The Simularium Viewer: an interactive online tool for sharing spatio-temporal biological models


We thank Johannes Schöneberg for his help in creating 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 collaborating with MCell; James Faeder for training at 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 sample 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 their collaboration in integrating their simulators and sample data; Ludovic Autin and Ivan Viola for visualization inspiration and discussion; Jonathan Alberts for his invaluable assistance in testing the prototype viewer with large trajectories; and Rick Horwitz for suggestions. Researchers at the Allen Institute for Cell Science would like to thank Allen Institute Founder Paul G. Allen for his vision, encouragement, and support. Please see Additional Acknowledgments to help us acknowledge a long list of additional contributors who helped with user testing, scientific and design feedback, implementation testing, and more.


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