here, there and everywhere - on integrating knime workflows · here, there and everywhere - on...

Here, There And Everywhere -On Integrating KNIME Workflows

Man-Ling Lee

KNIME User Group Meeting 02/13/2014

M. Lee KNIME User Group Meeting 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 programCommercial software wrapped as Java program

Commercial software

PHP program

Commercial software

Collaboration with C. Lu, J. Wolny


Start A KNIME Workflow From SMDI Application Dashbo ard 7

http://knimeServer/webportal/#/--SMDD_Portal/DMPK_Model_Validation/

PPB_Models

☺Use URL to start a workflow


PPB Model Validation Application 8

Collaboration with I. Aligas, A. Gobbi

Users can evaluate or compare the quality of models

using the data set of their interest

Project 1Project 2Project 3Project 4Project 6Project 7Project 8

none

Project 1

Cmpd ID_____none

Project 1

DMPK_Validation/123445678_345678/

Cmpd ID


PPB Model Validation Workflow 9

GUI GUICompute


Node Template: GenerateValidationData 10

Performance BoostRunning the computationin parallel on Linux cluster

Predict

Calculate Properties


Retrieve Kinase Selectivity Singlepoint Data 12

http://knimeServer/webportal/#/--SMDD_Portal/Kinase_Selectivity_Panel_Searches/

KS_Singlepoint

Collaboration with J. Moffat

Cmpd ID


Retrieve Kinase Selectivity Singlepoint Data 13

1234

2341

P1

P2

(KinaseX)

dummy

dummy

Cmpd ID


Execute A Workflow From The Principal Workflow 14

1234

2341

P1

P2

(KinaseX)

dummy

dummy

Cmpd ID



1234

2341

P1

P2

(KinaseX)

1234 2341

Kinase 1

Kinase 2

dummy

dummy

dummydummy

Cmpd ID



http://knimeServer/webportal/#/--Webservices/Kinase_Selectivity/

KS_GNumber_report&wv:ui_gnumber=1234,2341 &run &single

1234 2341

Kinase 1

Kinase 2

dummydummy



knimeServer/webportal/#/--SMDD_Portal/Kinase_Selectivity_Panel_Searches/KS_Singlepoint?exec=



http://knimeServer/webportal/#/--Webservices/Kinase_Selectivity/KS_GNumber_report

&wv:ui_gnumber=1234,2341 &run &single

knimeServer/webportal/#/--Webservices/Kinase_Selectivity/KS_Gnumber_report?exec=63e485790a


Generate The Report Page Of The Principal Workflow 19



‘http://knimeServer/webportal/#/’

‘—Websrvies/Kinase_Selectivity/KS_Gnumber_report’

‘&wv:ui_gnumber=‘ + gnums + ‘&run&single’;


Kinase Report With JavaScript 25

1234

2341

P1

P2

(KinaseX )

dummy

dummy

Cmpd ID


Project Vortex Session 27

Comp chemists create Vortex sessions for their proj ect teams.


iMatch – Supervised Molecular Matched Pair Analysis 28

Collaboration with C. Goliva, K. P. Clark, B. Wei, A. Gobbi

Does the change in core structure affect molecules’ properties?


iMatch – User’s Perspective 29

C. Goliva

Call KNIME workflow

Call Vortex iMatch Script


http://knimeSMDDWeb/KnimeWSExecutor

?action=EXECUTE&invocationMode=Synchronous

&launchURL=...&selectedWF../iMatch_webservice

&__UI__HIDDEN__username=manle&...

iMatch – Behind The Scene 30

C. Goliva







C. Goliva

Submitrequest toknimeSMDDWeb







C. Goliva

ExecuteKNIME workflow

Submitrequest toknimeSMDDWeb


iMatch Workflow – Top Tier 33


Write error message to a file for the knimeSMDDWeb t o pick up !


iMatch – Supervised Molecular Matched Pair Analysis 34


Exposing workflows in context where they are needed !


Take Home Message: Use URL to call KNIME Workflows 35




SMDIDashboard

KNIMEWebportal

LinuxKNIME

Webportal

SMDIDashboard

KNIMEWebportal

KNIMEWebportal

VortexSMDDWeb

KNIMEServer

LinuxKNIMEServer

VortexSMDDWeb


Acknowledgements 36

Application DevelopmentIgnacio AliagasKevin P. ClarkAlberto Gobbi

Chandra GolivaChinchih LuJohn MoffatBinQing Wei

Jakub Wolny (Roche ADMD)

Technical SupportSlaton LipscombSimran Hansrai

Thomas Gabriel (KNIME.com)Bernd Wieswedel (KNIME.com)


Unix Command For Computing PPB Model Prediction 38

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