Simon Süwer

Simon Süwer, Zoe Chervontseva, Kester Bagemihl et al.

The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by fragmented distribution, inconsistent documentation, complex dependencies, and difficult-to-reproduce execution environments. As a result, reusing published tools and workflow adaptation to own date remains technically demanding and time-intensive, even for experienced users. Here, we present PoSyMed, an open and modular platform for the controlled integration, composition, and execution of bioinformatics tools and workflows. PoSyMed combines a backend-centered platform architecture with formal tool descriptions, controlled container-based build and execution processes, persistent workflow state, and a dialogue-based user interface. Large language models (LLM) are integrated not as autonomous decision-makers, but as human-computer interface with bounded semantic assistants that help identify tools, propose workflow steps, and support parameterization within a typed, validated, and human-supervised execution environment. PoSyMed is designed to improve reproducibility, traceability, and transparency in practical biomedical analysis within one platform. We describe the system architecture and evaluate its behavior across representative biological software scenarios with respect to workflow support, interaction design, and platform extensibility. PoSyMed is publicly available at https://apps.cosy.bio/posymed.

Simon Süwer, Kester Bagemihl, Sylvie Baier et al.

Repurposing approved drugs offers a time-efficient and cost-effective alternative to traditional drug development. However, in silico prediction of repurposing candidates is challenging and requires the effective collaboration of specialists in various fields, including pharmacology, medicine, biology, and bioinformatics. Fragmented, specialized algorithms and tools often address only narrow aspects of the overall problem. Heterogeneous, unstructured data landscapes require the expertise of specialized users. Hence, these data services do not integrate smoothly across workflows. With ChatDRex, we present a conversation-based, multi-agent system that facilitates the execution of complex bioinformatic analyses aiming for network-based drug repurposing prediction. It builds on the integrated systems medicine knowledge graph (NeDRex KG). ChatDRex provides natural language access to its extensive biomedical knowledge base. It integrates bioinformatics agents for network analysis, literature mining, and drug repurposing. These are complemented by agents that evaluate functional coherence for in silico validation. Its flexible multi-agent design assigns specific tasks to specialized agents, including query routing, data retrieval, algorithm execution, and result visualization. A dedicated reasoning module keeps the user in the loop and allows for hallucination detection. By enabling physicians and researchers without computer science expertise to control complex analyses with natural language, ChatDRex democratizes access to bioinformatics as an important resource for drug repurposing. It enables clinical experts to generate hypotheses and explore drug repurposing opportunities, ultimately accelerating the discovery of novel therapies and advancing personalized medicine and translational research. ChatDRex is publicly available at apps.cosy.bio/chatdrex.