Lilly Workflow Now Available From KNIME Example Flow Server

Hi All,

I am pleased to announce that the workflow which was designed by Eli Lilly UK as part of the 5th KNIME UGM Meeting 1-3rd February 2012 is now available for download from the KNIME Example Workflow Server under 050_Applications and called 050006_ComplexSARAnalysis. The purpose of the workflow is to showcase the use of a number of chemistry related nodes from Erlwood Lilly UK, RDKit, and Indigo and how these can be combined together with the KNIME core nodes to provide real Medicinal Chemistry applications.

Workflow requires KNIME release v2.5.4 or higher, and uses a number of community nodes which must be installed in KNIME prior to usage;

- Erlwood Lilly nodes,
- RDKit nodes,
- Indigo nodes.

These nodes are highlighted with various colours inside the workflow.

Notes are provided in the workflow in light yellow and dark blue annotation boxes to try and explain the process in the workflow.


The applications this workflow provides are;

- Use of 2D/3D Viewer to measure R2 correlations.


- Use of Merging two datasets together.


- Murcko Scaffold and Carbon Framework Generation, as well as KNIME Hiliting.


- Generating Automatically Structural Matched Pairs.


- Generating Free Wilson Matrix for further SAR Analysis including;
     - Matched Pairs,

     - Substructure Searching via either RDKit or Indigo nodes,

     - Functional Group Trend Analysis.


- Generating Similarity Matched Pairs using Fingerprints.


- Generating Common Scaffolds using Clustering and Fingerprints.

 

Many thanks, and please enjoy the workflow.


Simon Richards, Eli Lilly UK.

Dear Simon,

Many thanks for this very useful workflow.  I have one question, all of the groupby nodes seem to have failed.  Any ideas on what might be the problem?  I get the following errors in the Knime console when I try and load the workflow.

Thanks,

A

 

ERROR     LoadWorkflowRunnable     Errors during load: Status: Error: Lilly_ComplexSARAnalysis 0:0 loaded with errors
ERROR     LoadWorkflowRunnable       Status: Error: Lilly_ComplexSARAnalysis 0:0
ERROR     LoadWorkflowRunnable         Status: Warning: Customized MetaNode 0:0:656
ERROR     LoadWorkflowRunnable           Status: Warning: MetaNode 1 : 1 0:0:656:467
ERROR     LoadWorkflowRunnable             Status: Warning: State has changed from EXECUTED to CONFIGURED
ERROR     LoadWorkflowRunnable           Status: Warning: Customized MetaNode 0:0:656:470
ERROR     LoadWorkflowRunnable             Status: Warning: Customized MetaNode 0:0:656:470:317
ERROR     LoadWorkflowRunnable               Status: Warning: MolConverter 0:0:656:470:317:305
ERROR     LoadWorkflowRunnable                 Status: Warning: Loading model settings failed: String for key "outoption" not found.
ERROR     LoadWorkflowRunnable               Status: Warning: MolConverter 0:0:656:470:317:306
ERROR     LoadWorkflowRunnable                 Status: Warning: Loading model settings failed: String for key "outoption" not found.
ERROR     LoadWorkflowRunnable           Status: Warning: Customized MetaNode 0:0:656:468
ERROR     LoadWorkflowRunnable             Status: Warning: Customized MetaNode 0:0:656:468:317
ERROR     LoadWorkflowRunnable               Status: Warning: MolConverter 0:0:656:468:317:305
ERROR     LoadWorkflowRunnable                 Status: Warning: Loading model settings failed: String for key "outoption" not found.
ERROR     LoadWorkflowRunnable               Status: Warning: MolConverter 0:0:656:468:317:306
ERROR     LoadWorkflowRunnable                 Status: Warning: Loading model settings failed: String for key "outoption" not found.
ERROR     LoadWorkflowRunnable         Status: Error: Customized MetaNode 0:0:657
ERROR     LoadWorkflowRunnable           Status: Warning: MetaNode 1 : 1 0:0:657:469
ERROR     LoadWorkflowRunnable             Status: Warning: MolConverter 0:0:657:469:309
ERROR     LoadWorkflowRunnable               Status: Warning: Loading model settings failed: String for key "outoption" not found.
ERROR     LoadWorkflowRunnable           Status: Error: Some node states were invalid
ERROR     LoadWorkflowRunnable         Status: Warning: Customized MetaNode 0:0:655
ERROR     LoadWorkflowRunnable           Status: Warning: Customized MetaNode 0:0:655:317
ERROR     LoadWorkflowRunnable             Status: Warning: MolConverter 0:0:655:317:309
ERROR     LoadWorkflowRunnable               Status: Warning: Loading model settings failed: String for key "outoption" not found.
ERROR     LoadWorkflowRunnable             Status: Warning: MolConverter 0:0:655:317:313
ERROR     LoadWorkflowRunnable               Status: Warning: Loading model settings failed: String for key "outoption" not found.
ERROR     LoadWorkflowRunnable         Status: Error: Some node states were invalid
ERROR     LoadWorkflowRunnable       Status: Error: Some node states were invalid

I uploaded the workflow again in 2.5 format (you will get an error while loading about some states of metanodes having changed; this is a bug that will be fixed in 2.6 but doesn't affect the functionality of the workflow itself)

Hi Angus,

The initial workflow which was uploaded required KNIME 2.6 or later which is why the GroupBy nodes were failing.

Thanks to the KNIME team, the workflow has been reuploaded to the KNIME Public Server now supporting KNIME 2.5.4 or later.

Please delete the workflow you downloaded, and redownload it from the KNIME Public Server. All the nodes will now run smoothly.

 

Many thanks,

Simon.