PoSyMed让生物信息学工具使用更简单，支持可复现的全流程分析。
Biomedical systems biology workflow orchestration and execution with PoSyMed
- 用容器化+形式化描述整合工具，实现稳定执行环境。
- 结合大模型作为助手，辅助选工具、定参数，提升交互效率。
- 适合需要可复现分析的科研人员，尤其擅长复杂流程管理。
生物信息学软件的快速扩张带来了实际应用障碍。尽管统计与人工智能方法日益普及，但因分发碎片化、文档不一致、依赖复杂和执行环境难复现，工具复用与流程适配仍耗时费力。为此，我们提出PoSyMed——一个开放、模块化的平台，用于生物信息工具与工作流的受控集成、组合与执行。该平台采用后端驱动架构，结合形式化工具描述、受控容器构建与执行、持久化工作流状态，以及基于对话的用户界面。大语言模型（LLM）作为人类-计算机接口中的语义助手，协助识别工具、建议步骤并支持参数配置，均在类型安全、验证且人工监督的环境中进行。该设计提升了生物医学分析的可复现性、可追溯性与透明度。我们阐述了系统架构，并在典型生物软件场景下评估其工作流支持、交互设计与平台扩展性。PoSyMed已公开，访问地址：https://apps.cosy.bio/posymed。
原文摘要 · Abstract (English)
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.
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