This reference guide describes standard operating procedures (SOP) for emLab projects. This SOP is organized into 5 different sections: (1) File Structure, (2) Data, (3) Code, (4) High Performance Computing, and (5) Reports and Publications. Section 1 covers file structure and storage; Section 2 describes file naming and metadata standards, as well as what the emLab data directory is composed of; Section 3 highlights best practices for coding; Section 4 covers high performance computing; and Section 5 outlines aspects of the publication process from emLab affiliations to preparing a public GitHub repository.