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01. Flow Variable - solution

Flow Variables Solution

Solution for "Flow Variable" exercise for advanced Life Science User Training
- Filtering rows by an attribute value
- Filtering rows by an attribute value that fulfils a condition and that is updated automatically
- substructure search based on a drawn reference molecule

Activity II: Using Flow Variable for Substructure SearchThe goal of this exercise is to find all compounds from the dataset that match a certain substurcture and prepare the dataset within an interactiveview including molecule highlighting. The RDKit Substructure Filter node expects a SMARTS to be entered to do the search. Use the Table Row to Variable node to pass the the chemical structure drawn in the Marvin Sketch node tothe RDKit Substructure Filter node as a variable SMARTS. To do so, go to the Flow Variable Tab in the RDKitSubstructure Filter node and select as smarts value your variable SMARTS. Activity I: Flow Variables - Filter the compound data to 1. contain the compounds that were tested in the highest number of assays2. contain only compounds tested for AssayID "CHEMBL853187" Filtering by SelectionIn this exercise, we will use Flow Variables to overwrite node configurations. Step 1Use the Table Reader node to load theChEMBLID228_SERT_ligands.table Step 2.2Use the Value Selection Configuration nodeand set the Default Column to "assay_chembl_id" Step 2.3Use the Row Filter node and connect the FlowVariable port from the Value Selection Configurationnode with the Flow Variable port of the Row Filter node.- Column to Test: "assay_chembl_id"- use pattern matching: "value-selection" Step 1.2Use the GroupBy node to group all the assayfor each compound. Groupby"molecule_chembl_id" and count the"assay_chembl_id".Use the Sorter node to sort by count of assaysin a descending order. Step 1.3Use the Table Row to Variable nodeconvert the first row of the table toFlow Variables Step 1.4Use the Row Filter node with Columnto Test set to "molecule_chembl_id"and select the Flow Variable"molecule_chembl_id" to use aspattern matching. Step 1Use the Table Row to Variablenode convert the drawn moleculeto a Flow Variable Step 2Pass the Flow Variable "SMARTS"to the "smarts_value" in the FlowVariable Tab Step 2.4Create a Component containingthe Value Selection Configurationnode and the Row Filter node CHEMBLID228_SERT_ligands.table Action needed: Select some compounds!Draw a referencemolecule for the similaritysearch.You can also paste the following sequence:CC(=O)N1CCNCC1Add SMARTS to create a substructuresearch Table Reader Row Filter GroupBy Sorter Table Rowto Variable Row Filter RDKit Canon SMILES RDKit DescriptorCalculation Tile View MarvinSketch Renderer to Image RDKit SubstructureFilter Table Rowto Variable RDKit MoleculeHighlighting Table Reader Value SelectionConfiguration Assay Selection Activity II: Using Flow Variable for Substructure SearchThe goal of this exercise is to find all compounds from the dataset that match a certain substurcture and prepare the dataset within an interactiveview including molecule highlighting. The RDKit Substructure Filter node expects a SMARTS to be entered to do the search. Use the Table Row to Variable node to pass the the chemical structure drawn in the Marvin Sketch node tothe RDKit Substructure Filter node as a variable SMARTS. To do so, go to the Flow Variable Tab in the RDKitSubstructure Filter node and select as smarts value your variable SMARTS. Activity I: Flow Variables - Filter the compound data to 1. contain the compounds that were tested in the highest number of assays2. contain only compounds tested for AssayID "CHEMBL853187" Filtering by SelectionIn this exercise, we will use Flow Variables to overwrite node configurations. Step 1Use the Table Reader node to load theChEMBLID228_SERT_ligands.table Step 2.2Use the Value Selection Configuration nodeand set the Default Column to "assay_chembl_id" Step 2.3Use the Row Filter node and connect the FlowVariable port from the Value Selection Configurationnode with the Flow Variable port of the Row Filter node.- Column to Test: "assay_chembl_id"- use pattern matching: "value-selection" Step 1.2Use the GroupBy node to group all the assayfor each compound. Groupby"molecule_chembl_id" and count the"assay_chembl_id".Use the Sorter node to sort by count of assaysin a descending order. Step 1.3Use the Table Row to Variable nodeconvert the first row of the table toFlow Variables Step 1.4Use the Row Filter node with Columnto Test set to "molecule_chembl_id"and select the Flow Variable"molecule_chembl_id" to use aspattern matching. Step 1Use the Table Row to Variablenode convert the drawn moleculeto a Flow Variable Step 2Pass the Flow Variable "SMARTS"to the "smarts_value" in the FlowVariable Tab Step 2.4Create a Component containingthe Value Selection Configurationnode and the Row Filter node CHEMBLID228_SERT_ligands.table Action needed: Select some compounds!Draw a referencemolecule for the similaritysearch.You can also paste the following sequence:CC(=O)N1CCNCC1Add SMARTS to create a substructuresearch Table Reader Row Filter GroupBy Sorter Table Rowto Variable Row Filter RDKit Canon SMILES RDKit DescriptorCalculation Tile View MarvinSketch Renderer to Image RDKit SubstructureFilter Table Rowto Variable RDKit MoleculeHighlighting Table Reader Value SelectionConfiguration Assay Selection

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: glandrum
Created at: 2015-02-07
On NodePit since: 2021-01-15
Last update: 2024-12-21
Created with KNIME version: v4.2.3
Tags: flow variableconfigurationworkflow automationworkflow controlworkflow abstractioncomponentuser selectioneducationlife science

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