Schrödinger KNIME Extensions allow scientists to protoype, validate, automate, and deploy multi-step workflows. In this installment of KNIME Questions and Answers, Schrödinger’s KNIME Extensions Associate Product Manager Jean-Christophe Mozziconacci talks about how to use KNIME to interactively edit tabular data and 3D structures, and how to keep track of your workflows. All of the referenced workflows are available for download from our KNIME workflows page.
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Q. I have custom data that I’d like to use as part of a workflow – is there a KNIME node that I can use to input this data into a workflow (instead of reading a text file) and easily edit the data when I need to?
A. Yes. The “Table creator” node is used to do exactly this. One or several columns can be filled with custom values as needed. For example, you could create a list of SMARTS patterns that constitute a custom ligand filter or compound list, and you could periodically edit this list as needs change. Alternately, you could supply a list of parameters that is used to run one or more jobs within a workflow.
For a good example of this, see the “Loop over docking parameters” workflow. This workflow will perform a variety of similar calculations using job settings that vary according to parameters supplied by the Table creator node. Other workflows that use the Table Creator node are the "Cluster by Fingerprint 1-4” and “Vendor database preparation” workflows.
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Q. I only need to operate on a certain subset of data in a table at any given time. Is there a good way for me to interactively select a specific subset of rows from that table to run some nodes on?
A. The best way to do this is with the “HiLite Filter” node. This node allows you to select certain rows within a table, and to use that selection in another branch of your workflow. Another related node, “HiLite Collector,” allows you to add annotations to any selected rows. For examples, see the “Phase Screening 1-2” and “Vendor database preparation 1-3” workflows.
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Q. I already know I can supply my own structures as input to a workflow using the various structure-reading nodes. But is it possible to interactively edit a structure in the middle of a KNIME workflow?
A. This useful feature was introduced as a new “Run Maestro 1:1” metanode. However, its usefulness is not just limited to structure editing. You can also use it to select atoms or residues, and in the case of the “Library enumeration” workflow you can even use it to select attachment points on a molecular scaffold. This metanode is easily extended since it’s based on a Python script node. (In other words, the metanode merely wraps a Python script that reads the input structure, launches Maestro, etc.) Give the new "Run Maestro 1:1" metanode a try and let us know what else you’d like to see in this node.
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Q. I recently started creating KNIME workflows for other chemists in my group. Between my own workflows and the projects I’ve helped others with, I now have more KNIME workflows than I can easily keep track of. How can I list the workflows I’ve recently worked on?
A. There’s no way to do this in the current version of the KNIME interface, but it can be done with a workflow called “Workflows in the current workspace” available on our workflow page. This is a generally useful workflow – for example if you’ve saved multiple similarly named versions of a complex workflow, it can help you find the most recent. It will also list workflows alphabetically, by size, or according to the specific nodes they contain. (The last example is helpful when searching for an old workflow that was used as a starting point to create a new workflow.) One especially nice feature of this workflow is the ability to find a workflow on the basis of the text that it contains. In the viewer output table, just choose “Navigation > Find in the Text.”
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