KNIME - BNNLab/BN_Group_Wiki GitHub Wiki

1. KNIME Analytics Platform Installation

The KNIME analytics platform and its cheminformatics extensions are a useful tool for a number of processes such as automatic atom-atom mapping (aam) of reactions. This page will walk through the installation of KNIME and some basic usage.

Download and install KNIME

  1. To download KNIME, you must visit: https://www.knime.com/downloads and fill in the information form. KNIME will then send some emails to your address to guide you through creating your first workflow (this may not be immediate). 

  2. After filling in the information form you are directed to an installation page, choose the correct operating system for your device and download the file (for windows, download the installer version). While the file is downloading there are useful links on the downloads page, I suggest reading through the 'Build a Workflow' page: https://www.knime.com/getting-started-guide

  3. Once the installation is complete, launch KNIME. It will ask you to provide a directory to which your workflows will be saved, you can use the default or set your own.

Now you have the KNIME GUI open and you are ready to begin building workflows. To use the cheminformatics based nodes we must first install them.

Installation of cheminformatics based extensions:

  1. Go to File>Install KNIME extensions...

  2. In the search box, type in the node names given in step 3 individually and check the boxes next to the extension, once you have all the boxes checked, proceed with the installation, accept the license agreement and KNIME will restart upon completion.

  3. Names of extensions: KNIME Base Chemistry Types & Nodes, KNIME-CDK, Lhasa reaction contributions, Lhasa public plugin, Lhasa metabolism feature, RDKit KNIME integration, RDKit KNIME Wizards.

2. Example Workflow for AAM

  1. Link to folder containing example KNIME workflow and input file. Access is only granted to those within the BN group.

  2. Download the folder and the accompanying .csv file, save the folder in the KNIME directory (where workflows are saved).

  3. Import the workflow by: File> Import KNIME Workflow...

  4. Navigate to the folder using the 'select root directory' option in the import menu and import the workflow.

  5. Configure the nodes (start with .csv file import)

  6. Execute the nodes

  7. To view the node output, right-click on the node and select the bottom option.