CSP Sequencing and Project Management

Before sequencing can begin, users must sign a formal User Agreement that defines legal responsibilities of the JGI and the User. Additionally, JGI Project Managers work with users and JGI scientists and technical staff to prepare a Statement of Work (SOW) document that defines the scope of sequencing and analysis and lays out roles and responsibilities. The SOW 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.

Once a project has been approved through the review process, and the Scope of Work and User Agreement documents have been signed, the sequencing project may begin. Essential elements of the project are entered into JGI’s Global Project Tracking System (GPTS) to allow staff to understand the requirements, history and status of any DOE JGI sequencing project. Active management of sequencing projects involves the following considerations:

Designation of a Project Manager within the JGI.

Designation of a principal collaborator or "Project Representative," not necessarily the original applicant, who will be the JGI's main point of contact throughout the duration of the sequencing project.
The collaborator must provide DNA, libraries, and other materials as described in the Statement of Work. Detailed guidelines for DNA submission are available. All materials described in the project proposal must be immediately available with the appropriate documentation. Failure of the collaborator to provide DNA, libraries, or other materials described in the proposal in a timely fashion may lead to cancellation of the project and/or return of the proposal to the review panels.
Project components each require separate documentation. Those projects that are a composite of various components (whole-genome shotgun, cDNAs, BACs, etc.), will require separate DNA QC documentation and sterility certificates (for BSL-2 or RG-2 projects) for each component, or for resubmissions of a component (from new source materials to make a new library).
All DNA/RNA/cDNA source materials must pass the JGI QC process. Work will not commence on a new or resubmitted project component until the source material has passed the QC process.
The JGI's Project Manager will communicate with the Project Representative to confirm, in a timely manner, when the initial sample data is of appropriate quality, free of contamination, etc.
Approved projects enter a queue, not a sequencer. When a sequencing component of an approved project is qualified for production, it enters the production queue. This queue is managed primarily on a first-in/first-out basis, so it can take weeks or months for actual production to begin on a project, depending on the current workload and the length of time required to prepare and quality control representative clone libraries. Scheduling of the sequencing will be at the discretion of the JGI, given the overall production sequencing queue and the need to optimize available resources. See Prioritization and Scheduling of Projects for details.
The post-sequencing analysis and publication plans must be coordinated and scheduled as specified in the Statement of Work.