Proteax® KNIME nodes

Proteax can be used from within the KNIME data mining tool via the Proteax KNIME nodes extension.

You can download a number of workflow examples here.

Source code for the Proteax KNIME nodes can be downloaded from here as a JAR file.

How to install


  • KNIME, of course. If you do not already have KNIME installed, it can be downloaded from the KNIME download site.
  • Proteax Desktop 2.0 should be installed, at least downloaded and unpacked. It can be downloaded from the Biochemfusion download site.

Note: If you already have Proteax for Spreadsheets 2.x installed and you run KNIME with a 32-bit Java on Windows, you do not need to install Proteax Desktop. You may to learn how to setup KNIME so it uses the Proteax library that comes with Proteax for Spreadsheets.

Installation - nodes

Install the Proteax KNIME node extension by adding the Biochemfusion KNIME update site to your list of KNIME software repositories, as shown below. The dialog below is shown by choosing "Install New Software..." from KNIME's Help menu.

[Image: Adding the Proteax KNIME node update site to KNIME.]

Once the Biochemfusion update site has been added, you can install the Proteax KNIME nodes from it.

[Image: Installing the Proteax KNIME nodes.]

After a restart of KNIME you should now see the Proteax nodes in the Node Repository tree.

[Image: Proteax KNIME nodes installed.]

Installation - Proteax configuration

If you have already done a full installation of Proteax Desktop 2.0 where you have set the environment variable PROTEAX_DESKTOP_5_HOME, then the Proteax KNIME nodes should already work now. You need not do more.

However, if you simply unpacked the Proteax Desktop download without additional configuration - or if you want to use a KNIME-specific Proteax Desktop installation - then KNIME needs to know where Proteax Desktop is located. Open the Proteax Preferences page in KNIME. It is located in the normal KNIME Preferences page that you open via "Preferences" from the File menu.

[Image: Proteax KNIME preferences.]

The location you set for "Proteax Desktop home" should be the directory that contains the folders as shown here.

[Image: Proteax home directory contents.]

This is also the location where you will find the Proteax license file proteax_desktop.license. To register your Proteax license, open the license file with a text editor, e.g. Notepad on Windows or gedit on Linux, paste your license key in, and save the file.

After changing the setting for "Proteax Desktop home" in KNIME you will need to restart KNIME.

You should now have working Proteax KNIME nodes. If you do not have working Proteax KNIME nodes after following these instructions you are most welcome to .