Knime Evaluation Smaller
description
Transcript of Knime Evaluation Smaller
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.