This reference guide describes standard operating procedures (SOP) for emLab projects. This SOP is organized into 6 different sections: (1) Project Management, (2) File Structure, (3) Data, (4) Code, (5) High Performance Computing, and (6) Reports and Publications. Section 1 provides an overview of the platforms we use and how to install them; Section 2 covers file structure and storage; Section 3 describes file naming and metadata standards, as well as what the emLab data directory is composed of; Section 4 highlights best practices for coding; Section 5 covers high performance computing; and Section 6 outlines aspects of the publication process from emLab affiliations to preparing a public GitHub repository.