The KNIME node for MolCompass project

Introduction

`MolCompassKnime` is a part of the `MolCompass` project. It is a KNIME extension that provides a pretrained parametric t-SNE model for molecular visualization. This extension generates X and Y coordinates for compounds, ensuring that similar compounds group together, forming well-recognizable clusters.

Installation

Installation from pre-build package (recommended)

To install MolCompassKnime from Zenodo, follow the instructions below:

1. Download the pre-compiled zip archive  for your KNIME version from Zenodo:
2. Open KNIME Analytics Platform.
3. Click on the Help menu and select Install New Software.
4. Click on Add and select Local to add the downloaded extension.
5. Select the path to the folder containing the extension and click on OK.
6. Select the extension and click on Next.
7. Follow the instructions to install the extension.
8. Restart KNIME Analytics Platform.

Building from scratch (optional, recommended only for developers)

To build MolCompassKnime from scratch, follow the instructions below:

1. Prepare the Building Environment for KNIME:

   conda create -n knime-ext-bundling -c knime -c conda-forge knime-extension-bundling
   conda activate knime-ext-bundling

2. Run the Build Command:

   python build_python_extension.py --knime-version [version] molcompass molcompass_build_[version]

   Replace [version] with the desired KNIME version (e.g., 5.2).

Also, you can clone the repo and run GitHub action for building.

Usage

You will see the MolCompass node in the Community Nodes/Pharmacoinformatics category. Using MolCompassKnime is straightforward. After building and installing the extension, you can incorporate it into your KNIME workflows.

Minimal Workflow

Drag and drop the MolCompassKnime node into your workflow. Connect it with, for example, a CSV reader and read a dataset. You can find the example in workflows folder.

Advanced Workflow

Support

For any questions, issues, or feedback, please refer to sergey.sosnin@univie.ac.at