DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Science Programs
    • Science Highlights
    • Scientists
    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

    More

    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

    More

    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    A panoramic view of a lake reflecting a granite mountain.
    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

    Listen

    A light green shrub with spiny leaves, up close.
    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

    Listen

    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    iPHoP image (Simon Roux)
    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

    More

    Abstract image of gold lights and squares against a black backdrop
    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

    More

    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

    More

    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

    More

    croppe image of the JGI helix sculpture
    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

    Listen

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

    More

    image from gif that shows where in the globe JGI fungal collaborators are located.
    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

    More

    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

    More

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 accepted proposals, sequencing, synthesis, metabolomics and analysis will be paid for by the Department of Energy’s funding of the JGI. There is no cost to the user and no granting of funds.

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

  • Calls for User Proposals
  • CSP Overview
  • FICUS Overview
    • FICUS JGI-EMSL
    • FICUS JGI-NERSC-KBase
  • Closed Calls
  • Review Process and Scoring Criteria
  • DOE Mission Relevance
  • Proposals FAQ

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2023 The Regents of the University of California