Proposals go through a two-step review process. First, they are evaluated for technical feasibility by JGI scientific staff. Second, proposals are considered by the scientific review panel. Each proposal is reviewed by three reviewers who each prepare written comments on the proposal’s strengths and weaknesses, keyed to the review criteria (listed below). The reviews are made available to the applicants. The mean score is used to rank proposals. Recommendations on which proposals will be approved are made by JGI senior management based on the rank order established by the scientific reviewers, and the sequencing capacity available. Final approval of the proposal list is made by the DOE after review of mission relevance. The Project Manager for each project then begins a consultative process with the proposer that culminates in the creation of a Statement of Work.
Proposals will be judged on the following scoring criteria:
- Scientific merit. An important goal of this program is to direct JGI’s sequencing and informatics capacity to scientific problems of great importance and of high impact on science and society. Scientific merit will be one of the most important criteria for scoring proposals, and scoring will include an evaluation of the importance of the scientific questions to be addressed and the likelihood that genomic sequencing efforts will answer them. For microbes this should include location in the phylogenetic tree.
- Relevance to DOE mission. Relevance to the DOE missions of carbon cycling, biogeochemistry, or alternative energy sources will be considered during the review of all proposals. Projects of strictly biomedical relevance are better suited for other sequencing programs, such as those funded by the National Institutes of Health. Because of the large commitment of resources required for shotgun sequencing of genomes larger than 250 Mb, applications for large genomes must establish clear relevance of the project to the DOE mission.
- Demonstrated capability of the applicant(s) and/or the scientific community to use the resource generated. Large-scale projects should be followed up in a timely fashion with analyses or further studies that answer important scientific questions. Proposals will be evaluated on whether scientists with expertise and the necessary skills will be ready to perform follow-up research and publications. The size and productivity of the user community will also be considered.
- Amount of DOE JGI resources to be allocated. The scale of each proposal should be commensurate with its stated scientific goals. Weight will be given to the effort required for each project in order to optimize the JGI’s overall contribution to scientific discovery. The JGI may suggest focusing or expanding the scope of the proposal to improve feasibility and/or project output.
- Technical feasibility. Sequencing projects vary in difficulty. Proposed projects will be evaluated for such factors as G+C content, polymorphism level, and repeat structure, as well as resources to overcome difficulties and improve the product, such as having physical and/or genetic maps, inbred strains, fingerprinted BAC libraries, cDNA libraries, etc.