Overview of the Community Science Program
What is the Community Science Program?
The Community Science Program (CSP) was created to provide the scientific community at large with access to high-throughput sequencing and other resources at the Department of Energy Joint Genome Institute (JGI) for projects of relevance to DOE missions. Projects will be chosen based on scientific merit--judged through independent peer review--and relevance to issues in global carbon cycling, alternative energy production, and biogeochemistry. Criteria for participation in this program, the review process, and interactions between JGI and participants are outlined on this web site. Through this program, the Department of Energy aims to advance genome science-based scientific research from a broad range of disciplines.
Important changes for the current proposal cycle are as follows:
- Small-scale microbial and metagenome proposals will be submitted as brief white papers rather than full proposals, will be accepted on a continuous basis, and will be reviewed every six months. Currently, proposals may include bacterial and archaeal epigenomes and metagenome samples (including iTags). Proposal requests for bacterial and archaeal isolate and single-cell sequencing projects, as well as RNA sequencing and resequencing projects are expected to resume in the fall of 2015.
- JGI has introduced a synthetic biology call. Proposals will be submitted as white papers, will be accepted on a continuous basis, and will be reviewed every six months.
- The CSP annual call seeks to encourage large-scale projects that make optimal use of JGI’s sequencing, synthesis and analysis capabilities.
- The Community Science Program has expanded to include a JGI-EMSL Collaborative Science Initiative. This annual call solicits pilot projects that integrate the genomics and molecular characterization resources of both JGI and EMSL.
How does the CSP Work?
CSP proposals for the annual call and the JGI-EMSL Collaborative Science Initiative begin with a letter of intent from a researcher, stating that they plan to send in a proposal to sequence DNA from an organism or group of organisms. Letters of intent allow JGI to plan for appropriate review and prevent full applications for projects outside of DOE mission areas, or outside one of the focus areas identified in the call. Letters are reviewed by JGI scientific staff and OBER program managers, and EML scientific staff for letters in response to the joint call. Nearly all letters of intent are accepted for full proposal submission. The major reason for disapproval is a lack of relevance to DOE mission areas. In some cases, a meritorious project does not fit within JGI’s capabilities. In these cases, JGI scientists will often be able to suggest an alternative strategy that meets the project objectives. (Proposals submitted to the small-scale microbial/metagenome or synthetic biology do not use the letter of intent; rather proposals are submitted in a single step.)
Following acceptance of a letter of intent (if required), the researcher submits a proposal for consideration in the next review cycle. All proposals undergo technical review by the JGI's scientific and technical staff, who consider technical feasibility and readiness to begin work, checking such factors as genome size, polymorphism level, sample quality and availability, etc. At peer review, proposals are evaluated and placed in rank order by the scientific reviewers. The ranked proposal list is then forwarded to DOE for final approval. Following DOE approval, project managers negotiate project specifics with PIs (including JGI scientists as needed), and the work plan is written into a Statement of Work document.
For sequencing projects, once work is under way, raw sequence data is released to NCBI’s Sequence Read Archive on a regular basis, in accordance with JGI's data release policy. Interactions with applicants and others who might be interested in the project are coordinated through JGI's Project Management Office. At the completion of a project, the JGI makes the assemblies, gene annotations, and analyses available to the community at large. In most cases where the JGI provides more than raw sequencing reads, the JGI also participates in publication of results.