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01. Flow Variable

Flow Variables

"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. Write the found molecules into an Excel file, which contains the execution time in the file name. Step 1Use the Table Row to Variablenode convert the drawn moleculeto a Flow Variable 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 1.4Use 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 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 1Use the Table Reader node to load theChEMBLID228_SERT_ligands.table Step 2.4Create a Component containingthe Value Selection Configurationnode and the Row Filter node Step 2.2Use the Value Selection Configuration nodeand set the Default Column to "assay_chembl_id" Filtering by SelectionIn this exercise, we will use Flow Variables to overwrite node configurations. 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" Step 1.3Use the Table Row to Variable nodeconvert the first row of the table toFlow Variables 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 Molecular Sketchercomponent to the RDKit Substructure Filter node as a variable Output. To do so, go to the Flow Variable Tabin the RDKit Substructure Filter node and select as smarts value your variable Output. Step 2Pass the Flow Variable "Output" tothe "smarts_value" in the FlowVariable Tab Step 5Write the filtered table into a XLSXfile (Excel Writer node)Tip: Use the Path flow variable thatyou created in 5 Step 3Create a flow variable with theexecution date (Date&TimeConfiguration node)Tip: Select "Date" for the settingoption type and activate thecheckbox "Use execution time". Step 4Create a Path flow variable to savethe filtered product file in adirectory of your choice (CreateFile/Folder Variables node)Tip: select the base location, enterthe file extension and provide thefilename as a flow variable. Draw a referencemolecule for the similaritysearch in the interactive view.You can also paste the following sequence:CC(=O)N1CCNCC1 Action needed: Select some compounds!Add SMARTS to create a substructuresearchadd execution time to file name Molecular Sketcher RDKit Canon SMILES RDKit DescriptorCalculation Tile View Renderer to Image RDKit SubstructureFilter RDKit MoleculeHighlighting Table Reader String Manipulation(Variable) Column Filter 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. Write the found molecules into an Excel file, which contains the execution time in the file name. Step 1Use the Table Row to Variablenode convert the drawn moleculeto a Flow Variable 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 1.4Use 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 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 1Use the Table Reader node to load theChEMBLID228_SERT_ligands.table Step 2.4Create a Component containingthe Value Selection Configurationnode and the Row Filter node Step 2.2Use the Value Selection Configuration nodeand set the Default Column to "assay_chembl_id" Filtering by SelectionIn this exercise, we will use Flow Variables to overwrite node configurations. 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" Step 1.3Use the Table Row to Variable nodeconvert the first row of the table toFlow Variables 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 Molecular Sketchercomponent to the RDKit Substructure Filter node as a variable Output. To do so, go to the Flow Variable Tabin the RDKit Substructure Filter node and select as smarts value your variable Output. Step 2Pass the Flow Variable "Output" tothe "smarts_value" in the FlowVariable Tab Step 5Write the filtered table into a XLSXfile (Excel Writer node)Tip: Use the Path flow variable thatyou created in 5 Step 3Create a flow variable with theexecution date (Date&TimeConfiguration node)Tip: Select "Date" for the settingoption type and activate thecheckbox "Use execution time". Step 4Create a Path flow variable to savethe filtered product file in adirectory of your choice (CreateFile/Folder Variables node)Tip: select the base location, enterthe file extension and provide thefilename as a flow variable. Draw a referencemolecule for the similaritysearch in the interactive view.You can also paste the following sequence:CC(=O)N1CCNCC1 Action needed: Select some compounds!Add SMARTS to create a substructuresearchadd execution time to file name Molecular Sketcher RDKit Canon SMILES RDKit DescriptorCalculation Tile View Renderer to Image RDKit SubstructureFilter RDKit MoleculeHighlighting Table Reader String Manipulation(Variable) Column Filter

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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: 2024-01-14
Last update: 2024-11-21
Created with KNIME version: v4.6.1
Tags: flow variableconfigurationworkflow automationworkflow controlcomponentuser selectioneducationworkflow abstractionlife science

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