Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Netherlands
- Institute for Computing and Information Sciences, Data Science, Radboud University, Netherlands
Figures
Box 1—figure 1
An example CPM grid with pixels belonging to the background (identity 0) or to one of two cells (identities 1 and 2).
Figure 1
Artistoo provides different levels of access depending on the audience.
Figure 2 with 1 supplement
Artistoo supports interactive, 'real time' simulations of diverse biological processes.
(A) Artistoo supports simulation of diverse biological processes; (B) users can interact with browser-based simulations via sliders, in real time. (C) Artistoo performance is comparable to that of the Morpheus framework. Data show wall times (mean ± SD of five runs) for four CPM models implemented in both frameworks (see Materials and methods for implementation details). (D) Scalability of the cell sorting simulation; simulation speed in Monte Carlo Steps per second (MCS/s) for different grid sizes (mean ± SD of five runs). Red line indicates 20 frames per second, a minimum speed required for a ‘real-time’ simulation for the human visual system. See also Appendix 1 for interactive versions of the simulations shown in (B)–(D). Artistoo Node.js scripts for the simulations in (C) and (D) are available on GitHub (Wortel and Textor, 2020).
Figure 2—figure supplement 1
Alternative representation of Figure 2D showing scaling with domain size.
Different plot of the data from Figure 2D showing wall time (s) for the entire simulation of 2500 MCS at different domain sizes (mean ± SD of five runs); simulation duration scales linearly with the number of pixels on the grid.
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Software, algorithm | Morpheus | Publication Starruß et al., 2014 | RRID:SCR_014975 | version 2.1.0 |
| Software, algorithm | Artistoo | This paper, see also https://artistoo.net | RRID:SCR_020983 | version 1.0.0 |
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Artistoo, a library to build, share, and explore simulations of cells and tissues in the web browser
eLife 10:e61288.
https://doi.org/10.7554/eLife.61288
