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 FY2010 will be accepted between December 15, 2008 and January 30, 2009 and should be submitted using the web-based Work Initiation Process (WIP) interface. Proposals for bacterial and archaeal isolates should be submitted as brief white papers beginning in January 2009, will be accepted on a continuous basis and will be reviewed every three months. Submitters whose letters of intent are approved will receive further instructions via email.

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 the CSP 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 within DOE’s mission areas. Proposals from researchers within the DOE National Laboratory system are accepted, and proposals from foreign investigators are also encouraged. Ultimately, the most important factor in determining whether a project will be accepted is its scientific merit.

In the application, JGI requests that applicants focus primarily on describing the science that will be enabled by completion of the project rather than the technical details of how sequencing will be carried out, because the former is the primary criterion and the latter is subject to change. Nonetheless, the CSP director does interact with ~50% of applicants to discuss technical details of their applications.

Sequencing projects will be judged on the following scoring criteria:

Scientific merit
The relevance to the DOE mission. The societal and economic importance of specific large-genome projects will also be considered.
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.

For the CSP2010 call, the JGI is targeting the following project types:

Bacterial and Archaeal isolates

Beginning in January 2009, brief white papers will be accepted on a continuous basis and reviewed every three months. Proposed organisms should broaden phylogenetic representation among sequenced organisms or participate in processes directly relevant to DOE missions. Organisms will be ranked by the panel and placed in a priority queue. Projects will be scheduled for sequencing when they reach the top of the queue. After approval, at an established time prior to project initiation, the proposer will be asked to prepare DNA according to JGI’s standard procedures with the goal of having received DNA within two months of approval. DNA of insufficient quality or quantity will delay or potentially defer approval for sequencing.

Bacterial resequencing

JGI also seeks proposals centered on resequencing of bacterial isolates for which a reference genome exists. Projects may focus on bacterial community structure, understanding gene function in bacteria under selective pressure or in mutagenized strains. We will also consider collections of highly related strains from nature that display differences in phenotypes related to DOE missions, e.g. lignocellulose degradation, fermentation of sugar substrates or metabolism of environmental toxins.

Metagenomes

Proposals are sought for sequencing and analysis of microbial communities relevant to DOE’s missions in alternative energy, biogeochemistry and global carbon cycling. Possible targets include rhizosphere communities, cellulosic biomass degrading communities, communities capable of degrading environmental toxins, or marine or terrestrial communities important in global carbon cycling. Goals of individual projects may be gene or pathway discovery or complete genome assembly, but should be driven by specific project goals rather than environmental surveys.

Eukaryotic resequencing

Proposals are sought for large-scale re-sequencing efforts that are appropriate for new short-read sequencing technologies. Appropriate targets include biomass feedstocks, model organism plants, biomass degrading fungi and plant pathogens for which a reference genome exists or is currently planned. Projects of up to 20 Gb will be considered.

Eukaryotic reference genomes

We are interested in obtaining target genomes less than 250 Mb in size that are appropriate for sequencing on new technology platforms. Ideal candidate genomes should be inbred, and have minimal polymorphism and repeat content. If this information is not currently available, applicants are encouraged to apply for pilot scale sequencing in order to acquire this basic genome information. As with other sequencing targets, these genomes should be relevant to DOE’s missions.

Additional information on proposal types:

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 (LOI), 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 LOI should be submitted using the web-based Work Initiation Process (WIP) form and should include proposal title, focus area (based on the project types requested in the CSP call), description, justification, sequence utilization, community interest and DOE mission relevance. The LOI 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 further 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 250Mb, 10 pages for 250Mb to 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)