Here, There And Everywhere - On Integrating KNIME · PDF fileHere, There And Everywhere - On...
Transcript of Here, There And Everywhere - On Integrating KNIME · PDF fileHere, 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
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?
M. Lee KNIME User Group Meeting 2014
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
M. Lee KNIME User Group Meeting 2014
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
M. Lee KNIME User Group Meeting 2014
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
M. Lee KNIME User Group Meeting 2014
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
M. Lee KNIME User Group Meeting 2014
Node Template: GenerateValidationData 10
Performance BoostRunning the computationin parallel on Linux cluster
Predict
Calculate Properties
M. Lee KNIME User Group Meeting 2014
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
M. Lee KNIME User Group Meeting 2014
Retrieve Kinase Selectivity Singlepoint Data 12
http://knimeServer/webportal/#/--SMDD_Portal/Kinase_Selectivity_Panel_Searches/
KS_Singlepoint
Collaboration with J. Moffat
Cmpd ID
M. Lee KNIME User Group Meeting 2014
Retrieve Kinase Selectivity Singlepoint Data 13
1234
2341
P1
P2
(KinaseX)
dummy
dummy
Cmpd ID
M. Lee KNIME User Group Meeting 2014
Execute A Workflow From The Principal Workflow 14
1234
2341
P1
P2
(KinaseX)
dummy
dummy
Cmpd ID
M. Lee KNIME User Group Meeting 2014
Execute A Workflow From The Principal Workflow 15
1234
2341
P1
P2
(KinaseX)
1234 2341
Kinase 1
Kinase 2
dummy
dummy
dummydummy
Cmpd ID
M. Lee KNIME User Group Meeting 2014
Execute A Workflow From The Principal Workflow 16
http://knimeServer/webportal/#/--Webservices/Kinase_Selectivity/
KS_GNumber_report&wv:ui_gnumber=1234,2341 &run &single
1234 2341
Kinase 1
Kinase 2
dummydummy
M. Lee KNIME User Group Meeting 2014
Execute A Workflow From The Principal Workflow 17
knimeServer/webportal/#/--SMDD_Portal/Kinase_Selectivity_Panel_Searches/KS_Singlepoint?exec=
M. Lee KNIME User Group Meeting 2014
Execute A Workflow From The Principal Workflow 18
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
M. Lee KNIME User Group Meeting 2014
Generate The Report Page Of The Principal Workflow 23
‘http://knimeServer/webportal/#/’
‘—Websrvies/Kinase_Selectivity/KS_Gnumber_report’
‘&wv:ui_gnumber=‘ + gnums + ‘&run&single’;
M. Lee KNIME User Group Meeting 2014
Kinase Report With JavaScript 25
1234
2341
P1
P2
(KinaseX )
dummy
dummy
Cmpd ID
M. Lee KNIME User Group Meeting 2014
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
M. Lee KNIME User Group Meeting 2014
Project Vortex Session 27
Comp chemists create Vortex sessions for their proj ect teams.
M. Lee KNIME User Group Meeting 2014
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?
M. Lee KNIME User Group Meeting 2014
iMatch – User’s Perspective 29
C. Goliva
Call KNIME workflow
Call Vortex iMatch Script
M. Lee KNIME User Group Meeting 2014
http://knimeSMDDWeb/KnimeWSExecutor
?action=EXECUTE&invocationMode=Synchronous
&launchURL=...&selectedWF../iMatch_webservice
&__UI__HIDDEN__username=manle&...
iMatch – Behind The Scene 30
C. Goliva
M. Lee KNIME User Group Meeting 2014
http://knimeSMDDWeb/KnimeWSExecutor
?action=EXECUTE&invocationMode=Synchronous
&launchURL=...&selectedWF../iMatch_webservice
&__UI__HIDDEN__username=manle&...
iMatch – Behind The Scene 31
C. Goliva
Submitrequest toknimeSMDDWeb
M. Lee KNIME User Group Meeting 2014
http://knimeSMDDWeb/KnimeWSExecutor
?action=EXECUTE&invocationMode=Synchronous
&launchURL=...&selectedWF../iMatch_webservice
&__UI__HIDDEN__username=manle&...
iMatch – Behind The Scene 32
C. Goliva
ExecuteKNIME workflow
Submitrequest toknimeSMDDWeb
M. Lee KNIME User Group Meeting 2014
iMatch Workflow – Top Tier 33
Collaboration with C. Goliva, K. P. Clark, B. Wei, A. Gobbi
Write error message to a file for the knimeSMDDWeb t o pick up !
M. Lee KNIME User Group Meeting 2014
iMatch – Supervised Molecular Matched Pair Analysis 34
Collaboration with C. Goliva, K. P. Clark, B. Wei, A. Gobbi
Exposing workflows in context where they are needed !
M. Lee KNIME User Group Meeting 2014
Take Home Message: Use URL to call KNIME Workflows 35
�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
SMDIDashboard
KNIMEWebportal
LinuxKNIME
Webportal
SMDIDashboard
KNIMEWebportal
KNIMEWebportal
VortexSMDDWeb
KNIMEServer
LinuxKNIMEServer
VortexSMDDWeb
M. Lee KNIME User Group Meeting 2014
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)