FPbase has a DOI through Zenodo and may be cited as follows:
Lambert, T. (2018) tlambert03/FPbase. Zenodo. doi:10.5281/zenodo.1244328
The source code is available and can be referenced at GitHub: https://github.com/tlambert03/FPbase
If you have used a set of fluorescent proteins in your publication, consider creating a public protein collection on FPbase, and providing the collection URL in your publication. (collection IDs in the URL will be static over time). This creates a single page where readers can see the attributes of the fluorescent proteins used in your study, and links where they can easily download the properties and spectra of your protein collection. For example from the Remus-Emsermann lab, see:
As an addition to listing the fluorescence filter sets used on your microscope in your methods section, consider linking to a custom microscope configuration on FPbase (microscope IDs and URLs will also be static). In addition to part numbers and vendor links, readers can see the complete filter spectra for every specific optical configuration used in your experiment. Microscopes can also be paired with protein collections for tidy presentation of the conditions used in your paper.