JGI Technology Development Pilot Program (TDP)

Purpose

JGI's current main User Program, the Community Sequencing Program (CSP) is intended for large (terabase-) scale sequencing projects, with an annual review cycle befitting the large commitment made to these projects. The CSP offers users access to the latest generation of sequence-based technologies at a scale that requires the capabilities of a large genome center, focusing on methods that are sufficiently well-established at the JGI to be utilized in a "data production" setting.

To complement the CSP, the Technology Development Program (TDP) was designed to provide users with early access to nascent technologies at the JGI and in close collaboration with onsite scientists. Projects supported through the TDP are expected to use groundbreaking methods that are currently emerging (and not offered through the CSP program) to address questions of immediate DOE mission relevance. High-risk/high-reward projects exploring the very limits of current technology in the context of cutting-edge scientific questions are encouraged.

Capabilities

sequencing machine at work Sequencing Technologies:

Third Generation Long Read Single Molecule Sequencing

3kb + Average Read Lengths
100Ks of Reads

Prokaryotic methyl-Adenosine Detection

Molecular Technologies:

Micro and other emerging RNA Libraries
ChIP-Seq (RNA pol-II; Histone Modifications; other)
DNase Sensitivity (FAIRE; DNase I)
Bi-sulfite Methylation Detection
Community Suggestions

Anticipated Scale

While an upper limit of sequencing allocated to each proposal has not been established, a total annual sequencing capacity of 2.5TB will be available for the entire program. Approved projects are expected to be of pilot scale and their size will be more often limited by complexity of library creation or data analysis to be carried out by JGI. The proposed scale should be sufficient to demonstrate feasibility and result in publication upon completion.

DOE Relevance

Proposed projects should address problems within DOE's mission areas of bioenergy, global carbon and nutrient cycling, and biogeochemistry. A more complete discussion of DOE mission relevance can be found at www.jgi.doe.gov

Mechanism of Application

Proposals can be submitted through JGI's electronic submission system using the myJGI logon. New users must register with the system before an application can be submitted. Proposals are limited to 3 pages and should include:

a brief description of the problem to be addressed including DOE relevance,
JGI capabilities to be exploited and any new capabilities that will be developed,
thespecific number of samples to be provided to JGI and a timeline for obtaining them,
an analysis plan,
alist of project collaborators and their roles.

The PI should append a biosketchin NIH, NSF or similar format.

Pre-proposal Inquires

Contact:

Len Pennacchio, Deputy Director for Genomic Technologies
LAPennacchio@LBL.GOV

Proposal Review

To account for the rapid advances in technology development in this area, proposals can be submitted at any time and will be reviewed by senior management at JGI, generally within 2 weeks of submission. Review criteria include responsiveness to program guidelines, novelty and potential value of the project if successful, capacity and staffing availability, and ability of the users to provide required materials in a timely fashion. JGI-approved proposals will be reviewed by BER program managers for final approval.