SocialViruses: integrating quantitative phage-bacteria and phage-phage interaction networks for rational cocktail design.

Motivation: Phage therapy is emerging as a promising alternative to antibiotics in biomedical research, highlighting the growing need for computational tools to rationally design effective phage cocktails. However, its clinical potential is often compromised by the evolution of heritable bacterial resistance, which is frequently exacerbated by repeated phage exposure. This can lead to broad-spectrum cross-resistance and reduced long-term efficacy. Existing approaches typically rely on host range matrices but often overlook viral interference and the complex, non-binary nature of virus-host interactions. Results: We present SocialViruses, a tool for designing optimized phage cocktails selecting up to twelve viruses and using two alternative algorithms. SocialViruses integrates quantitative host range infection and virus-virus interaction matrices to guide cocktail design. It produces a detailed report with key quality metrics and allows users to define multiple cocktails while minimizing viral interference and managing co-infection redundancy. Availability and implementation: SocialViruses is freely available as a Cytoscape application and can be downloaded from: https://apps.cytoscape.org/apps/SocialViruses.