DOE Joint Genome Institute

  • COVID-19
  • About
  • Phones
  • Contacts
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Products
    • Science Highlights
    • Scientists
    Screencap of green algae video for PNAS paper
    Green Algae Reveal One mRNA Encodes Many Proteins
    A team of researchers has found numerous examples of polycistronic expression – in which two or more genes are encoded on a single molecule of mRNA – in two species of green algae.

    Read more

    Advances in Rapidly Engineering Non-model Bacteria
    CRAGE is a technique for chassis (or strain)-independent recombinase-assisted genome engineering, allowing scientists to conduct genome-wide screens and explore biosynthetic pathways. Now, CRAGE is being applied to other synthetic biology problems.

    Read more

    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.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • 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.

    More:

    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.

    Read more

    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

  • Data & Tools
    • IMG
    • Genome Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    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.

    More

    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.

    More

    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.

    Read more

  • User Programs
    • Calls for User Proposals
    • Special Initiatives & Programs
    • User Support
    • Submit a Proposal
    screencap long reads webinar_ Metagenome Program
    Utilizing long-read sequencing for metagenomics and DNA modification detection webinar
    Watch the webinar on how the JGI employs single-molecule, long-read DNA sequences to aid with genome assembly and transcriptome analysis of microbial, fungal, and plant research projects.

    More

    SIP engagement webinar
    “SIP technologies at EMSL and JGI” Webinar
    The concerted stable isotope-related tools and resources of the JGI and the Environmental Molecular Sciences Laboratory (EMSL) may be requested by applying for the annual “Facilities Integrating Collaborations for User Science” (FICUS) call.

    Read more

    martin-adams-unsplash
    CSP Functional Genomics Call Ongoing
    The CSP Functional Genomics call helps users translate genomic information into biological function. Proposals submitted by July 31, 2021 will be part of the next review.

    Read more

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)
    A Team Effort Toward Targeted Crop Improvements
    A multi-institutional team has produced a high-quality reference sequence of the complex switchgrass genome. Building off this work, researchers at three DOE Bioenergy Research Centers have expanded the network of common gardens and are exploring improvements to switchgrass.

    More

    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 .

    More

    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.

    More

User Programs
Home › User Programs › User Program Info › FAQ

FAQ

Where can I find instructions and templates for submitting proposals?

Review the list of open calls; click on the call link to see specific details including project types supported, sample/capacity limits, and instructions.  Many of the submissions are done using web-based forms.  To view the proposal templates, go to the proposal submission page in WIP, login using your JGI account (create one here if you don’t already have an account) and click the “begin” button for the call you are interested in.

All proposals must be written in English.

Are there example proposals that I can view?

Yes.  While the details of the proposal templates may have changed slightly since these were submitted, the format is largely the same.  These proposals were shared with the permission of the PI.

CSP New Investigator proposal – example

CSP Annual Letter of Intent – example 1, example 2, example 3

Who is eligible to submit CSP and FICUS proposals?

The CSP and FICUS calls are open to both domestic and international applicants from any institution type and at any career stage. Generally, most users are able to work with Berkeley Lab. However, users from certain countries (Iran, North Korea, Cuba, and Syria), need DOE permission and authorization from other U.S. Government agencies to work with Berkeley Lab, a process which can take 6 months or longer to obtain with no guarantee of approval.   JGI staff are not eligible to submit proposals, or to be listed as co-PIs or collaborators.  JGI’s standard User Agreement must be signed before work can begin, and all CSP proposals are subject to JGI policies on Data Release and Publication.  Except for applicants to the CSP New Investigator call, investigators may have existing proposals with the JGI.

How can I increase my chance of success?

Get tips on how to submit an effective proposal here: https://jgi.doe.gov/webinar-successfully-apply-for-csp-proposal/  This webinar is targeted to the New Investigator call, but many of the suggestions can be applied to JGI’s other calls as well.  The number one tip: contact us in advance for advice!

What can I request from the CSP and FICUS programs?

The deliverables can range from raw sequence data to well-annotated assembled genomes to synthesized DNA constructs to metabolomics data, depending on the specific product types covered in the call.   If you have technical questions, we encourage you to contact us in advance for advice.

How much will it cost me to sequence or synthesize my target or obtain metabolomics data?

For accepted proposals, sequencing, synthesis, metabolomics and analysis will be paid for by the Department of Energy’s funding of the JGI.

Should I include budget information in my proposal?

No, the proposal is only for sequencing, metabolomics and/or synthesis effort at JGI. There is no cost to the user and no granting of funds.

Where do I go to get sequence data from an approved proposal?

A complete listing of approved proposals can be found here.  All sequence data will be accessible on the JGI Portal.

I am applying for a research grant. I would like to request genomic resources from the JGI for this research grant. Can I get technical information, deliverables, and perhaps a support letter from the JGI?

Yes. You should indicate this in the proposal so we can select the project provisionally. If your project makes it successfully through the scientific review and is selected, we will provide you with the information you need for the grant.

If I have ongoing research funding to carry out functional studies using the proposed sequencing data, should I mention it in the proposal?

Yes. You should use it to demonstrate that you have the capability to perform the plans described in your proposal.

Will the JGI provide other types of genomic resources such as construction of cDNA libraries, BAC libraries, or genotyping?

While, in general, requests will be for sequencing and its analysis, investigators are encouraged to contact the JGI concerning other genomic resource needs.

Am I allowed to submit NIH-oriented projects to the CSP and FICUS calls?

Scientific merit is the major criteria used in evaluating proposals; however, the proposal must demonstrate relevance to DOE missions.  USDA, NSF, and NIH operate sequencing programs, and potential users are urged to contact these agencies for projects when appropriate.

I am in a competitive field. I do not want my competitors to know that I am submitting a proposal to the JGI. What degree of confidentiality do I have?

The review process is confidential. Once a project is selected, however, we will post the PIs’ names and the proposal title. All data will be released in accordance with the JGI Data Release Policy.

What are the JGI’s sample material requirements?

Sample requirements for sequencing projects can be found here.  The quality of the starting material is one of the greatest predictors of a successful sequencing project.

What should be included in the “sample regulatory compliance” section of the proposal?

Utilization or transfer of any genetic resource may be covered by local, national or international regulation.  These requirements apply whether the use is for non-profit or for-profit activity. A few examples include:

Convention on Biological Diversity Nagoya Protocol on Access and Benefit Sharing

Benefits sharing in the US National Parks

USDA Animal and Plant Health Inspection Service permits

US Fish and Wildlife permits

These examples may apply to your samples, but do not serve as a comprehensive list of regulatory requirements. The user is responsible for determining which regulations or permit requirements are appropriate and ensuring compliance before any materials are transferred to JGI.

What format should I use for my CV?

JGI does not require a specific format; many investigators use a format similar to the NIH or NSF biosketches.  In general, CVs should not exceed three pages.

Who can I contact with questions?

We encourage submitters to contact JGI to discuss their proposals prior to submission!  Specific contact info is available on the individual call pages, or please contact us with your general questions.

  • Calls for User Proposals
  • CSP Overview
  • FICUS Overview
  • Closed Calls
  • Review Process and Scoring Criteria
  • DOE Mission Relevance
  • FAQ

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Podcasts
  • Webinars
  • CSP Plans
  • Featured Profiles
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Emergency Info
  • Accessibility / Section 508 Statement
  • RSS feed
  • Flickr
  • LinkedIn
  • 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

© 1997-2021 The Regents of the University of California