Workflow Snippets

Simple workflows that demonstrate how to solve specific tasks.

External Tools

The External Tools Node lets you call executable files for other applications. It's especially useful for working with Shell scripts and Window’s executables so that you can integrate KNIME with your existing processes and applications.

View on KNIME Hub

View and download all Workflow Snippets on the KNIME Hub.

Previous Workflow Snippets

BIRT Report for bioactivity prediction

Always wanted to generate beautiful reports with the Business Intelligence and Reporting Tool (BIRT) and never dared to try? This workflow snippet gives you an excellent opportunity to learn how to transfer several different data elements to a BIRT report using KNIME Report Designer.

 

knime-workflow-snippet-birt-report-bioactivity

 

⇒ Download BIRT report for bioactivity prediction

Retry Database Connection

Connecting to a Database could fail for multiple reasons such as network related issues, too many connections to the server at a time, etc. It is desirable to automatically retry connecting to a database a couple of times to avoid a failure of workflow execution due to a temporary glitch. This workflow snippet shows one way of doing that.

 

 

⇒ Download Retry Database Connection from KNIME Hub

Standardizing Molecular Structures

Ever got impressed by the many different ways in which chemists can represent the same thing? In this workflow snippet we show how to use the open-source RDKit nodes to standardize molecular structures. In particular we have a look at the Remove Hs, Salt Stripper and Structure Normalizer nodes.

 

 

⇒ Download Standardizing Molecular Structures from KNIME Hub

Query GraphQL API

This workflow snippet demonstrates an example query to a GraphQL API. The Open Targets Platform provides a GraphQL API, which supports queries for a single target, disease/phenotype, drug, or target-disease association. Here, we are using Ensembl Gene IDs to query more information, e.g. description, genomic location, associated disease, ...

 

 

⇒ Download Query GraphQL API from KNIME Hub

Model Prediction Chemistry

This workflow snippet demonstrates how to use an already trained model on new data to predict bioactivity. Simply load the trained model with the Model Reader node and provide this to the corresponding Predictor Node, in our case this is the Random Forest Predictor node.

 

workflow-snippet-chemistry-prediction

 

⇒ Download Model Prediction Chemistry from KNIME Hub

Machine Learning Chemistry

Did you even wonder how you can train a bioactivity model using chemical structures? Take a look at this workflow snippet, to learn how to transform chemical structures into hashed bit-based fingerprints, which serve as an input for a Random Forest model to predict CDPK1 bioactivity. Evaluate the model performance using the ROC Curve and the confusion matrix.

 

workflow-snippet-chemistry-model-training

 

⇒ Download Machine Learning Chemistry from KNIME Hub

Time-to-Event Analysis using the Kaplan-Meier Plot

This workflow snippet shows how a time-to-event analysis can be easily done using KNIME Analytics Platform. You simply upload a file containing the corresponding data from a clinical study, e.g. in .xpt format, and after a small column manipulation the event is ready to be analyzed in the Kaplan-Meier Plot.

 

workflow-snippet-kaplan-meier-plot

 

⇒ Download Time-to-Event Analysis using the Kaplan-Meier Plot from KNIME Hub

Count Elements in Molecule

This workflow snippet counts the number of atoms in a molecule for an element of choice. This is done by first getting the molecular formula and using regex to extract the number of atoms.

 

workflow-snippet-count-elements-in-molecule

 

⇒ Download Count Elements in Molecule from KNIME Hub

Assign Custom Colors to a Chart

Sometimes special colors are needed to let your report shine! This workflow shows you how to customize colors in your chart using KNIME Analytics Platform.

 

workflow-snippet-custom-color-to-chart

 

⇒ Download Assign Custom Colors to a Chart from KNIME Hub

Create Hyperlinks in Table View

This workflow shows you how to create a clickable hyperlink in the Table View. It takes PubMed IDs as input and manipulates them into a certain format. This makes your interactive views even more interactive and allows you to open other pages right away from the Table View.

 

workflow-snippet-hyperlinks-in-table-view

 

⇒ Download Create Hyperlink in Table View from KNIME Hub

Sanitizing Query SMARTS

This workflow snippet is meant as a sequel to the previous one, where we showed you how to align molecules. There are some cases where the alignment might not have worked for you right away, e.g. when your drawn structure contains aromaticity. Learn in this snippet how to sanitize SMARTS for any kind of queries (or well, to finally align your molecules).

 

workflow-snippet-sanitizing-query-smarts

 

⇒ Download Sanitizing Query SMARTS from KNIME Hub

Align the Orientation of Molecules

Your molecules all contain the same substructure, but they are not aligned accordingly and deep down it’s driving you somehow nuts? Check out this workflow snippet that shows you how to align the orientation of molecules according to a drawn substructure. Using the SMARTS thereof we can then generate 2D coordinates for all the molecules. If you run into trouble with the SMARTS, check out the next workflow snippet where we will show you how to sanitize them.

 

workflow-snippet-align-orientation-molecule

 

⇒ Download Align the Orientation of Molecules from KNIME Hub

Manipulate Several Columns at Once

The Table Manipulator node is rarely used, although it combines quite some functionalities. You can use it to rename columns, resort the column order, change the column types and select which columns to include or exclude from your table. Have a look at this workflow snippet to see the Table Manipulator node in action.

 

workflow-snippet-table-manipulator

 

⇒ Download Manipulate Several Columns at Once from KNIME Hub

Add Colors to Table Cells

Would you like to color individual cells in your data table based on a certain value? This workflow snippet shows how to customize the individual cells in the table using the HTML color groups.

