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04. 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 thedataset within an interactive view including molecule highlighting. Write the found molecules into an Excel file, whichcontains the execution time in the file name. Step 1Use the Table Row toVariable node convert thedrawn molecule to a FlowVariable Step 1.2Use the GroupBy node to group allthe assay for each compound.Groupby "molecule_chembl_id" andcount the "assay_chembl_id".Use the Sorter node to sort bycount of assays in a descendingorder. Step 1.4Use the Row Filter nodewith Column to Test set to"molecule_chembl_id" andselect the Flow Variable"molecule_chembl_id" to useas pattern matching. Step 2.3Use the Row Filter node and connect theFlow Variable port from the ValueSelection Configuration node with theFlow Variable port of the Row Filter node. - Column to Test: "assay_chembl_id"- use pattern matching: "value-selection" Step 1Use the Table Reader node toload theChEMBLID228_SERT_ligands.table Step 2.4Create a Componentcontaining the ValueSelection Configurationnode and the Row Filternode Step 2.2Use the Value SelectionConfiguration node and set theDefault 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 toVariable node convert thefirst row of the table to FlowVariables The RDKit Substructure Filter node expects a SMARTS to be entered to do thesearch. Use the Table Row to Variable node to pass the the chemical structure drawn inthe Molecular Sketcher component to the RDKit Substructure Filter node as avariable Output. To do so, go to the Flow Variable Tab in the RDKit SubstructureFilter node and select as smarts value your variable Output. Step 2Pass the Flow Variable"Output" to the"smarts_value" in theFlow Variable Tab Step 6Write the filtered table intoa XLSX file (Excel Writernode)Tip: Use the Path flowvariable that you createdin 5 Step 4Create a flow variable withthe execution date(Date&Time Configurationnode)Tip: Select "Date" for thesetting option type andactivate the checkbox"Use execution time". Step 5Create a Path flowvariable to save thefiltered product file in adirectory of your choice(Create File/FolderVariables node)Tip: select the baselocation, enter the fileextension and provide thefilename as a flowvariable. Draw a referencemolecule for the similaritysearch in the interactive view.You can also paste the following sequence:CC(=O)N1CCNCC1Action 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 thedataset within an interactive view including molecule highlighting. Write the found molecules into an Excel file, whichcontains the execution time in the file name. Step 1Use the Table Row toVariable node convert thedrawn molecule to a FlowVariable Step 1.2Use the GroupBy node to group allthe assay for each compound.Groupby "molecule_chembl_id" andcount the "assay_chembl_id".Use the Sorter node to sort bycount of assays in a descendingorder. Step 1.4Use the Row Filter nodewith Column to Test set to"molecule_chembl_id" andselect the Flow Variable"molecule_chembl_id" to useas pattern matching. Step 2.3Use the Row Filter node and connect theFlow Variable port from the ValueSelection Configuration node with theFlow Variable port of the Row Filter node. - Column to Test: "assay_chembl_id"- use pattern matching: "value-selection" Step 1Use the Table Reader node toload theChEMBLID228_SERT_ligands.table Step 2.4Create a Componentcontaining the ValueSelection Configurationnode and the Row Filternode Step 2.2Use the Value SelectionConfiguration node and set theDefault 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 toVariable node convert thefirst row of the table to FlowVariables The RDKit Substructure Filter node expects a SMARTS to be entered to do thesearch. Use the Table Row to Variable node to pass the the chemical structure drawn inthe Molecular Sketcher component to the RDKit Substructure Filter node as avariable Output. To do so, go to the Flow Variable Tab in the RDKit SubstructureFilter node and select as smarts value your variable Output. Step 2Pass the Flow Variable"Output" to the"smarts_value" in theFlow Variable Tab Step 6Write the filtered table intoa XLSX file (Excel Writernode)Tip: Use the Path flowvariable that you createdin 5 Step 4Create a flow variable withthe execution date(Date&Time Configurationnode)Tip: Select "Date" for thesetting option type andactivate the checkbox"Use execution time". Step 5Create a Path flowvariable to save thefiltered product file in adirectory of your choice(Create File/FolderVariables node)Tip: select the baselocation, enter the fileextension and provide thefilename as a flowvariable. Draw a referencemolecule for the similaritysearch in the interactive view.You can also paste the following sequence:CC(=O)N1CCNCC1Action 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: 2023-09-08
Last update: 2024-04-27
Created with KNIME version: v4.4.2
Tags: flow variableconfigurationworkflow automationworkflow controlcomponentuser selectioneducationworkflow abstractionlife science

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