RISK (RISK Infers Spatial Kinships) is a next-generation tool designed to streamline the analysis of biological and non-biological networks. RISK enhances network analysis with its modular architecture, extensive file format support, and advanced clustering algorithms. It simplifies the creation of publication-quality figures, making it an important tool for researchers across disciplines.
RISK is compatible with Python 3.8 and later versions and operates on all major operating systems. Install RISK via pip:
pip install risk-network
We applied RISK to a Saccharomyces cerevisiae protein–protein interaction network, revealing both established and novel functional relationships. The visualization below highlights key biological processes such as ribosomal assembly and mitochondrial organization.
RISK successfully detected both known and novel functional clusters within the yeast interactome. Clusters related to Golgi transport and actin nucleation were clearly defined and closely located, showcasing RISK's ability to map well-characterized interactions. Additionally, RISK identified links between mRNA processing pathways and vesicle trafficking proteins, consistent with recent studies demonstrating the role of vesicles in mRNA localization and stability.
If you use RISK in your research, please cite the following:
Horecka, et al., "RISK: a next-generation tool for biological network annotation and visualization", [Journal Name], 2024. DOI: 10.1234/zenodo.xxxxxxx
RISK features a streamlined, modular architecture designed to meet diverse research needs. Each module focuses on a specific task—such as network input/output, statistical analysis, or visualization—ensuring ease of adaptation and extension. This design enhances flexibility and reduces development overhead for users integrating RISK into their workflows.
In benchmarking tests using the yeast interactome network, RISK demonstrated substantial improvements over previous tools in both computational performance and memory efficiency. RISK processed the dataset approximately 3.25 times faster, reducing CPU time by 69%, and required 25% less peak memory usage, underscoring its efficient utilization of computational resources.
We welcome contributions from the community. Please use the following resources:
If you encounter issues or have suggestions for new features, please use the Issues Tracker on GitHub.
RISK is freely available as open-source software under the GNU General Public License v3.0.
Note: For detailed documentation and to access the interactive tutorial, please visit the links provided in the Documentation and Tutorial section.
FAQs
A Python package for biological network analysis
We found that risk-network demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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