CSP Review Process and Contract Documents

Review Process

Proposals will go through a three-step review process. First, they are evaluated for technical feasibility (based on the required letter of intent) by the JGI's scientific staff. Second, proposals are considered by the Proposal Study Panel (PSP). The PSP reviews and scores the proposals based on an objective set of criteria (listed below) and recommends project priorities to the Scientific Advisory Committee (SAC). Finally, proposals are reviewed by the SAC, which approves them for sequencing based on the rank order established by the PSP and the sequencing capacity available. The project coordinator managing each project then begins a consultative process with the proposer that culminates in the creation of a Scope of Work .

Project proposals are reviewed at least yearly. A letter of intent is required to submit a proposal to the CSP. Applicants with concerns about the suitability of their projects for this program are urged to contact the CSP prior to writing a proposal.

Scoring Criteria

Proposals will be scored on the following factors:

Relevance to DOE mission. Relevance to the DOE missions of carbon sequestration, bioremediation, 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 to the large-genome program must establish clear relevance of the project to the DOE mission.
Scientific merit. An important goal of this program is to direct the 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.
Demonstrated capability of the applicant(s) and/or the scientific community to use the genome sequence. Large-scale sequencing 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 JGI resources to be allocated. Weight will be given to the effort required for each project in order to optimize the JGI's overall contribution to scientific discovery.
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.

Scope of Work and User Agreement

After a proposal has been approved through the technical and scientific review process, the principal investigator of each proposal will engage in a discussion (collaborate) with JGI project managers to define a project plan. This discussion will culminate in a written "Scope of Work" that defines the expectations and mutual responsibilities for the project. Work will not commence on a project until a signed Scope of Work is in place and all required documents are approved (DNA QC, sterility certification, etc.). The Scope of Work includes the following items:

Defined source, protocols, and timeline for the provision of DNA, libraries, and any other resources needed to initiate the project, including required ancillary documentation (e.g., experimental data supporting genome size estimates, BAC library sizes, etc.).
Approximate quantity of JGI sequencing to address the scientific goals of the project, and timeline for the generation of this data, including responsibilities for analysis of early sample data to assess sequence for contamination, uniformity, and other quality control checks at the initial stages of the project. If contamination or cloning is a problem at this stage, the project may be suspended until suitable DNA is available.
Defined plan for maintaining regular communication between the JGI and collaborators through the duration of the project.
Defined responsibilities for collaborators and the JGI after the completion of sequencing, including genome assembly, automated and/or manual annotation, and other analyses, and initial plan for experimental and/or computational studies needed to address the specific scientific aims of the project.
The initial publication plan, including a provisional timeline and anticipated authorship. To the extent that JGI scientists contribute scientific and/or technical expertise or leadership to the project, it is expected that they will participate in the publication.
Acknowledgment of JGI Data Release policies, and affirmation that the project will conform to applicable safety regulations, including regulations that govern organisms that are pathogenic or could potentially be used as bioweapons.
Other relevant interactions between collaborators and the JGI, coordination with other related projects, etc. will be addressed as necessary to make the Scope of Work as comprehensive as possible.

A formal User Agreement outlining the legal responsibilities of JGI and the user must also be signed before sequencing begins.