Company Confidential

© 2014 Eli Lilly and Company

KNIME Nodes Update

KNIME UGM - Zurich 2014

• Last release late 2011

• Major internal refactoring since then

• Planed new release mid 2014

• Pending legal agreement/sign off

• Few final refactoring issues (Molecule type)

• Aiming for further meaningful periodic updates to include

• Utilisation of KNIME molecular container type

• Bug fixes (especially for new nodes)

• feature requests where aligned with internal development

aims

• New nodes suitable for opensource release

KNIME Nodes

Internal & Opensource Code Evolution

Opensource

Nodes

Lilly

Nodes

Internal

Lilly Nodes Lilly Internal Nodes

Multiple Developer

Groups

Consolidation

Tests

Infrastructure Authentication

Refactoring

2012

2013

Multiple Projects

2011

2014

Lilly

Nodes

Open

Source

Open

Source

Release

Open

Source

Release

Nodes 2011 2014

9 Nodes Deprecated

5 Nodes Branched

• 9 Nodes deprecated due complexity of ongoing support

• 5 Nodes associated with Reaction Vectors have been updated significantly by James Wallace at Sheffield University

• Lilly will help support James as he releases these nodes independently

• We’ll maintain support for the Desirability and Pareto Ranking Nodes that are necessary/useful with the reaction vectors code

• All nodes updated (bugs/features)

Nodes 2011 2014

Mutiple New Nodes • Core (non-node) code associated with

Webservice authentication released to KNIME.com for NTLM Auth including sharepoint

• 3 new Nodes released to handle authentication (File list, read, write)

• Molecule Difference Checker Node (Testing)

• Multi-molecule Chemical Sketcher

• Improved Matched Pairs node (Replaces Matched Pairs Detector & Finder)

• Free-Wilson Matched Pairs Node

• Atom Selector Node

• PBF (Plane of Best Fit) Node

Multi-molecule sketcher

• Based on Marvin sketcher

• Configure to sketch and edit multiple structures or reactions

• Output multiple structures (port_0) or reactions (port_1) on node execution

• Internally reuse code for sketcher applet in webportal

Matched Pairs Node

• Multiple bugs fixed (e.g.:

MolID set to RowID causes

null pointer)

• UI enhancements (layout

and scroll bars)

• Option to specify atom

attachment point format

(useful for later enumeration)

• More control over the format

of the property / activity data

comparison for each pair

(R/L & R-L or L/R & L-R)

Plane of Best Fit Node

• Plane of best fit (PBF) - quantitative

measure of how far removed a

molecule is from a flat 2D plane.

• PBF node can calculate Plane of Best

Fit values from SDF input.

• Option to include or remove

Hydrogen's in calculation.

J. Chem. Inf. Model., 2012, 52 (10), pp 2516–2525

• Designed for our internal test system but has other utilities

• Compares molecule columns on input tables • Row by row comparison of all molecule type columns (sort sensitive)

• Immediately fails if number of rows different or molecules in row are different

• Reports first that shows a different molecule

• Uses Chemaxon molecule “isSimilarTo”

• Node output: Input tables with Mol columns removed for further difference checking

• Suggestions / enhancements welcome • Could easily extend to specific Molecule Difference Node

Molecule Difference Checker

INFO

MoleculeDifferenceCheckerNodeMo

del Including molecule column

Molecule

ERROR Molecule Difference

Checker Execute failed: Cell

content differs in row #1('Row1')

column #0('Molecule'): CellPort0=‘

---print SDF block here---

'

List / Download / Write Files

with Authentication

• Generic Webservice node enhanced to

handle NTLM authentication . Code

released to KNIME.com • Option to retrieve raw XML output allows crude

SharePoint integration

• Authenticated file list/read/write nodes can

access protected windows network shares • Upload/Download nodes simply copy any existing

file type on/off network share. Extension of

KNIME.com list files nodes

• Need network.credentials (see also preferences)

• Further enhances server usage where workflows

utilise ‘computer’ accounts and non public,

scheduled workflows to automate many tasks

(e.g.: AT instrumentation dashboard presented at

KNIME London UGM)

• All utilise Java CIFS Client Library -

http://jcifs.samba.org/

Excel Writer (a)

• Old but very popular in house

feature. Can define colour range

values for individual columns on

XLS write

Excel Writer (b)

• New feature allows write of merged cells and write to authenticated

file share. Simple functionality opens up full integration of Roambi

mobile reporting. KNIME Server automates workflow execution and

writes xls files formatted for Roambi to push to mobile device

http://www.roambi.com/

Web viewer panel

• Web Viewer panel

allows display of

internal or external

webpage

• Used for internal

support by pointing

to Lilly ‘service layer

dashboard’

• Preferences panel

allows user to set

URL and optional

refresh interval

• Mike Bodkin’s C3 UK Group • Original Code base by Mike’s group, particularly Niko Fechner

• Testing & Multiple ongoing features/bug requests

• Roger Robinson • Plane of Best Fit Node

• Simon Richards • Testing & Multiple ongoing features/bug requests

• Luke Bullard • Complete Refactoring and code standardisation (sonar rules) 2012-2014

• Core Authentication Code for NTLM auth

• Many Node enhancements & Bug fixes

• Tom Wilkin • Authenticated File List/Read/Write

• Molecule Difference Checker

• Dashboard

• Gary Sharman • 2D/3D Scatterplot & bug fixes

Acknowledgements