uniquesmiles,UniqueGtlecheck,Ligfilter,Alignbindingsites,RMSD,Volumeoverlapmatrix...
Nodesofgeneraluse-DatamanipulaDonandviewers• Lookupandaddcolumns• RunSpreadsheetviewer(OpenOffice/Excel)• Tableviewer
KNIMEWorkflowsAvailableforDownload
http://www.schrodinger.com/knimeworkflows
OtherKNIMEWorkflowsCheminformaDcs• ClusterbyFingerprint• DatabaseAnalysis• MaximumCommonSubstructureSearch(MCS)• SelectDiverseMolecules• SimilaritySearch• SubstructureSearch
DockingandPost-Processing• DockingandScoring• EnsembleDocking• LoopOverDockingParameters• ProteinPreparaGonandGlideGridGeneraGon• ValidateDockingParameters• VirtualScreening• SiteMap
PharmacophoreModeling• PhaseHypothesisIdenGficaGon• PhaseScreening• ShapeScreening
MolecularDynamics:
• DesmondSimulaGon
MolecularMechanics
• CompareConformaGonalSearchMethods
• ConformaGonalSearchandPost-Processing
Quantummechanics
• ConformaGonalSearchandQMRefinement
• ESPCharges
• JaguarpKa
• QuantumMechanicalProperGes
• Semi-empiricalOpGmizaGon
LibraryDesign
• LibraryEnumeraGon
ProteinModeling
• InducedFitDockingProtocol
• ModelBuilding
Workbench
• GroupByUse-cases
• GroupLooper
• Unpivot
RealWorldExamples
• BindingSiteShapeClustering
• SitemapandGlideGridGeneraGon
• VendorDatabasePreparaGon
Labs• GlideGridWriter• ParameterFlowVariableUse-cases• RunMaestro1:1Use-casesGeneraltools• ChemistryExternalToolUse-cases• EnsureMoleculeTitleUniqueness• OutputColumnStructureOpGonPhilosophy• ProteinStructureAlignment• PythonScriptNodeUse-cases• RunMaestroCommandNodeUse-cases• RunPyMOL• SplitandAlignMulGmers• Webservice• WorkflowsintheCurrentWorkspacehttp://www.schrodinger.com/knimeworkflows/
Schrödingernodes ►
• Chemistrytoolnodes• Pythonnodes• Rowiteratorloopstart• Lookupandaddvs.Joinernode• Miscellaneousnodes:Compareligands,SetmoleculeGtle
Intermediate
KNIMEworkbench-GUI ►-Nodes ►
Schrödingerextensions
-SpecificiGes ►-Schrödingernodes ►
◄ Getstarted►AdvancedfuncGonaliGes
KNIMEworkbenchGUI ◄ • Preferences• AdvancednodefuncGonaliGes• Errors,warningsandConsoleinformaGon• Flowvariablesandworkflowvariables• Metanodes• Memorylimit• Tipsandtricks
Preferences>KNIME• Directoryfortemporaryfiles(SeealsoSchrödingerpreferences ►)• KNIMEGUI-disablethenodereset,deleGonandreconnecGonconfirmaGon• KNIMEGUI-Consoleviewloglevel:recommendedtochangetoINFO.ExampleofinformaGonprovidedbySchrödingernodes►
AdvancednodefuncDonaliDes• Hoveringoveraninputconnectortellsyouwhatthenodetakesasinput(egMoleculesinMaestro,SMILESorSDformat)
• Hoveringoveranoutputconnectorreportsthenumberofrowsandcolumnsintheoutputtable
• Commentaworkflow:Nodepop-upmenu>NodenameanddescripGon• Datatable>changetherenderer
Errors,warningsandConsoleinformaDon• Popup-menu>ViewStdoutput/error• WarningsignabovethenodestatuswhenthenodecompletedwithpotenGalerrors.
