Biomedical systems biology workflow orchestration and execution with PoSyMed

TL;DR

PoSyMed is a modular platform that streamlines the integration, execution, and management of bioinformatics workflows, enhancing reproducibility and user interaction with AI-assisted tools.

Contribution

It introduces a formal, container-based, human-supervised system architecture that incorporates large language models for improved bioinformatics workflow management.

Findings

PoSyMed improves reproducibility and traceability in biomedical workflows.

The platform supports complex biological software scenarios effectively.

Large language models assist users in tool identification and workflow parameterization.

Abstract

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.