FY2019 JGI-EMSL Collaborative Science Call (Status: CLOSED)
Letters of Intent (LOI) for collaborative research applications with the Environmental Molecular Sciences Laboratory (EMSL) and the Joint Genome Institute (JGI) are being accepted until March 21, 2018. This call is part of the Facilities Integrating Collaborations for User Science initiative (FICUS) – a collaboration that was developed between user facilities stewarded by the Department of Energy (DOE) Office of Biological and Environmental Research (BER). FICUS was established in 2014 to encourage and enable researchers to more easily integrate the expertise and capabilities of multiple user facilities into their research. The FICUS call between EMSL and DOE JGI represents a unique opportunity for researchers to combine the power of genomics and molecular characterization in one proposed research project.
FICUS applications follow a proposal package guidance, schedule, and review process that is tailored to meet the requirements of the facilities involved. Applications begin with a required LOI, and requests for full proposals will be transmitted by April 9. Returning users especially are advised to carefully review the unique elements of this joint program as some of the procedures have changed.
Successful applications will address high risk/high payoff projects in the focus topic areas that can be completed in an 18-24 month timeline; use a range of the capabilities of each facility; and generate datasets beyond what each of these facilities could generate by itself. Because this program offers a diverse but integrated set of capabilities, applicants are strongly encouraged to talk to facility staff in advance to design a set of analyses that is directed at their research goals. For more details regarding the initiative application process, sample limits or the capabilities available at either facility, please check our frequently asked questions (FAQ).
Focused Topic Areas
- Biofuels and bioproducts – Projects should be aimed at characterizing biological processes that are relevant to biofuels and bioproducts, and connecting these processes to genomics-based analyses in organisms of interest (plants, fungi, microbes and algae). Relevant biological processes include plant polymer biosynthesis and deconstruction, especially lignin and production of metabolites that are precursors of biofuels and/or bioproducts. Proposals for projects investigating organisms and/or biological products involved in plant-microbial interactions that impact biofuel feedstock productivity are also encouraged.
- Biogeochemistry – Projects should focus on the cycling and transport of elements and molecular compounds in soils, aquatic sediments and the subsurface, or on their involvement in plant or microbial regulatory/metabolic processes. Proposals should seek to illuminate critical biogeochemical processes, including those through which bacteria, archaea, fungi, and/or plant and/or microbial communities/consortia influence the transformation and transport of metals or the cycling of C, N, and P. Such projects should seek to link microbial populations, genes and traits to molecular biochemistry.
- Inter-organismal interactions – Projects should explore the exchange of carbon, nitrogen and other elements among plants and microbes in above and below ground ecosystems as well as investigate signaling, cooperation or competition via physical or chemical means. Proposals for projects studying the impact of genetic diversity within plant populations on plant-associated microbial communities and plant-microbial interactions are also encouraged, as are those structurally or functionally characterizing secondary metabolites potentially involved in cell-cell interactions.
- Novel applications of molecular techniques – Projects should be aimed at stretching the boundaries of scientific integration of EMSL and JGI capabilities, touching on DOE/BER missions involving biofuels, bioproducts, environmental processes, plant-microbe interactions, soil-atmospheric interactions, soil/subsurface/aquatic sediment biogeochemical processes, nutrient traffic, and transformations, and other BER-aligned topics, and may include relevant organisms such as bacteria, archaea, fungi, algae, protists, soil organisms, plants, and viruses and phages. The scale of such projects should be limited to proof-of-principle with the possibility of expanded support upon demonstration of novel results. This work could involve radically different experimental or computational approaches or application of expertise and/or approaches from other research domains.
Accepted projects must address or be aligned with 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 capabilities that can be applied to proposals under this call, including a variety of in-situ probes for NMR, advanced electron microscopy in quiet space including a dynamic transmission electron microscope, super resolution fluorescence microscopy for live cells, high-resolution mass spectrometers including a 21 Tesla FTICR, nonlinear optical spectroscopy (sum frequency generation), a 3.4 petaflop supercomputer, interactive data visualization tools, NanoSIMS, and Atom Probe Tomography.
