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Visualization Example

Introduction to KNIME

If this is the first time that you work in KNIME, please read this small introduction on how to configure and run nodes. Useful links will be provided below.

First thing to know is that KNIME uses particular subunit called 'nodes' to perform simple actions. Every node can be configured according to your necessities (right button - 'configure' or simple double-click on the node). To execute the node, you can click the green button (like a 'play' button) on the toolbar at the top of the window or right-click then 'execute'. Some nodes have a JavaScript Visualization mode. The output of this nodes can be interactively explored and eventually selection of the visualized data can be done.

If the node is not yet configured you will see a red light, then yellow light when the node is configured and a green light when the node is properly executed. Errors are displayed through a yellow triangle with an esclamation point in it.

If you need to add a specific node you can search it throgh the Node Repository in the bottom-left part of the window.

Feel free to play around and discover the functionalities of KNIME. Further information, courses and a forum can be found on the KNIME HUB link provided below.

INTRODUCTIONWelcome! This is the first KNIME workflow for Celeris Therapeutics. The aim of this workflowis guiding you through a series of helpful tools that you can use and adapt to your ownpurposes. Before continuing and applying the workflow, I suggest you to check thedescription box on the right with all the basic instructions on how to run the nodes. Data Access Preprocessing Data Visualization and Selection Export selected molecules asimages MCS Visualization and R-GroupDecomposition (Beta Version) Data Access Workflow instructions Please read these instructions before proceeding:1) Open the configuration mode of the SDF Reader (right-click -> configure) and insertyour data file in the node. Then execute the node. The last option in the menu (right-click) will show you the output table of your file. 2) Then execute the preprocessing without any further doings. The preprocessing willremove duplicates and apply some filters to remove undesidered data. RdKitdescriptors are also computed.3) Probably you do not need to save all the molecules contained in a SDF file, then youneed to select some molecules of your interest. To do this, you need first to select therange of colors with the Color Manager: in the default settings is on PTPN1/PTPN2selectivity. You can always do it in the configuration mode of the node. Then you canvisualize the properties of your molecules and the table with the Data Visualizationand selection component interactively. For doing this right-click -> Interactive View. Forfurther details please click Ctrl/Cmd/Strg + left button. Then you can execute the RowFilter and the PNG Image to ImgPlus nodes without any further doings. 4) Open the Image Writer node's configuration mode to insert your images' desiredlocation. Optional: - Your starting point is a CSV file: use the CSV Reader node. It works identically to the SDF Reader. - Use the Structure Sketcher node to generate a picture or an SDF file directly from a hand-designed molecule or a SMILES. Double-click on the node and a graphical editor will appear with several functions. - You want to parse your data according a MCS and display the different R-groups: use the MCS visualization component. For further details please click Ctrl/Cmd/Strg + left button. Read the sdf and extract propertiesFilter selected nodesSave images as png filesApply colors according to a columnCalculate RdKit descriptors and renders imagesNode 29Node 30Node 36SDF Reader Row Filter Image Writer PNG Imageto ImgPlus Color Manager Data Visualizationand selection Preprocessing MCS visualization Structure Sketcher CSV Reader INTRODUCTIONWelcome! This is the first KNIME workflow for Celeris Therapeutics. The aim of this workflowis guiding you through a series of helpful tools that you can use and adapt to your ownpurposes. Before continuing and applying the workflow, I suggest you to check thedescription box on the right with all the basic instructions on how to run the nodes. Data Access Preprocessing Data Visualization and Selection Export selected molecules asimages MCS Visualization and R-GroupDecomposition (Beta Version) Data Access Workflow instructions Please read these instructions before proceeding:1) Open the configuration mode of the SDF Reader (right-click -> configure) and insertyour data file in the node. Then execute the node. The last option in the menu (right-click) will show you the output table of your file. 2) Then execute the preprocessing without any further doings. The preprocessing willremove duplicates and apply some filters to remove undesidered data. RdKitdescriptors are also computed.3) Probably you do not need to save all the molecules contained in a SDF file, then youneed to select some molecules of your interest. To do this, you need first to select therange of colors with the Color Manager: in the default settings is on PTPN1/PTPN2selectivity. You can always do it in the configuration mode of the node. Then you canvisualize the properties of your molecules and the table with the Data Visualizationand selection component interactively. For doing this right-click -> Interactive View. Forfurther details please click Ctrl/Cmd/Strg + left button. Then you can execute the RowFilter and the PNG Image to ImgPlus nodes without any further doings. 4) Open the Image Writer node's configuration mode to insert your images' desiredlocation. Optional: - Your starting point is a CSV file: use the CSV Reader node. It works identically to the SDF Reader. - Use the Structure Sketcher node to generate a picture or an SDF file directly from a hand-designed molecule or a SMILES. Double-click on the node and a graphical editor will appear with several functions. - You want to parse your data according a MCS and display the different R-groups: use the MCS visualization component. For further details please click Ctrl/Cmd/Strg + left button. Read the sdf and extract propertiesFilter selected nodesSave images as png filesApply colors according to a columnCalculate RdKit descriptors and renders imagesNode 29Node 30Node 36SDF Reader Row Filter Image Writer PNG Imageto ImgPlus Color Manager Data Visualizationand selection Preprocessing MCS visualization Structure Sketcher CSV Reader

Nodes

Extensions

Links

Download

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

Download Workflow
Created by: user
Created at: 2022-06-01
On NodePit since: 2023-07-25
Last update: 2024-11-21
Created with KNIME version: v4.6.0

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