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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

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    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

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    • Legacy Projects
    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

    Read more

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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  • User Programs
    • Calls for User Proposals
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    • Submit a Proposal
    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

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    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

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    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

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User Programs
Home › User Programs › User Program Info › FICUS Overview

FICUS Overview

The “Facilities Integrating Collaborations for User Science” (FICUS) initiative was established in 2014 to encourage and enable researchers to more easily integrate the expertise and capabilities of multiple Department of Energy Office of Science National User Facilities into their research. In recognition of the increasingly collaborative and multidisciplinary nature of DOE mission science projects, this initiative aims to encourage innovative research exploiting a range of capabilities.

Previously researchers had to apply to each facility with separate review schedules and selection processes, making it difficult to propose projects that truly integrated the capabilities of more than one facility. The FICUS initiative not only simplifies and streamlines this process, but enables scientists to conduct fundamental science experiments in ways they couldn’t with projects undertaken separately at either user facility. Future calls are expected to continue to expand the range of facilities and capabilities accessible through the program.

  • FICUS JGI-EMSL Collaborative Science Initiative
  • FICUS JGI-NERSC-KBase Biological Data Science

How does FICUS Work?

Proposals for the annual FICUS call with EMSL begin with a Letter of Intent (LOI) from a researcher, briefly describing the project motivation, experimental design, capabilities to be used and DOE mission relevance. LOIs allow JGI and EMSL to plan for appropriate review and prevent full applications for projects outside of DOE mission areas or outside the scope of the call. Letters are reviewed by JGI and EMSL scientific staff, and nearly all LOIs 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 or EMSL’s capabilities. In these cases, staff scientists will often be able to suggest an alternative strategy that meets the project objectives.

Proposals submitted to the JGI-NERSC-KBase call do not use the Letter of Intent; rather proposals are submitted in a single step.

The researcher then submits a proposal for consideration in the next review cycle. All proposals undergo technical review by JGI staff as well as staff at the other participating facilities, who consider technical feasibility and readiness to begin work, checking such factors as genome size, polymorphism level, sample quality and availability, etc.  During scientific peer review, proposals are evaluated and placed in rank order by the reviewers. The ranked proposal list, along with a recommendation from management at JGI and the other participating facilities, 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 customized analysis, the JGI also participates in publication of results.

Approved FICUS plans for past years

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