SBMLNetwork: A framework for standards-based visualization of biochemical models

Adel Heydarabadipour, Lucian Smith, Joseph L Hellerstein and Herbert M Sauro

PLOS Computational Biology, 2025, vol. 21, issue 9, 1-19

Abstract: 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.Author summary: We developed SBMLNetwork, a software tool that enables researchers to create standardized visualizations of biological models with minimal effort. Currently, scientists studying complex biological systems face the major challenge that different software tools store visualization data in incompatible formats. This makes it difficult to share model diagrams or reproduce them across platforms, creating unnecessary barriers to collaboration and slowing scientific progress. Our solution builds on an established standard format for visualizing biological models, while removing the technical complexity that has limited its widespread use. SBMLNetwork automatically generates diagrams of biological networks and stores all visualization details in the standard format alongside the model data in a single file. We demonstrated our tool’s capabilities by producing clear, standards-based diagrams that accurately represent biological pathways and can incorporate relevant data. By making standards-based model diagrams easier to create and share, we aim to enhance reproducibility and accelerate the communication of biological models within the systems biology community.

Date: 2025
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1013128

DOI: 10.1371/journal.pcbi.1013128

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