The Neurosphere Simulator: An educational online tool for modeling neural stem cell behavior and tissue growth

Abstract

Until very recently, distance education, including digital science labs, served a rather small portion of postsecondary students in the United States and many other countries. This situation has, however, dramatically changed in 2020 in the wake of the COVID-19 pandemic, which forced colleges to rapidly transit from face-to-face instructions to online classes. Here, we report the development of an interactive simulator that is freely available on the web (http://neurosphere.cos.northeastern.edu/) for teaching lab classes in developmental biology. This simulator is based on cellular automata models of neural-stem-cell-driven tissue growth in the neurosphere assay. By modifying model parameters, users can explore the role in tissue growth of several developmental mechanisms, such as regulation of mitosis or apoptotic cell death by contact inhibition. Besides providing an instantaneous animation of the simulated development of neurospheres, the Neurosphere Simulator tool offers also the possibility to download data for detailed analysis. The simulator function is complemented by a tutorial that introduces students to computational modeling of developmental processes.

Keywords: Cellular automata; Digital science lab; Modeling; Neural stem cells; Neurosphere assay; Simulations.

Fig. 1

Search trends in the United States for queries in Google Search using the terms “remote learning” and “online learning” over the period of July 26, 2015 and July 25, 2020. The search volume for each of these terms is normalized to the peak popularity of the “remote learning” query. Note that the start of the surge in queries for both strings coincides with the announcement of the times when U.S. President Donald Trump officially declared a national emergency in wake of the COVID-19 pandemic (March 13, 2020) and when the New York City’s public school system announced that it would close (March 15, 2020).

Fig. 2

Home page of the Neurosphere Simulator Toolbox.

Fig. 3

Dashboard of the Neurosphere Simulator Tool page.

Fig. 4

Simulated neurosphere at iteration step 100 (a). Development of its cellular populations (b). The structure was grown using the default settings of the Neurosphere Simulator. Red, active stem cell; orange, progenitor cells; blue, differentiated cells; black, dead cells; green, BTSCs (not present).