How to Propose a CSP Project

How do I submit my proposal?

A letter of intent is required to submit a proposal to the CSP. Letters for sequencing in FY2009 are no longer being accepted. The next call for proposals will be in November 2008.

What types of projects will the JGI accept?

The JGI is interested in accepting a wide range of projects for the Community Sequencing Program. In fact, the primary goal of this program is to provide access to high-throughput sequencing to the broadest possible community of researchers and to expand the diversity of disciplines using sequence data to address scientific questions. Proposals from researchers within the DOE National Laboratory system are accepted, and proposals from foreign investigators are particularly encouraged. Ultimately, the most important factor in determining whether a project will be accepted is its scientific merit.

Sequencing projects will be judged on the following scoring criteria:

the relevance to the DOE mission. The societal and economic importance of specific large-genome projects will also be considered.
scientific merit.
the demonstrated capability of the applicant(s) and/or the scientific community to use the genome sequence.
the amount of JGI resources required for project completion.
technical feasibility.

Resequencing Projects

JGI has significantly expanded capacity for resequencing with 454 FLX (250-bp reads) and Illumina (40-bp reads) platforms. Projects of modest scope are encouraged. Investigators considering such a proposal should contact JGI (csp@jgi.doe.gov) to discuss scale and scope.

Whole-Genome Shotgun Sequencing

Requests for draft sequencing of whole organisms will be carried out by whole-genome shotgun sequencing to 8X depth. Draft assembly and initial annotation are expected as part of the proposal. This year, JGI will only accept whole-genome shotgun projects for organisms whose genome has been demonstrated to be less than 200 Mb.

Directed Sequencing Projects

Sequencing projects that are not expected to result in completed genomes also will be considered. Acceptable directed sequencing projects include (but are not limited to)

shotgun sequencing of microbial communities.
large-scale EST sequencing.
sequencing of selected BAC or fosmid clones.
sequencing of PCR-amplified genomic segments.

Proposals that Require Gap Closure

The JGI's capacity for draft sequencing is far greater than for finishing. By producing end sequences from mixed clone sizes the JGI can produce draft sequence assemblies with contiguity and accuracy sufficient for most projects. However, some projects requiring an additional effort for gap closure will also be accepted.

For genomes larger than 50 Mb, requests for gap closure finishing will be accepted only after the draft sequence is complete.

For genomes less than 50 Mb, you can choose whether to include finishing in the project proposal. Unless you specify finishing as a strict project requirement, it will be considered separately from the rest of the proposal. This will ensure that the JGI proceeds with the draft sequencing process without delays associated with other resource contingencies.

Projects Contingent on Additional Funding

In some cases, a project that involves a large sequencing effort might not be approved without additional funding to accomplish other necessary studies. At the applicant's request, projects can be selected provisionally, contingent on acquiring additional funds from other sources. With no additional funding, these projects will expire two years after being selected by the Scientific Advisory Committee.

What information should I include in my CSP proposal?

A letter of intent, informing us that you plan to submit a proposal for consideration in the next round, must be sent to JGI before the submission of a proposal. The letter helps us to plan for review and allows us to help you with the details of your proposal. Submitters whose letters of intent are approved will receive instructions via email.

Proposals for CSP sequencing projects should include details about the scientific merits and technical issues associated with the project. Proposals should also highlight the ability of the proposed study to advance our understanding of the natural world.

The proposal should include the following sections:

Section A, Brief Description (limit 1 page)

Abstract: Introduce the project, and briefly describe its scientific merits.

Scope of Work: Include specific expectations from JGI beyond generating the raw sequencing reads (e.g., assembly, annotation, human validation, gene annotation jamborees, collaboration regarding interpretation, additional efforts at gap closure, etc), along with justifications.

Section B, Background Information (limit 4 pages)

Technical Information: Specific information on genome size, G+C content, polymorphism level, and repeat structure with details about how these are known.

Available Resources: Genomic resources already in place to aid this project. e.g., physical maps, genetic maps, fingerprinted BAC or EST libraries, etc.

Scientific Importance: The importance of this project to the scientific community, including an estimate of the size of the beneficiary research community.

Relevance to DOE Mission: For large-genome proposals, this section should include a discussion of DOE relevance.

Post-sequencing Plans: Plans in place for follow-on studies using this data, including information on the competence of the proposers to perform this work or plans for collaboration with JGI or others to achieve scientific goals of the project.

Technical Challenges: List any potential technical difficulties.

Scheduling Requirements: Specify any relevant scheduling requirements.

Section C, Project Description (limit 5 pages for total requests less than 400Mb, 10 pages for 400Mb to 2Gb, 15 pages for more than 2Gb)

Project Description: Use this section to emphasize the scientific merits of your project. Your description should highlight the scientific questions to be addressed or answered, the importance of the research, and the ability of the proposed research to advance our understanding of the natural world.

Section D, References (no page limit)

Section E, CVs of Lead Investigators (limit 3 pages per investigator)

Section F, Letters of Support (no page limit)