• ConsoleinformaGon:INFO HierarchicalClusteringNodeModel Preparinginputfile'/tmp/HierarchicalClustering_in_423741.mat'
INFO HierarchicalClusteringNodeModel FinishedpreparingfileGme0.35seconds
INFO HierarchicalClusteringNodeModel 10:42:4511.17.2009:
Runningcmdline[0]='=/usr/local/schro-latest/uDliDes/canvasHC-imHierarchicalClustering_in_4116794508031023741.mat-otHierarchicalClustering_in_4116794508031023741.tree-ogHierarchicalClustering_in_4116794508031023741.csv-linkageschrodinger-n123'
INFO HierarchicalClusteringNodeModel CompletedGme1.626seconds
INFO HierarchicalClusteringNodeModel Preparingoutput
INFO HierarchicalClusteringNodeModel Finishedpreparingoutput:Gme0.06seconds
INFO LocalNodeExecuGonJob HierarchicalClustering(fromMatrix)0:2:50Endexecute(2secs)
Flowvariablesandworkflowvariables• TheFlowvariablesareusedpassdatabetweennodesontopoftheconnecGons.• IntheflowvariabletabortheconfiguraGonpanelforacoupleofnodes:
• Globalvariablescanalsobeset:withtheJavasnippetnode► OrintheWorkflowprojectrepositoryselecttheworkflowandWorkflowvariablesinthe
pop-upmenu.SeealsoSchrödingerspecificiGes►andnodestoeditvariables►
Metanodes• Tohidethecomplexityandorganizeaworkflow• Chosethenumberandtypeofinput/output• Themetanodesopenupinnewtabs
Memorylimit• Checkthememorylimit:Help>AboutKnime>InstallaGondetails>ConfiguraGonand
searchforalinestarGngwith"eclipse.vmargs=-Xmx"(closetothetop).• IncreasethememoryallocatedtoKNIME:
– $SCHRODINGER\knime-maxHeap4096m– knime–Xmx4096m(aslastopGoninthecommandline)– in $SCHRODINGER\knime-v*\bin\*\knime.ini: change -Xmx1024M into 2048M (orhigheron64bit)
• Theerrormessageusuallycontain"Javaheapspace“whenthereisaKNIMEisrunningoutofmemory.
• Preferences>General>Showheapstatusandusethegarbagecollector.• KnimeandSchrödingertools(egCanvas)don'tcompeteformemory.
Tipsandtricks• Copyandpastesomenodestoaspecificplace:Select,copythenodes(Ctrl+C),rightclickwhereyouwanttopastethenodesandselectPasteinthepop-upmenu.UsingCtrl+Vinsteadthenodeswillbepastedali#lebelowtheoriginalones.
• Thekeyboardshortcutsforitemsonthemenusarelistedasusualwiththemenuitem.InFile>Preferences>General>Keysyoucanviewallthekeybindingstocommands,modifythebindings,andcreateyourownshortcuts.
• AllthebranchescanberunatthesameGmeusingtheGUItoolbarExecuteallexecutablenodesbu#on.SeealsoCancelallrunningnodes.
Knownissues• Ifyoucan´tsavetheworkflowwithaJavaheapspaceerrortrytodisconnectthelastnodeorrunthegarbagecollector.
KNIMEworkbenchGUI ► • Reportdesigner• Globalvariables• BatchexecuGon• Tipsandtricks
KNIMEworkbenchnodes ◄ • KNIME.comLabsnodes• ScripGngandrunathirdpartytool• Javasnippetuse-cases• ManipulatethetablerowIDsusingtheRowIDnode• AggregaGonusingtheGroupBynode• Miscellaneousnodes:InteracGvetable,Mathformula,CDKSketcher• PlopngfaciliGes• LoopingfuncGonaliGes-Basics• Modelbuildingnodes
KNIME.comLabsnodes• PipelinePilotConnector(otherwayaround?)• WebServiceclient,etcSpecificupdatesite:h#p://labs.knime.org/
ScripDngandrunathirdpartytool• Javasnippet► • JythonandSchrödingerPythonnodes► • PerlscripGng• ExternaltoolandSchrödingerChemistryexternaltoolnodes► • RunMaestrocommands►
Javasnippetuse-cases• Duplicatenumericorstringcolumns• Createanewcolumnfromscratch(egatag)• Combinecolumns(andflowvariables)butusetheCombinernodeforsimple
tasks egreturn"prefix-"+$$FlowVar$$+"_ref_"+$Col1$;
• Addarowindex(seealsoSetMAEindex)Seethecorrespondingworkflowexample.
