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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 aninteractive view including molecule highlighting. Write the found molecules into an Excel file, which contains the execution time in thefile name. The RDKit Substructure Filter node expects a SMARTS to be entered to do the search. Use the Molecular Sketcher component and the Table Row to Variable node to pass the the chemical structure drawn in the MolecularSketcher component to the RDKit Substructure Filter node as a variable Output. To do so, go to the Flow Variable Tab in the RDKitSubstructure Filter node and select as smarts value your variable Output.Hint: KNIME-verified components can be found on the Hub or on the Example Server. 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 toload theChEMBLID228_SERT_ligands.table Step 2.2Use the Value SelectionConfiguration node and set theDefault Column to "assay_chembl_id" 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 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 1.3Use the Table Row toVariable node convert thefirst row of the table to FlowVariables 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 1Use the Table Row toVariable node convert thedrawn molecule to a FlowVariable Step 2Pass the Flow Variable"Output" to the"smarts_value" in theFlow Variable Tab Step 2.4Create a Componentcontaining the ValueSelection Configurationnode and the Row Filternode Step 3Create a flow variable with theexecution date (Date&TimeConfiguration node)Tip: Select "Date" for the setting optiontype and activate the checkbox "Useexecution time". Step 4Create a Path flow variable to save thefiltered product file in a directory ofyour choice (Create File/FolderVariables node)Tip: select the base location, enter thefile extension and provide the filenameas a flow variable. Step 5Write the filtered table into a XLSXfile (Excel Writer node)Tip: Use the Path flow variable thatyou created in 5 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 substructuresearchCHEMBLID228_SERT_ligands.tableadd execution time to file name Molecular Sketcher Row Filter GroupBy Sorter Row Filter RDKit Canon SMILES RDKit DescriptorCalculation Tile View Renderer to Image RDKit SubstructureFilter RDKit MoleculeHighlighting Value SelectionConfiguration Assay Selection Table Rowto Variable Table Rowto Variable Table Reader Table Reader Date&TimeConfiguration String Manipulation(Variable) Create File/FolderVariables Excel Writer 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 aninteractive view including molecule highlighting. Write the found molecules into an Excel file, which contains the execution time in thefile name. The RDKit Substructure Filter node expects a SMARTS to be entered to do the search. Use the Molecular Sketcher component and the Table Row to Variable node to pass the the chemical structure drawn in the MolecularSketcher component to the RDKit Substructure Filter node as a variable Output. To do so, go to the Flow Variable Tab in the RDKitSubstructure Filter node and select as smarts value your variable Output.Hint: KNIME-verified components can be found on the Hub or on the Example Server. 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 toload theChEMBLID228_SERT_ligands.table Step 2.2Use the Value SelectionConfiguration node and set theDefault Column to "assay_chembl_id" 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 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 1.3Use the Table Row toVariable node convert thefirst row of the table to FlowVariables 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 1Use the Table Row toVariable node convert thedrawn molecule to a FlowVariable Step 2Pass the Flow Variable"Output" to the"smarts_value" in theFlow Variable Tab Step 2.4Create a Componentcontaining the ValueSelection Configurationnode and the Row Filternode Step 3Create a flow variable with theexecution date (Date&TimeConfiguration node)Tip: Select "Date" for the setting optiontype and activate the checkbox "Useexecution time". Step 4Create a Path flow variable to save thefiltered product file in a directory ofyour choice (Create File/FolderVariables node)Tip: select the base location, enter thefile extension and provide the filenameas a flow variable. Step 5Write the filtered table into a XLSXfile (Excel Writer node)Tip: Use the Path flow variable thatyou created in 5 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 substructuresearchCHEMBLID228_SERT_ligands.tableadd execution time to file name Molecular Sketcher Row Filter GroupBy Sorter Row Filter RDKit Canon SMILES RDKit DescriptorCalculation Tile View Renderer to Image RDKit SubstructureFilter RDKit MoleculeHighlighting Value SelectionConfiguration Assay Selection Table Rowto Variable Table Rowto Variable Table Reader Table Reader Date&TimeConfiguration String Manipulation(Variable) Create File/FolderVariables Excel Writer Column Filter

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Created by: glandrum
Created at: 2015-02-07
On NodePit since: 2022-05-17
Last update: 2024-11-18
Created with KNIME version: v4.5.2
Tags: flow variableconfigurationworkflow automationworkflow controlworkflow abstractioncomponentuser selectioneducationlife science

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