RISK Documentation

This repository offers a detailed guide to using Regional Inference of Significant Kinships (RISK), a next-generation tool for biological network annotation and visualization. It walks users through core features and practical workflows for network analysis.

• Full Documentation: riskportal.github.io/risk-docs
• Figure Gallery: riskportal.github.io/risk-docs/8_figure_gallery
• Try in Browser (Binder):
• Source Code: github.com/riskportal/risk

For a full description of RISK and its applications, see:
Horecka, I., and Röst, H. (2026)
RISK: a next-generation tool for biological network annotation and visualization
Bioinformatics. https://doi.org/10.1093/bioinformatics/btaf669

Yeast Protein–Protein Interaction (PPI) Network Demonstration

We applied RISK to a Saccharomyces cerevisiae protein–protein interaction (PPI) network (Michaelis et al., 2023; 3,839 proteins, 30,955 interactions). RISK identified compact, functional modules overrepresented in Gene Ontology Biological Process (GO BP) terms (Ashburner et al., 2000), revealing biological organization including ribosomal assembly, mitochondrial organization, and RNA polymerase activity.

RISK workflow overview and analysis of the yeast PPI network. Clusters are color-coded by overrepresented GO Biological Process terms (p < 0.01).

Setting Up Python and Jupyter for RISK

Step 1: Install Python 3.8+

Download and install Python 3.8 or later (recommended) from the official Python website. RISK is tested on Python 3.8+.

• On Windows, ensure you check the box that says Add Python to PATH during installation. If you missed this step, follow this guide to manually set the PATH.

Step 2: Create a Virtual Environment (Optional but Recommended)

Set up a virtual environment to manage dependencies for RISK:

• For Windows:

  python -m venv risk-env
  risk-env\Scripts\activate

• For macOS/Linux:

  python3 -m venv risk-env
  source risk-env/bin/activate

Step 3: Configure Jupyter to Use the Virtual Environment

Follow this guide to link your virtual environment with Jupyter.

After setup, select the virtual environment in Jupyter Notebook:

1. Click Kernel in the menu.
2. Choose Change kernel.
3. Select your virtual environment (e.g., risk-env).

Step 4: Install Jupyter

With your virtual environment activated, install Jupyter Notebook:

pip install jupyter

Step 5: Clone Repository

To install the dependencies for this tutorial, run:

git clone https://github.com/riskportal/risk-docs.git
cd risk-docs

Step 6: Install Dependencies

To install the dependencies for this tutorial, run:

pip install -r requirements.txt

Step 7: Launch Jupyter Notebook

Start Jupyter Notebook to run the RISK tutorial:

jupyter notebook

Citation

Primary citation

Horecka, I., and Röst, H. (2026)
RISK: a next-generation tool for biological network annotation and visualization
Bioinformatics. https://doi.org/10.1093/bioinformatics/btaf669

Software archive

RISK software for the published manuscript.
Zenodo. https://doi.org/10.5281/zenodo.17257418

License

This tutorial follows the GPLv3 License.