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# The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models | Nature Methods

**URL:** https://www.nature.com/articles/s41592-022-01442-1

**Saved:** 2025-08-23T22:17:46.459Z

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Correspondence
Published: 04 April 2022
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models
Blair Lyons, Eric Isaac, Na Hyung Choi, Thao P. Do, Justin Domingus, Janet Iwasa, Andrew Leonard, Megan Riel-Mehan, Emily Rodgers, Lisa Schaefbauer, Daniel Toloudis, Olivia Waltner, Lyndsay Wilhelm & Graham T. Johnson

Nature Methods 
volume
 19, 
pages
513–515 (2022)Cite this article

6267 Accesses

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To the Editor — We present the Simularium Viewer, a user-friendly, open-source application that makes it easy to share and interrogate interactive three-dimensional (3D) visualizations of biological simulation trajectories directly in a web browser at https://simularium.allencell.org. The primary goal of the Simularium project is to facilitate collaborations among experimental and computational biologists by removing challenges to sharing, accessing and comparing simulation results. As a new arrow in the modeling community’s quiver, the Simularium Viewer provides a platform to share simulation outputs in an easy-to-use interface that requires no computational expertise from end users. With a relatively small effort, any modeling researcher can use our conversion package to save their data as a Simularium file and generate a link that anyone can use to interactively investigate their simulation trajectories and related plots immediately in a browser, instead of spending time downloading, installing and learning to use tools specific to any given model.

Spatial simulations are a powerful tool for investigating biological phenomena at different scales;1,2 however, by surveying researchers, educators and students in the field of cell biology, we have identified several pain points that restrict their utility and adoption. In general, simulation tools are often difficult for non-computational biologists to use, provide limited options for the easy sharing of interactive visualizations, and must be downloaded and run as independent desktop software—often with challenging installation processes. Many require users to write code or to run software from a terminal window and offer only a limited user interface or no graphical user interface. Most visualization tools for spatial modeling are either specialized to support atomic coordinates and/or image data or built to support visualization for one particular modeling engine (Supplementary Table 1), making it challenging to compare models that were created using different engines. The common practice of developing new visualization software from scratch often results in redundant efforts to solve common challenges that take developer time and expertise away from addressing unsolved problems in the field.

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Code availability

The software described here is available under a modified BSD license at https://github.com/simularium and is free for non-commercial use.

References

Osborne, J. M., Fletcher, A. G., Pitt-Francis, J. M., Maini, P. K. & Gavaghan, D. J. PLOS Comput. Biol. 13, e1005387 (2017).

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Johnson, M. E. et al. Mol. Biol. Cell 32, 186–210 (2021).