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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 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 the search. Use the Table Row to Variable node to pass the the chemical structure drawn in the Molecular Sketcher component to theRDKit Substructure Filter node as a variable Output. To do so, go to the Flow Variable Tab in the RDKit Substructure Filter nodeand select as smarts value your variable Output. Step 2Pass the Flow Variable"Output" to the"smarts_value" in theFlow Variable Tab Step 5Write the filtered table intoa XLSX file (Excel Writernode)Tip: Use the Path flowvariable that you createdin 5 Step 3Create a flow variable with the executiondate (Date&Time Configuration node)Tip: Select "Date" for the setting optiontype and activate the checkbox "Useexecution time". Step 4Create a Path flow variable to savethe filtered product file in a directoryof your choice (Create File/FolderVariables 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)N1CCNCC1Action needed: Select some compounds!Add SMARTS to create a substructuresearchadd execution time to file nameNode 503Node 504Node 505Node 506Node 507 Molecular Sketcher RDKit Canon SMILES RDKit DescriptorCalculation Tile View Renderer to Image RDKit SubstructureFilter RDKit MoleculeHighlighting Table Reader String Manipulation(Variable) Column Filter Table Reader GroupBy Sorter Table Rowto Variable Row Filter 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 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 the search. Use the Table Row to Variable node to pass the the chemical structure drawn in the Molecular Sketcher component to theRDKit Substructure Filter node as a variable Output. To do so, go to the Flow Variable Tab in the RDKit Substructure Filter nodeand select as smarts value your variable Output. Step 2Pass the Flow Variable"Output" to the"smarts_value" in theFlow Variable Tab Step 5Write the filtered table intoa XLSX file (Excel Writernode)Tip: Use the Path flowvariable that you createdin 5 Step 3Create a flow variable with the executiondate (Date&Time Configuration node)Tip: Select "Date" for the setting optiontype and activate the checkbox "Useexecution time". Step 4Create a Path flow variable to savethe filtered product file in a directoryof your choice (Create File/FolderVariables 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)N1CCNCC1Action needed: Select some compounds!Add SMARTS to create a substructuresearchadd execution time to file nameNode 503Node 504Node 505Node 506Node 507 Molecular Sketcher RDKit Canon SMILES RDKit DescriptorCalculation Tile View Renderer to Image RDKit SubstructureFilter RDKit MoleculeHighlighting Table Reader String Manipulation(Variable) Column Filter Table Reader GroupBy Sorter Table Rowto Variable Row Filter assay selection

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Created by: glandrum
Created at: 2015-02-07
On NodePit since: 2022-05-17
Last update: 2024-04-25
Created with KNIME version: v4.5.2
Tags: flow variableconfigurationworkflow automationworkflow controlcomponentuser selectioneducationworkflow abstractionlife science

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