The DOE Joint Genome Institute (JGI) is first and foremost a DOE National User Facility making large-scale genomics available to users studying DOE-relevant problems in energy and environment. The JGI User Programs receive an annual target resource allocation decided upon through discussion with DOE program managers, and all user proposals are reviewed for scientific merit and DOE relevance. The JGI offers users a number of standard sequencing, synthesis and metabolomics products. Following approval, user proposals are broken into component parts (“projects”) that correspond to these products for the purpose of scoping, scheduling and tracking. This process serves both to facilitate the production process as well as to allow the resulting data to be integrated through standardized analysis pipelines.

Proposals come to the JGI through its user programs, and approved proposals are carried out by the Genomic Technologies Division in coordination with the JGI’s five Science Programs: Plant, Fungal, Microbial, Metagenome, and DNA Synthesis Science. These administrative divisions allow the considerable work of scoping, managing and carrying out the required analysis to be distributed in a way that is logical and flexible enough to be responsive to user needs. To reflect overlap in analytical approaches and pipelines, the Microbial and Metagenome Programs fall under the umbrella of the Prokaryotic Super Program and the Plant and Fungal Program make up the Eukaryotic Super Program. The DNA Synthesis Science Program oversees projects involving design of synthetic DNA and engineering of hosts. The Metabolomics Platform provides functional annotation of genomes and improved understanding of the role of small molecules in diverse biological systems relevant to DOE missions.