Applications are not limited to these EMSL capabilities and may request any combination of EMSL’s capabilities, but they must provide adequate information to demonstrate the plan for integration and justify the amount of time or other resources requested. Applicants are strongly urged to discuss their resource needs with the respective Capability Lead or Instrument Scientist 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.
Researchers interested in learning more about EMSL and specific instruments can view a dozen different instruments in four of EMSL’s laboratories through a panning 360-degree virtual tour. The tour includes lab and instrument overviews available through text, images, video and web pages. It features EMSL’s surface science instruments, nuclear magnetic resonance spectrometers, ion mobility mass spectrometers, and cell isolation and surface analysis tools.
DOE JGI primarily employs next-generation short-read sequencing platforms augmented by 3rd generation single-molecule/long-read capabilities (read lengths in the 6-10kb range). The capabilities available for this call are listed below. Proposals should request no more than 1 Tb of sequencing, 500 Kb of synthesis and up to 200 samples for metabolomics polar analysis and 500 samples for nonpolar analysis. Researchers are encouraged to review JGI’s sample submission guidelines to obtain additional information about the amounts of material that are required for various product types. Individual proposals may draw from one or more of these capabilities as needed to fulfill project goals. Successful projects frequently exploit a combination of capabilities:
- Core Capabilities Include:
- De novo sequencing and annotation of plant, fungal, bacterial, and archaeal genomes
- Resequencing for variation detection
- Fluorescence activated cell sorting for targeted metagenomics and single-cell genomics
- Microbial community DNA/RNA sequencing and annotation
- Comprehensive transcriptome analysis including coding transcript annotation, non-coding RNA (both small and long ncRNA) characterization and expression profiling
- Target enriched re-sequencing
- Whole genome DNA methylation analysis
- Chromatin analysis including FAIRE and ChIP-seq
- DNA/gene synthesis
- Analysis pipelines for the datasets above
- High throughput metabolomics for functional genomics
- DOE JGI also has limited capacity for the following developing capabilities:
- Flow cytometric sorting and genomic analysis of metabolically active microbes labeled via Bio-Orthogonal Non-Canonical Amino acid Tagging (BONCAT). Close consultation with JGI scientists regarding goals and experimental design is necessary.
- Custom genome analysis of generated datasets
- Access to high-performance computing at the National Energy Research Scientific Computing Center (NERSC)
Submitted LOIs will be reviewed by members of both EMSL and DOE 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 7, 2018. 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, and approved projects will start on October 1, 2018.
Questions regarding FICUS or specifics related to this Call may be directed to the contacts listed below.
For general LOI or full proposal inquiries – Terry Law (firstname.lastname@example.org, 509-371-6003)
For EMSL inquiries – Mary Lipton (email@example.com, 509-371-6589)
For Joint Genome Institute inquiries – Susannah Tringe (SGTringe@lbl.gov, 925-296-5813)
To respond to the FY18 call, a Letter of Intent (LOI) is required before submitting a proposal. Letters of intent will only be accepted electronically and should be submitted via the EMSL Portal from Jan 10 – Mar 21, 2018. Applicants will be advised by email whether to prepare a full proposal, and full proposals will be due May 7, 2018. Guidance for submitting full proposals will be included in the email notification to invited applicants.
The full FY18 schedule is below:
|Calls for proposals issued||January 10, 2018|
|Letters of intent received||March 21, 2018|
|Invitation of proposals||April 9, 2018|
|Proposals received||May 7, 2018|
|Technical and scientific review||June 21, 2018|
|Approval and rejection notices sent||July 31, 2018|
|Prepare user agreements||September 2018|
|Projects start||As soon as user agreement is finalized|