SiliFish: A desktop application to model swimming behavior in developing zebrafish (Danio rerio)

Abstract

Summary: SiliFish is an open-source desktop application to model and study zebrafish swimming. Here, we explain how to define the general parameters of the model, define cell populations, place them within the spinal cord, and define their projections. We explain how to run a simulation and how to visualize the network output and single-cell activity. The choice of C# as the programming language allows higher speed performance, simulating models with larger spinal circuits in less time.For complete details on the use and execution of this protocol, please refer to Roussel et al. (2021).1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Keywords

• Bioinformatics
• Model Organisms
• Neuroscience
• Computer sciences