NeuroDeRisk Toolbox Installation

The NeuroDeRisk toolbox can be installed on all common operating systems (Windows, Linux, macOS). If you are not familiar with KNIME, we recommend to install the complete toolbox at once, as described in the next section.

Installing the Complete Toolbox

Inte:Ligand provides a bundled package, that combines the KNIME Analytics Platform with all NeuroDeRisk node extensions, that form the toolbox. By using this package, you can install the complete toolbox at once.

This installation variant of the toolbox is summarized by the following illustration:

Tip

If you are familiar with KNIME, or even have it installed already, you can install the different parts of the NDR Toolbox directly within KNIME. Please refer to variant 2 for more details.

Please see the below sections for instructions on how to install the package for your operating system. After you finished the installation, please continue with the Getting Started section.

Windows

Download the package at
https://www.inteligand.com/ndr/download/knime-ndr-toolbox-win-v0.1.zip

Then, use an Archive Manager, such as 7-Zip or WinRAR to unpack it. You can put the resulting folder to a location of your choice. After unpacking, you can use the knime.exe executable to start the NDR Toolbox. This executable is located at the root of the extracted folder.

Linux

Download the package at
https://www.inteligand.com/ndr/download/knime-ndr-toolbox-linux-v0.1.tar.gz

Next, unpack the downloaded archive to a location of your choice. To do this on the command-line, you can use the following command:

tar -xzf knime-ndr-toolbox-linux-v0.1.tar.gz

Most Linux distributions include also a GUI-based archive manager. Alternatively to using the command-line, you can right-click the knime-ndr-toolbox-linux-v0.1.tar.gz file and use Extract Here.

After unpacking the archive, open the new directory and run knime. Or on the command-line:

./knime

macOS

Download the package at
https://www.inteligand.com/ndr/download/knime-ndr-toolbox-mac-v0.1.zip

Then, double-click the file toolbox-mac-latest.zip. macOS will unpack it at the current location. After unpacking is complete, open the newly created folder knime-ndr-toolbox-v0.1. This folder contains an install script install.sh, which creates a launcher in your /Applications folder and moves the downloaded toolbox contents into this launcher. To execute this script, open the Terminal application and navigate to the knime-ndr-toolbox-v0.1 folder:

cd /path/to/knime-ndr-toolbox-v0.1

Then, make the script executable and run it using the following commands on the Terminal:

chmod a+x install.sh
./install.sh

Tip

On some systems, it is enough to double-click the install.sh file in the Finder to run it. However, the above method will work on all systems.

After the script has finished, you can close the terminal pop-up and start the toolbox from your /Applications folder. The launcher is named KNIME NDR Toolbox.

Info

If you have problems with this installation method, get in touch for support or refer to the second installation variant described below.

Installing Extensions Separately

This alternative option to install the NeurDeRisk in-silico toolbox is recommended for users familiar with the KNIME platform. If there is an existing KNIME installation on your computer, you can integrate the different parts of the toolbox into this installation.

This installation variant of the toolbox is summarized by the following illustration:

Install KNIME

A prerequisite for the FAERS Drug selection installation is to have KNIME up and running. It can be downloaded for all platforms (Windows, Linux, macOS) from the official KNIME website at the following location: https://www.knime.com/downloads/download-knime
The installation should follow familiar steps depending on your system. For more information, please refer to the official KNIME installation instructions.

Installing Inte:Ligand Extensions

The Inte:Ligand NDR Toolbox Extensions can be installed as any other KNIME node extension:

1. In the KNIME graphical user interface (GUI), go to Help->Install New Software
2. Click the Add... button in the top-right of the dialog

3. Add the update site URL for the Inte:Ligand NDR Toolbox Extensions in the Location field:

   https://www.inteligand.com/ndr/knime
   

   

4. Click the OK button

5. Select Inte:Ligand NeuroDeRisk Extensions for the KNIME Workbench in the table
6. Click Finish and follow the instructions

After the installation is finished, KNIME will ask to be restarted. When this is done, you will be ready to use the Inte:Ligand NDR Toolbox Extensions.

For usage documentation, please refer to the respective part of this documentation or read the node descriptions within KNIME.

Installing Biovista Extensions

The installation procedure for the Biovista extensions is very similar to the procedure described above. The update site URL is

https://neuroderisk.biovista.com/knime/

For more details, please refer to the detailed documentation provided by Biovista.

Updating

You can update your KNIME installation and also the different parts of the NeuroDeRisk computation toolbox via File->Update KNIME. First KNIME will check if there are any updates for the platform itself. Then, a list with available updates for all installed node extensions is shown. This list will include updates from Biovista and Inte:Ligand, and other consortium partners that publish extensions for the NDR toolbox.

Info

This update method will work for both installation variants described above.