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AnEvaluation Study

 

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Why Knime

Approach for Evaluation

Demo

Goals, Challenges & Open Issues

Summary

Agenda

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Introduction to Knime

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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?

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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

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Features of Knime

KNIME

MachineLearning

Data

Mining

PredictiveAnalytics

LifeSciences

Image

Processing 

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Knime Extensions

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Approach

Input -Excel

Output -CSV/HTML

DatabaseAccess

Read/Write/ Update

SDF File

input andCalculate 

Mol. Wt andFormula

Web

Serviceintegration

usingWSDL

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Protocol 1 - Metabolism Plate Preparation

OutputsInstrument File  – CSV & HTML

Necessary

InstrumentInformation

Formula &StandardsFormula.

ESMPlatemap

File

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Video 1

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Protocol 1 – Outputs

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• 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

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Protocol 2 - Purif Accord Loader

SD File

Data

fromDatabase

OutputsDatabase Insertsof Structures and

Tabular Data

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Video 2

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• SDF Reader and DatabaseReader

Read / Extract SDF& UpdateDatabase

• Molecular Properties NodesExtractingMolecular data

•No Node to capturemolecular formulaOpen Issues

Protocol 2 – Goals, Challenges & Open Issues

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Protocol 3 – Automate LIMS Requesting

WebServices

Accord

File

Outputs Database

Inserts ofStructures andTabular Data

Creating LIMSRequest 

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Protocol 3 – Goals, Challenges & Open Issues

• Generic Web Service ClientRead BioRails/ 

LIMS WSDL

• RPC Encoded WSDL notSupportedOpen Issues 

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Enterprise Server Demo

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Video 3

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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

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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 (?)

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Thank You

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References

• www.knime.org • T. Naumann’s Presentation on Knime Vs. Scitegic