DOE Joint Genome Institute

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    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.

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

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    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.

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    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.

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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    • GOLD
    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.

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    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.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    • Submit a Proposal
    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.

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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

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    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.

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    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.

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    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.

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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

CSP Functional Genomics proposal – example

FICUS proposal (JGI/EMSL) – example 1, example 2

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.

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