Heydarabadipour Adel, Smith Lucian, Hellerstein Joseph L, Sauro Herbert M
Department of Bioengineering, University of Washington, Seattle, 98195, WA, USA.
eScience Institute, University of Washington, Seattle, 98195, WA, USA.
bioRxiv. 2025 May 11:2025.05.09.653024. doi: 10.1101/2025.05.09.653024.
SBMLNetwork is an open-source software library that makes the SBML Layout and Render packages practical for standards-based visualization of biochemical models. Current tools often manage model visualization data in custom-designed, tool-specific formats and store it separately from the model itself, hindering interoperability, reproducibility, and the seamless integration of visualization with model data. SBMLNetwork addresses these limitations by building directly on the SBML Layout and Render specifications, automating the generation of standards-compliant visualization data, offering a modular implementation with broad integration support, and providing a robust API tailored to the needs of systems biology researchers. We illustrate the capabilities of SBMLNetwork across key visualization tasks, including SBGN-compliant visualization, application of predefined style templates, layout arrangement to reflect pathway logic, and integration of model data into network diagrams. These examples demonstrate how SBMLNetwork enables high-level visualization features and seamlessly translate user intent into reproducible outputs that support both structural representation and dynamic data visualization within the SBML model. SBMLNetwork is freely available at https://github.com/sys-bio/SBMLNetwork under the MIT license.
SBMLNetwork是一个开源软件库，它使SBML布局和渲染包能够实际用于基于标准的生化模型可视化。当前的工具通常以自定义设计的、特定于工具的格式管理模型可视化数据，并将其与模型本身分开存储，这阻碍了互操作性、可重复性以及可视化与模型数据的无缝集成。SBMLNetwork通过直接基于SBML布局和渲染规范构建，自动生成符合标准的可视化数据，提供具有广泛集成支持的模块化实现，并提供针对系统生物学研究人员需求定制的强大API，来解决这些限制。我们展示了SBMLNetwork在关键可视化任务中的功能，包括符合SBGN的可视化、预定义样式模板的应用、反映通路逻辑的布局安排以及将模型数据集成到网络图中。这些示例展示了SBMLNetwork如何实现高级可视化功能，并将用户意图无缝转换为可重复的输出，这些输出支持SBML模型中的结构表示和动态数据可视化。SBMLNetwork可在https://github.com/sys-bio/SBMLNetwork上根据MIT许可免费获取。
