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8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 1/23
AnEvaluation Study
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 2/23
Why Knime
Approach for Evaluation
Demo
Goals, Challenges & Open Issues
Summary
Agenda
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 3/23
Introduction to Knime
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 4/23
Scitegic Pipeline Pilot Alternative
Lower cost of Product and Support
Open Source Platform with GPL license
Frankfurt Investigation Underway
Feasibility Analysis and impact of Migration
Why Knime?
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 5/23
Functions of Prime Importance
• Excel • Database
• SDF
I/O Access
• SDF Fileextraction
• MolecularData Access
BasicChemistry
• SOAP
• SharepointIntegration
Scalability
• Limited User
intervention• Server Based
access
Web PortFunctionality
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 6/23
Features of Knime
KNIME
MachineLearning
Data
Mining
PredictiveAnalytics
LifeSciences
Image
Processing
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 7/23
Knime Extensions
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 8/23
Approach
Input -Excel
Output -CSV/HTML
DatabaseAccess
Read/Write/ Update
SDF File
input andCalculate
Mol. Wt andFormula
Web
Serviceintegration
usingWSDL
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 9/23
Protocol 1 - Metabolism Plate Preparation
OutputsInstrument File – CSV & HTML
Necessary
InstrumentInformation
Formula &StandardsFormula.
ESMPlatemap
File
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 10/23
Video 1
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 11/23
Protocol 1 – Outputs
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 12/23
• KNIME LabsRead/Write Excel,CSV, HTML
• Cell Splitter & Concatenatenodes
Slice and DiceData
• Data processing is handledthrough Java Snippets
Open Issues
Protocol 1 – Goals, Challenges & Open Issues
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 13/23
Protocol 2 - Purif Accord Loader
SD File
Data
fromDatabase
OutputsDatabase Insertsof Structures and
Tabular Data
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 14/23
Video 2
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 15/23
• SDF Reader and DatabaseReader
Read / Extract SDF& UpdateDatabase
• Molecular Properties NodesExtractingMolecular data
•No Node to capturemolecular formulaOpen Issues
Protocol 2 – Goals, Challenges & Open Issues
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 16/23
Protocol 3 – Automate LIMS Requesting
WebServices
Accord
File
Outputs Database
Inserts ofStructures andTabular Data
Creating LIMSRequest
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 17/23
Protocol 3 – Goals, Challenges & Open Issues
• Generic Web Service ClientRead BioRails/
LIMS WSDL
• RPC Encoded WSDL notSupportedOpen Issues
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 18/23
Enterprise Server Demo
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 19/23
Video 3
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 20/23
Demonstrated Assumed Unsure Comments
Excel read/Write
CSV
SDF Read
SDF Write SDF Read/Write nodes available.
Accord Read/Write Not a Native node, most likely to be a
vendor extension
DB Read/Insert/ Update
DB Delete DB Delete is assumed to be donethrough DB query node
HTML Write
Molecular Wt Calc
Molecular FormulaCalc
Did not investigate all chemistryplugins to find this functionality
PDF Report
Web Portal
Summary
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 21/23
Conclusions
Evaluation
• Basic Functions
• Comparable Web Portal
• Migration of Utilities
Pendinginvestigation
• Chemistry Extensions
• Large Volumes of Data
• SharePoint integration
• Sophisticated Reporting
• Enumeration
NextSteps
• SDI evaluation Results
• In-depth analysis (?)
• Migration of apps (?)
• Local server Installation (?)
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 22/23
Thank You
8/3/2019 Knime Evaluation Des
http://slidepdf.com/reader/full/knime-evaluation-des 23/23
References
• www.knime.org • T. Naumann’s Presentation on Knime Vs. Scitegic