Joint Call for Exploratory Collaborations between EMSL and the Joint Genome Institute
EMSL and the Joint Genome Institute's Call for Exploratory Collaborations is now closed. This supplemental call to EMSL's annual Call for Proposals was open February 11 - April 8, 2013, and followed an unique proposal guidance and review processes as detailed below.
In addition to EMSL's Call for Science Theme proposals, EMSL and the Joint Genome Institute (DOE-JGI) launched their first-ever joint call to facilitate the integration of their capabilities. Both user facilities, which are stewarded by the Department of Energy Office of Biological and Environmental Research, play critical roles in supporting DOE's energy, environment and basic research missions.
Applications were accepted for pilot projects that integrate DOE-JGI and EMSL capabilities to address the following:
- Biofuels production – Projects that explore plant, fungal and microbial physiology and that enable improved production of biofuel and chemical intermediates.
- Carbon cycling – Projects that enhance our understanding of terrestrial carbon cycling with an emphasis on plant and soil associated fungal and microbial interactions and physiology.
These applications should be modest in scope, focused on high risk/high payoff projects that can be completed in 18 months, and generate datasets unique to these two facilities and beyond what each could generate by itself. An individual application should not request more than 300 Gb of DOE-JGI sequencing, in addition to the EMSL resources necessary for the proposed work. Accepted projects must broadly address DOE/BER missions, but proof of concept for the demonstration of a technology that would be applicable to a DOE mission is appropriate.
EMSL provides a wide range of unique and state-of-the-art resources that can be applied to proposals under this Call. Applications may request any combination of resources, but must provide adequate information to demonstrate the plan for integration and justify the amount requested. Applicants are strongly urged to discuss their resource needs with the respective Capability Leads or Instrument Scientists prior to responding to the Call. Contact information for these individuals is available on the resource description pages, or interested applicants may contact the User Support Office for assistance.
DOE-JGI employs almost exclusively next-generation short read sequencing platforms, with limited 3rd generation long-read capabilities (3+kb and 10kb). The capabilities available for this call are listed below. Individual proposals may draw from one or more of these capabilities as needed to fulfill project goals but if longer read sequencing is needed, the burden is on the submitter to justify the request. Successful projects frequently exploit a combination of capabilities:
- Core Capabilities Include:
- De novo sequencing of plant, fungal, bacterial, and archaeal genomes
- Resequencing for variation detection
- Single-cell DNA sequencing
- Microbial community DNA/RNA sequencing
- Comprehensive transcriptome analysis including coding transcript annotation, non-coding RNA (both small and long ncRNA) characterization and expression profiling
- Laser capture micro-dissection (LCM) coupled RNA-Seq
- Target enriched re-sequencing
- Whole genome DNA methylation analysis
- Chromatin analysis including FAIRE, histone modifications through ChIP-seq
- DNA/gene synthesis
- Analysis pipelines for the datasets above
- DOE-JGI also has limited capacity for the following developing capabilities:
- 3rd generation single-molecule sequencing
- Fluorescence activated cell sorting, including single-cell sorting and amplification
- Micromanipulation for isolation of single cells
- Multiplex emulsion PCR amplicon sequencing
- Transposon mutagenesis of bacteria
- Custom genome analysis of generated datasets
Submitted Letter of Intent (LOI)s will be reviewed by members of both EMSL and JGI scientific staff and management for relevance to DOE mission areas. Submitters whose letters of intent are approved will be notified via email to submit full proposals through EMSL's User Portal by May 28. Proposals will be peer-reviewed and ranked following the published review criteria for EMSL and DOE-JGI, using a combined panel of EMSL and DOE-JGI independent reviewers. Final decisions based on ranking for these proposals will be made by EMSL and DOE-JGI management. Approved projects will start on October 1, 2013. The full schedule, including LOI and proposal format requirements, are below.
|Call for Proposals Issued:||February 11|
|Letters of Intent Due:||April 8|
|Invitation of Proposals:||April 22|
|Full Proposals Due:||May 28|
|Technical and Scientific Review:||June 26-28|
|Decision notices sent:||Mid-July|
|Projects start:||October 2013|
Letter of Intent
Letters of intent will be reviewed by members of both EMSL and JGI scientific staff and managers. LOIs allow both facilities to plan for appropriate reviewers and prevent full applications for projects outside of DOE mission areas or any specific focus area identified in the 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.
Full Proposals (invited only)
Applicants, whose letters of intent are approved, will be notified via email to submit full proposals through EMSL's User Portal by May 28. The proposal package and review process will be different than EMSL's standard process for General and Science Theme proposals, and returning users are urged to closely review the details provided in the Guidance for Full Proposals. Proposals failing to meet these requirements will not be considered. Applicants are encouraged to submit proposals early to allow time to resubmit should issues be identified in the proposal screening process.
For information regarding this joint EMSL-DOE-JGI Call, contact: