These files are related to our course-based research use of per3-luciferase zebrafish embryos. Here we show several projects from different course years. One project looks at the impact of housing the zebrafish in an incubator under either a light:dark (LD) cycle or keeping them in constant darkness (DD) prior to measuring circadian rhythms. Another project looks at fish of two genotypes. Many projects are possible, and students can design and conduct these experiments. The data files are difficult to handle in Excel, which can motivate students to turn to R statistical programming. The posted command files can help students struggling with how to display and manipulate their data, but purposefully are not complete, to allow creative work from each student as they analyze the data. The use of chemical modulators to alter zebrafish larvae circadian rhythms in a biomathematics course is described here: https://curenet.cns.utexas.edu/projects/responses-circadian-clock-chemical-compounds When we were setting this up, we compared different plate readers. We looked for a reader that could hold temperature steady over multiple days, and that could detect the signal from each moving zebrafish larva. We settled on the SpectraMaxL from Molecular Devices. This is the major expense of this project, so it is good for instructors to share information on which readers will work.