ManipulatethetablerowIDsusingtheRowIDnode• UsedatatablecolumnvaluesasrowIDsandstoreRowIDsinacolumn.Use-cases:– beforetransposingadatatable– SetthelabelstobeusedbythePlo#ernode
• EnsurerowIDuniqueness– egforCanvastoolsbeforecreaGngamatrix)
AggregaDonusingtheGroupBynodeSomeoftheaggregaGonmethods:
- first,last
- max,min
- Mean
- Sum
- Concatenate
- (unique)count
- List
- Set
Miscellaneousnodes• InteracGvetable:Find&FindNextequivalenttotheSchrödingerTextviewernode
thathavemorefuncGonaliGes
• Mathformula• CDKStructuresketcherorMarvinsketch
(freeofchargefromInfocom)
PloingfaciliDes
• DataViews:Plo#er,Histogram…• Mining>Scoring:Enrichmentplo#er,ROCcurve• AdvancedcapabiliGesavailableinKNIMEReportdesigner ►
LoopingfaciliDes-Basics• Loopstart…Loopend• Injectandextractvariables• TableRow/Columntoandfromvariables• Prebuiltprotocols
• Schrödingernode:Rowiteratorloopstart►
Modelbuildingnodes
+FutureCanvasnodes
(alreadysomeprototypes)
KNIMEworkbenchnodes ►
• EditvariablesandadvancedloopingfuncGonaliGes• HilitefuncGonaliGes• Databasenodes• Miscellaneoususefulnodes
SchrödingerextensionsspecificiDes ◄ • Schrödinger preferences • Start-up script options • Access to the flow variables
SchrödingerPreferences• AspecificscratchdirectorycanbespecifiedforSchrödingernodes• DeletetemporaryfilesaXeranodesuccessfullyexecutesToggledofftorunthecalculaGonthroughthecommandlineagain
Start-upscriptopDonsTopassuser/machine/OS-specificparameters-maxHeap Maximumheapsize eg2048for2G-maxThreads Maximumworkingthreads-tempDir Schrödingerextensionstemporarydirectory-defaultHost Defaulthost-deleteTempFilestrue/false Deletetemporaryfilesonoroff.-ooCmd<value> Excel/OpenOfficeSpreadsheetcommandegoocalcorC:\ProgramFiles(x86)\MicrosoXOffice\Office12\EXCEL.EXE
Andmore(seeknime–hmessage)
Accesstotheflowvariables• AccesstotheflowvariablesintheFlowvariabletabincludingtheChemistryexternaltoolsnodes(using%flow_n%)
• VariablebasedGlidegridreader
Schrödingernodes ◄ • Chemistrytoolnodes• Pythonnodes• Rowiteratorloopstart• Lookupandaddvs.Joinernode• Miscellaneousnodes:Compareligands,SetmoleculeGtle,GetPDB
Chemistryexternaltoolnodes• Input/outputtypes:
– Maestro,SD,mol2,Smiles
– Double,Integer– String,Text– Sequence,alignment– FingerPrint,CanvasMatrix
– PhaseHypothesis,GlideGrid
Pythonnodes
• Input/outputconnectors:0:1,1:1,1:2,2:2
• Schrödinger’sAPIs• PossibilitytoincludethirdpartyAPIs
Rowiteratorloopstart
Lookupandaddvs.Joinernode• Takeadvantageonly1column,concatenatecolumnsTheJoinernodeistheeasiestwaytoconcatenatecolumnswhenthetablehavethesamenumberofrowsandsamerowIDs.
