Here, There And Everywhere - On Integrating KNIME Workflows Man-Ling Lee

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1 Here, There And Everywhere - On Integrating KNIME Workflows Man-Ling Lee KNIME User Group Meeting 02/13/2014

2 Tools Used In Drug Discovery 2

3 Tools Used In Drug Discovery 3

4 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?

5 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

6 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

wrapped as Java program Commercial software wrapped as Java program

7 Start A KNIME Workflow From SMDI Application Dashboard 7 Use URL to start a workflow --SMDD_Portal/DMPK_Model_Validation/ PPB_Models

8 PPB Model Validation Application 8 Project 1 Cmpd ID none DMPK_Validation/ _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

Project 6 Project 7 Project 8 Project 1 Cmpd ID none Users can evaluate or

9 PPB Model Validation Workflow 9 GUI Compute GUI

10 Node Template: GenerateValidationData 10 Predict Performance Boost Running the computation in parallel on Linux cluster Calculate Properties

11 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

12 Retrieve Kinase Selectivity Singlepoint Data SMDD_Portal/Kinase_Selectivity_Panel_Searches/ KS_Singlepoint Cmpd ID Collaboration with J. Moffat

13 Retrieve Kinase Selectivity Singlepoint Data 13 Cmpd ID (KinaseX) dummy 1234 P1 dummy 2341 P2

14 Execute A Workflow From The Principal Workflow 14 Cmpd ID (KinaseX) dummy 1234 P1 dummy 2341 P2

15 Execute A Workflow From The Principal Workflow 15 Cmpd ID (KinaseX) dummy 1234 P1 dummy dummy dummy 2341 P Kinase 1 Kinase 2

16 Execute A Workflow From The Principal Workflow Webservices/Kinase_Selectivity/ KS_GNumber_report &wv:ui_gnumber=1234,2341&run&single dummy dummy Kinase 1 Kinase 2

17 Execute A Workflow From The Principal Workflow 17 knimeserver/webportal/#/--smdd_portal/kinase_selectivity_panel_searches/ks_singlepoint?exec=

18 Execute A Workflow From The Principal Workflow 18 knimeserver/webportal/#/--webservices/kinase_selectivity/ks_gnumber_report?exec=63e485790a --Webservices/Kinase_Selectivity/KS_GNumber_report &wv:ui_gnumber=1234,2341&run&single

19 Generate The Report Page Of The Principal Workflow 19

20 Generate The Report Page Of The Principal Workflow 20

21 Generate The Report Page Of The Principal Workflow 21

22 Generate The Report Page Of The Principal Workflow 22

23 Generate The Report Page Of The Principal Workflow 23 Websrvies/Kinase_Selectivity/KS_Gnumber_report &wv:ui_gnumber= + gnums + &run&single ;

24 Generate The Report Page Of The Principal Workflow 24

25 Kinase Report With JavaScript 25 Cmpd ID (KinaseX) dummy 1234 P1 dummy 2341 P2

26 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

27 Project Vortex Session 27 Comp chemists create Vortex sessions for their project teams.

28 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

29 imatch User s Perspective 29 Call Vortex imatch Script Call KNIME workflow C. Goliva

30 imatch Behind The Scene 30 &launchurl=...&selectedwf../imatch_webservice & UI HIDDEN username=manle&... C. Goliva

31 imatch Behind The Scene 31 &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=.

32 imatch Behind The Scene 32 &launchurl=...&selectedwf../imatch_webservice & UI HIDDEN username=manle&... Submit request to knimesmddweb Execute KNIME workflow C. Goliva

33 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

34 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

35 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

36 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)

38 Unix Command For Computing PPB Model Prediction 38

What s Cooking in KNIME

What s Cooking in KNIME Thomas Gabriel Copyright 2015 KNIME.com AG Agenda Querying NoSQL Databases Database Improvements & Big Data Copyright 2015 KNIME.com AG 2 Querying NoSQL Databases MongoDB & CouchDB