Biomedical systems biology workflow orchestration and execution with PoSyMed

2026-04-21

AI Summary

This work addresses the pervasive challenges in bioinformatics tooling—such as fragmentation, complex dependencies, inconsistent documentation, and irreproducible environments—that severely hinder method reuse and adaptation. To overcome these limitations, the authors propose PoSyMed, an open modular platform that integrates biomedical workflows through formalized tool descriptions, containerized execution, a persistent workflow engine, and a conversational interface. Innovatively, a large language model is incorporated as a semantic assistant within a typed, validated, and human-supervised framework to support tool discovery, pipeline construction, and parameter configuration. This design significantly enhances analytical transparency and reproducibility. The platform’s efficacy is demonstrated in representative biomedical use cases, and it has been released as open-source software.

Technology Category

• Constraint Satisfaction and Optimization: Solvers and Tools
• Computer Vision: Medical and Biological Imaging
• Data Mining & Knowledge Management: Conversational Systems for Recommendation & Retrieval

Application Category

• Systems and Infrastructure for Web, Mobile and WoT: Experiences and lessons learnt from Web-based algorithms and system deployments
• Semantics and Knowledge: Scalable techniques for the creation, curation, publication, maintenance, and consumption of large, Web-based, structured, reusable, knowledge graphs and ontologies
• Security and Privacy: Data transparency and provenance

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.

Problem

• workflow orchestration
• reproducibility
• bioinformatics tools
• execution environment
• software integration

Innovation

• workflow orchestration
• container-based execution
• large language models
• reproducibility
• biomedical systems biology