Miscellaneousnodes• GetPDB:easywaytogetoneorseveralstructures usethe|symbolasadelimiterforthelistofcodes
• SetmoleculeGtle• Compareligands:themodesareFirstonly,both,either
Schrödingernodes ► • Simpleworkflowexamples• Workflowdevelopmentsupportforcustomers• AutomaGcproteinpreparaGon• ScienGficallyrelevantapplicaGonoftheworkflowexamples• InteracGveworkwithKnimeusingtheHiLitefuncGonaliGes• Useaworkflowagain
Advancedfunc+onali+es
KNIMEworkbench-GUI ►-Nodes ►
Schrödingerextensions
-Advancedworkflowexamples ►
◄ Intermediate
KNIMEworkbenchGUI ◄
• Reportdesigner• Globalvariables• BatchexecuGon• Tipsandtricks
Reportdesigner• Fromknime.combutfreeofcharge.IncludedinourdistribuGon• IncludeToreportnode(s)intheworkflow(can’tbeinmetanodes)andswitchtothe
Reportdesignermode
Reportdesigner-templatemode
Reportdesigner-Canvas2DrendererThestructurescanbeshowninareportusingCanvas2Drendererusingthefollowingprocedure:
• 1.Intheworkflow,addaMAE-to-smilesnodeandaToreportnode.
• 2.InReporGngmode,intheLayouttab,addatabletothereport(draganddropfromtheDatasetview).
• 3.Insertinthe"[smiles]"cell(Table-detailrow)anImagewidgetfromtheReportItemslist.
• 4.Configurethewidget(using"Edit"onthewidget),select"Dynamic image",andpress"Select ImageData..."toselectthesourcecolumn(whichshouldbetheSmilescolumn).Delete"[smiles]"ifyouwantjusttheimageandnoSMILES.YoumaywanttoalterthesizeofthecellbydraggingtheborderverGcallyandhorizontallyifnecessary.
• 5.Changethesizeoftheimagetosomethinglike300x300,whichisdonebyediGngtheDatasetview(rightclick->Edit->Parameters),andchanging(orcreaGngnewParameterstypedasintegeriftheydon'texistyet)theknime-image-heightandknime-image-widthparameters.
• 6.ChecktheviewinthePreviewtab
Globalvariables• IntheWorkflowprojectlist,right-clickontheworkflow,underWorkflowvariables
BatchexecuDon• $SCHRODINGER/knime-batch–reset–nosplash-nosave
-workflowFile=<path>/<wkf>.zipor-workflowDir=<path>/<workspace>/<wkf>
• Altersomesepngs-opDon=nodeNumber,valueName,value,type
-opGon=7,filename,"/tmp/new-molprops.csv",String (int,doubleorString)
FindthenodenumberintheconfiguraGonpanelheader(addthemetanodenumbers)
eg123/456/78forthenode78inthemetanode456inthemetanode123
FindtheopGonnameintheworkspacedirectory:<workflow>/node_name(#7)/node.xml eg:
<configkey="DataURL">
<entrykey="array-size"type="xint"value="1"/>
<entrykey="0"type="xstring"value="/C:/serotonin_unique.sdf"/>
-opGon=2,DataURL\0,"file:/tmp/new-input.mae",String
Whentheinputisanarray
• Passsomevariables:-workflow.variable=name,value,type(int,doubleorString)
• WorkflowscanberunfromMaestrousingasimplePythonscriptwrapper
Tipsandtricks• Rearrangethepanels• WorkflowMeta-Infos• TrytoopenaworkflowmodifiedwithanewerversionofKNIMEalterthe2
followinglinesofthefile<workspace>/<workflow>/workflow.knime:<entrykey="created_by"type="xstring"value="2.0.3.0021120"/>
<entrykey="version"type="xstring"value="2.0.0"/>
KNIMEworkbenchnodes ◄ • EditvariablesandadvancedloopingfuncGonaliGes• HilitefuncGonaliGes• Databasenodes• Miscellaneoususefulnodes
EditvariablesandadvancedloopingfuncDonaliDes
• Extractvariable(data)andInjectvariable(data)• TableRowtoVariable(usethefirstrow),VariabletoTableRowandVariabletoTableColumn
