Here, There And Everywhere - On Integrating KNIME Workflows Man-Ling Lee KNIME User Group Meeting 02/13/2014
Tools Used In Drug Discovery 2
Tools Used In Drug Discovery 3
KNIME WebPortal 4 Good entry point for KNIME workflows Not all tools are KNIME workflows Any alternative ways to expose KNIME workflows along with other tools?
Three Ways Of Accessing KNIME Workflows 5 Here - Start a workflow from SMDI Application Dashboard There - Execute a workflow from another KNIME workflow Everywhere - Execute a workflow as a web service from Vortex
SMDI Application Dashboard 6 One entry point for SMDD applications and documents KNIME workflows Java program KNIME workflows Commercial software wrapped as Java program Commercial software wrapped as Java program Commercial software Commercial software PHP program Collaboration with C. Lu, J. Wolny
Start A KNIME Workflow From SMDI Application Dashboard 7 Use URL to start a workflow http://knimeserver/webportal/#/ --SMDD_Portal/DMPK_Model_Validation/ PPB_Models
PPB Model Validation Application 8 Project 1 Cmpd ID none DMPK_Validation/123445678_345678/ Project 1 Project 2 Project 3 Project 4 Project 6 Project 7 Project 8 Project 1 Cmpd ID none Users can evaluate or compare the quality of models using the data set of their interest Collaboration with I. Aligas, A. Gobbi
PPB Model Validation Workflow 9 GUI Compute GUI
Node Template: GenerateValidationData 10 Predict Performance Boost Running the computation in parallel on Linux cluster Calculate Properties
Three Ways Of Accessing KNIME Workflows 11 Here - Start a workflow from SMDI Application Dashboard There - Execute a workflow from another KNIME workflow Everywhere - Execute a workflow as a web service from Vortex
Retrieve Kinase Selectivity Singlepoint Data 12 http://knimeserver/webportal/#/ --SMDD_Portal/Kinase_Selectivity_Panel_Searches/ KS_Singlepoint Cmpd ID Collaboration with J. Moffat
Retrieve Kinase Selectivity Singlepoint Data 13 Cmpd ID (KinaseX) dummy 1234 P1 dummy 2341 P2
Execute A Workflow From The Principal Workflow 14 Cmpd ID (KinaseX) dummy 1234 P1 dummy 2341 P2
Execute A Workflow From The Principal Workflow 15 Cmpd ID (KinaseX) dummy 1234 P1 dummy dummy dummy 2341 P2 1234 2341 Kinase 1 Kinase 2
Execute A Workflow From The Principal Workflow 16 http://knimeserver/webportal/#/ --Webservices/Kinase_Selectivity/ KS_GNumber_report &wv:ui_gnumber=1234,2341&run&single dummy dummy 1234 2341 Kinase 1 Kinase 2
Execute A Workflow From The Principal Workflow 17 knimeserver/webportal/#/--smdd_portal/kinase_selectivity_panel_searches/ks_singlepoint?exec=
Execute A Workflow From The Principal Workflow 18 knimeserver/webportal/#/--webservices/kinase_selectivity/ks_gnumber_report?exec=63e485790a http://knimeserver/webportal/#/ --Webservices/Kinase_Selectivity/KS_GNumber_report &wv:ui_gnumber=1234,2341&run&single
Generate The Report Page Of The Principal Workflow 19
Generate The Report Page Of The Principal Workflow 20
Generate The Report Page Of The Principal Workflow 21
Generate The Report Page Of The Principal Workflow 22
Generate The Report Page Of The Principal Workflow 23 http://knimeserver/webportal/#/ Websrvies/Kinase_Selectivity/KS_Gnumber_report &wv:ui_gnumber= + gnums + &run&single ;
Generate The Report Page Of The Principal Workflow 24
Kinase Report With JavaScript 25 Cmpd ID (KinaseX) dummy 1234 P1 dummy 2341 P2
Three Ways Of Accessing KNIME Workflows 26 Here - Start a workflow from SMDI Application Dashboard There - Execute a workflow from another KNIME workflow Everywhere - Execute a workflow as a web service from Vortex
Project Vortex Session 27 Comp chemists create Vortex sessions for their project teams.
imatch Supervised Molecular Matched Pair Analysis 28 Does the change in core structure affect molecules properties? Collaboration with C. Goliva, K. P. Clark, B. Wei, A. Gobbi
imatch User s Perspective 29 Call Vortex imatch Script Call KNIME workflow C. Goliva
imatch Behind The Scene 30 http://knimesmddweb/knimewsexecutor?action=execute&invocationmode=synchronous &launchurl=...&selectedwf../imatch_webservice & UI HIDDEN username=manle&... C. Goliva
imatch Behind The Scene 31 http://knimesmddweb/knimewsexecutor?action=execute&invocationmode=synchronous &launchurl=...&selectedwf../imatch_webservice & UI HIDDEN username=manle&... Submit request to knimesmddweb C. Goliva
imatch Behind The Scene 32 http://knimesmddweb/knimewsexecutor?action=execute&invocationmode=synchronous &launchurl=...&selectedwf../imatch_webservice & UI HIDDEN username=manle&... Submit request to knimesmddweb Execute KNIME workflow C. Goliva
imatch Workflow Top Tier 33 Write error message to a file for the knimesmddweb to pick up! Collaboration with C. Goliva, K. P. Clark, B. Wei, A. Gobbi
imatch Supervised Molecular Matched Pair Analysis 34 Exposing workflows in context where they are needed! Collaboration with C. Goliva, K. P. Clark, B. Wei, A. Gobbi
Take Home Message: Use URL to call KNIME Workflows 35 Here - Start a workflow from SMDI Application Dashboard SMDI Dashboard KNIME Webportal Linux KNIME Webportal There - Execute a workflow from another KNIME workflow SMDI Dashboard KNIME Webportal KNIME Webportal Everywhere - Execute a workflow as a web service from Vortex Vortex SMDD Web KNIME Server Linux KNIME Server SMDD Web Vortex
Acknowledgements 36 Application Development Ignacio Aliagas Kevin P. Clark Alberto Gobbi Chandra Goliva Chinchih Lu John Moffat BinQing Wei Jakub Wolny (Roche ADMD) Technical Support Slaton Lipscomb Simran Hansrai Thomas Gabriel (KNIME.com) Bernd Wieswedel (KNIME.com)
Unix Command For Computing PPB Model Prediction 38