2025-08-23_151743_nature_s41592-022-01442-1

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

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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

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

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Acknowledgements

We thank Johannes Schöneberg for help building example models and discussion; Moritz Hoffmann, Christoph Fröhner and Frank Noé for training and development with ReaDDy; Adam Husar, Tom Bartol and Jacob Czech for training and collaboration using MCell; James Faeder for training in BioNetGen and BNGL; François Nédélec for training and development with dynamic cytoskeletal fibers and membranes in Cytosim and Matthew Akamatsu and Daniel Serwas for insight, testing and example data; Leslie Loew, Michael Blinov, Ann Cowen, Ion Moraru, Aniruddha Chattaraj, Steve Andrews, Garegin Papoian, Paul Macklin, Randy Heiland, Ryan Spangler and Eran Agmon for collaboration to integrate their simulators and example data; Ludovic Autin and Ivan Viola for visualization inspiration and discussion; Jonathan Alberts for extensive help testing the prototype viewer with large trajectories; and Rick Horwitz for suggestions. Researchers from the Allen Institute for Cell Science wish to thank the Allen Institute founder, Paul G. Allen, for his vision, encouragement and support. Please see the Supplementary Acknowledgements to help us thank a long list of additional contributors who helped with user testing, scientific and design feedback, implementation testing and more.

Author information Authors and Affiliations

Allen Institute for Cell Science, Animated Cell, Seattle, WA, USA

Blair Lyons, Eric Isaac, Na Hyung Choi, Thao P. Do, Justin Domingus, Andrew Leonard, Megan Riel-Mehan, Emily Rodgers, Lisa Schaefbauer, Daniel Toloudis, Olivia Waltner, Lyndsay Wilhelm & Graham T. Johnson

University of Utah, Biochemistry, Salt Lake City, UT, USA

Janet Iwasa

Contributions

B.L., J.I., and G.T.J. conceived the project; B.L., E.I., J.D., M.R.-M., and D.T. designed the software architecture; B.L., E.I., N.H.C., J.D., M.R.-M. and D.T. wrote the software and A.L. helped with debugging; L.S. designed user interfaces and conducted user tests; T.P.D. contributed illustrations and managed analytics data; T.P.D. and L.W. refined user interface designs; E.R. and O.W. helped test the software; G.T.J. supervised the project.

Corresponding author

Correspondence to Graham T. Johnson.

Ethics declarations Competing interests

The authors declare no competing interests.

Peer review Peer review information

Nature Methods thanks Zaida Luthey-Schulten and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Supplementary information Supplementary Information

Supplementary Tables 1–3, Supplementary References and Supplementary Acknowledgements

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Lyons, B., Isaac, E., Choi, N.H. et al. The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models. Nat Methods 19, 513–515 (2022). https://doi.org/10.1038/s41592-022-01442-1

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Published 04 April 2022

Issue Date May 2022

DOI https://doi.org/10.1038/s41592-022-01442-1

Subjects Biological models Computational biophysics Computational models Computational platforms and environments Databases