 

workflow-snippet-add-colors-to-cells

 

⇒ Download Add Colors to Table Cells from KNIME Hub

Python View Example

Do you want to use your favorite python library to create highly customized plots from the KNIME Analytics platform? This example workflow shows how to create a 2D kernel density estimate (KDE) plot using the seaborn (https://seaborn.pydata.org/) python data visualization library.

 

workflow-snippet-python-view

 

⇒ Download Python View Example from KNIME Hub

Multiple Columns as Flow Variable

Learn how to apply a flow variable with multiple columns. Using the example of filtering multiple columns, we extract the column names of our data, create a collection column containing the desired column names, and then generate a variable that we use in the column filter node.

 

workflow-snippet-multiple-column-flow-variable

 

⇒ Download Multiple Columns as Flow Variables from KNIME Hub

Matched Molecular Pair Analysis

Discover in this workflow snippet how to do matched molecular pairs analysis in KNIME. Check the preprocessing of the molecules happening in the metanode, and find matches in your data set with the nodes from the Vernalis community extension.

 

workflow-snippet-matched-molecular-pairs

 

⇒ Download Matched Molecular Pair Analysis from KNIME Hub

Excel Formatting

This workflow snippet to format your Excel file might appear very complex in the beginning, but once you get the hang of it, you can easily automate your Excel formatting and reduce your manual work. More time to do fun stuff.

 

workflow-snippet-excel-formatting

 

⇒ Download Excel Formatting from KNIME Hub

Write Images to Excel

Did you know that the Excel Writer node does not only export strings and numerical values to your Excel file, but also images? This comes in handy when you want to export images of your molecules. Simply use the Renderer to Image node and export your PNGs to Excel.

 

workflow-snippet-images-to-excel

 

⇒ Download Write Images to Excel from KNIME Hub

Explore Molecular Properties

Interested in finding hidden relationships in your data and demonstrating it to your colleagues in a clear and concise way? This workflow snippet shows how to visually explore a dataset with molecules and their properties.

 

workflow-snippet-explore-molecular-properties

 

⇒ Download Explore Molecular Properties from KNIME Hub

Fetch Data from Database

Do you want to fetch data from a database without loading a complete database table? You are interested in just a couple of columns and some rows meeting a certain criteria? This workflow snippet shows how to get only the attributes & records you need as a KNIME table.

 

workflow-snippet-fetch-data-from-database

 

⇒ Download Fetch Data from Database from KNIME Hub

Simple R View

Do you want to combine the power of KNIME with your favourite R library? Learn in this easy workflow snippet how to import a R package and create a simple R plot.

 

workflow-snippet-simple-r-view

 

⇒ Download Simple R View from KNIME Hub

Generating Chemical Fingerprints

Wondering what a whole row of 0s and 1s have to do with chemical structures? Want to investigate the similarity of molecules? Have a look at this workflow snippet demonstrating how to compute molecular fingerprints in KNIME and giving some background information.

 

workflow-snippet-chemical-fingerprint

 

⇒ Download Generating Chemical Fingerprints from KNIME Hub

3D View of PDB Structures

Good things come to those who wait! Of course, with “good things” we mean finally being able to explore molecules in 3D with KNIME. Have a look at this workflow snippet demonstrating how to query the Protein Data Bank (PDB) and visualising the results in 3D using the 3D Molecule Viewer component. This was definitely worth the wait!

 

workflow-snippet-3D-molecule-view

 

⇒ Download 3D View of PDB Structures from KNIME Hub

Sketching a Molecule

Don't have a ChemAxon license and miss the MarvinSketch node? Try this component to draw molecules, chemical structures and reactions. Depending on your choice, the output is available in two different chemical data formats. And as a cherry on top, you can even supply input SMILES by flow variable!

 

workflow-snippet-molecule-sketcher

 

⇒ Download Sketching a Molecule from KNIME Hub

Streaming - Text Processing

Have you ever heard of Streaming in KNIME? No, we did not integrate Netflix. Streaming in KNIME enables you to execute certain nodes in a section of your workflow concurrently, instead of node by node. This way, the results of one node are instantly provided as input to downstream nodes, which cuts down memory usage and speeds up your calculations.

 

workflow-snippet-streaming-text-processing

 

⇒ Download Streaming - Text Processing from KNIME Hub

GET Request (Life Sciences)

Did you ever wonder how to retrieve data from a (public) web service like mygene.info or maybe ChEMBL? Just use the GET Request node of KNIME and enter the URL as demonstrated in this workflow snippet. The JSON Path node or XML Path node will help you to parse the retrieved data. And off you go with the latest data for your use case!

 

workflow-snippet-get-request

 

⇒ Download GET Request (Life Sciences) from KNIME Hub

Create an Interactive View

If you want to combine several plots to one interactive view, have a look at this workflow snippet! It shows an interactive view "Explore Data" generated from several JavaScript nodes (Parallel Coordinates Plot, Table Editor, Pie/Donut Chart, Tile View and Scatter Plot). By combining several JavaScript nodes that operate on the same data table in one component, the interactivity of the combined view is automatically achieved.

 

workflow-snippet-create-interactive-view

 

⇒ Download Create an Interactive View from KNIME Hub

Convert a String to SMILES

The Molecule Type Cast node can be sometimes overlooked, but it is important if you want to convert a string column into any molecule type, such as Mol2, PDB, SDF, CML, HELM, SLN, SMILES, SMARTS or RXN. This workflow snippet demonstrates the use of the Molecule Type Cast node to convert a string to the SMILES data format. In a second step, a RDKit node is used to canonicalize the SMILES.

 

workflow-snippet-molecule-type-cast

 

⇒ Download Convert a String to SMILES from KNIME Hub

LinkedInTwitterShare