HilitefuncDonaliDes• HiLitefilterandHiLitecollectornodes• Color,SizeandShapeManager/Appendernodes
Databasenodes• Seesimpleexamples(notontheWorkflowpageyet)
Timeseriessupport• Seesimpleexamples(notontheWorkflowpageyet)
Miscellaneousnodes:Cellspliker,Numericbinner• Referencerowfilter,Referencecolumnfilter,Nominalvaluerowfilter• Missingvalues• CreatecollecGoncolumnandSplitcollecGon• TextmanipulaGon:Stringreplacer,Caseconverter,Cellspli#er• Rowsampling,ParGGoning,Shuffle• Numericbinner
KNIMEworkflowexamples ◄
• KNIMEworkflowpage• Workflowdevelopmentsupportforcustomers• WorkflowexamplepresentaGon
Homologymodeling• ModelbuildingandrefinementLibrarydesign• LibraryenumeraGonincludingaRunMaestro1:1prototype
RealWorldExamples• VendordatabasepreparaGonGeneraltools• Pythonscriptnodeuse-casesincludingaRunPyMOLprototype
• Chemistryexternaltoolnodeuse-cases• Runmaestrocommandnodeuse-cases• OutputcolumnstructureopGonphilosophyKNIMEworkbench• WorkflowsinthecurrentworkspaceKNIMEworkbench-looper• GroupLooperSimplest,mostexciDng,newandimprovedworkflows
KNIMEworkflowpage-h#p://www.schrodinger.com/knimeworkflows/
CheminformaDcs• SubstructureSearch• Clustering,diversityselecGon,similaritysearch• Databaseanalysis• MaximumCommonSubstructureDockingandpost-processing• ProteinpreparaGon andGlidegridgeneraGon• Dockingandscoring,Virtualscreening,Ensembledocking,Induced
FitDocking• Loopoverdockingparameters• ValidatedockingparametersPharmacophoremodeling• PhaseShapescreening• PhasehypothesisidenGficaGon• Phasedatabasescreening
MolecularMechanics• CompareconformaGonalsearchmethodsQuantummechanics
• ConformaGonalsearchandQMopGmizaGonUsingtheReportdesigner
WorkflowdevelopmentsupportforcustomersCombineorexpandtheworkflowexamples• Hierarchicalclusteringanddiversecompoundsfromeachcluster
WaiDngfornewnodestobedeveloped
• CombiGlidelibraryenumeraGon,MacroModelcoordinatescan(nowavailable)
• PCAonperresidueinteracGons (Chemistryexternaltoolnode)
• DistancemeasurementinproteinandrunscriptinMaestro,descriptorcalculaGon,createproteinmutants(Pythonscriptnode)
Specificworkflows• VariousMacroModelprotocolsusingthePythonnodeforaccessingadvancedfuncGonaliGes(egcontraints)
• PrimeMM-GB/SAonasetofcomplexes(liganddetecGon,flexibleresidues)• SimplifyingcompounddockingwithKNIME,Dr.RobertHappel,BoehringerIngelheim,Vienna
h#p://www.schrodinger.com/seminarprior/19/26/
• CrisGuimaraesMM-GB/SApaperreproducGonandimprovements
h#p://www.schrodinger.com/Download.php?type=seminarentry&type2=slides&ident=105
• ProteinpreparaGonprotocol
RealWorldCaseStudy:BindingSiteClusteringandEnsembleDocking
ReallifeapplicaDons...
WorkflowexamplepresentaDonFeelfreetorequestthisotherpresentaGonincluding:• Simpleexamples• MoreadvancedexamplesfromtheWorkflowpage• ScienGficallyrelevantapplicaGons
SchrödingerKNIMEExtensions
KNIMEExtensionsProductManager: Jean-ChristopheMozziconacci
VicePresidentofTechnology: VolkerEyrich([email protected])
MainDeveloper: RavikiranKuppuraj
andthePyDevdevelopmentteam
QA: SimonFoucher
TechnicalSupport: KatalinPhimister,PavelGolubkov
MarkeDng: JarredYacob
