Konstanz Information Miner (KNIME)

AnEvaluation Study

Vijay Jayaraman Duraiswamy

Why Knime

Approach for Evaluation

Demo

Goals, Challenges & Open Issues

Summary

Agenda

Introduction to Knime

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?

Functions of Prime Importance

• Excel• Database• SDF

I/O Access

• SDF File extraction

• Molecular Data Access

Basic Chemistry

• SOAP• Sharepoint

Integration

Scalability

• Limited User intervention

• Server Based access

Web Port Functionality

Features of Knime

KNIME

Machine Learning

Data Mining

Predictive Analytics

Life Sciences

Image Processing

Knime Extensions

Approach

Input - Excel

Output - CSV/HTML

Database Access

Read/Write/ Update

SDF File input and Calculate

Mol. Wt and Formula

Web Service

integration using WSDL

Protocol 1 - Metabolism Plate Preparation

OutputsInstrument File – CSV & HTML

Necessary Instrument

Information

Formula & Standards Formula.

ESM Platemap

File

Video 1

Protocol 1 – Outputs

• KNIME LabsRead/Write Excel,

CSV, HTML

• Cell Splitter & Concatenate nodes

Slice and Dice Data

• Data processing is handled through Java Snippets

Open Issues

Protocol 1 – Goals, Challenges & Open Issues

Protocol 2 - Purif Accord Loader

SD File

Data from

Database

Outputs

Database Inserts of Structures and

Tabular Data

Video 2

• SDF Reader and Database Reader

Read / Extract SDF & Update Database

• Molecular Properties NodesExtracting Molecular data

• No Node to capture molecular formula

Open Issues

Protocol 2 – Goals, Challenges & Open Issues

Protocol 3 – Automate LIMS Requesting

Web Services

Accord File

Outputs Database Inserts of

Structures and Tabular Data Creating LIMS

Request

Protocol 3 – Goals, Challenges & Open Issues

• Generic Web Service ClientRead BioRails/ LIMS WSDL

• RPC Encoded WSDL not SupportedOpen Issues

Enterprise Server Demo

Video 3

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 done through DB query node

HTML Write

Molecular Wt Calc

Molecular Formula Calc

Did not investigate all chemistry plugins to find this functionality

PDF Report

Web Portal

Summary

Conclusions

Evaluation

• Basic Functions• Comparable Web Portal• Migration of Utilities

Pending investigation

• Chemistry Extensions• Large Volumes of Data• SharePoint integration• Sophisticated Reporting• Enumeration

Next Steps

• SDI evaluation Results• In-depth analysis (?)• Migration of apps (?)• Local server Installation (?)

Thank You

References

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

Kindly do not use the presentation for commercial purposes.