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    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

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    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

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    Algae growing in a bioreactor. (Dennis Schroeder, NREL)
    Refining the Process of Identifying Algae Biotechnology Candidates
    Researchers combined expertise at the National Labs to screen, characterize, sequence and then analyze the genomes and multi-omics datasets for algae that can be used for large-scale production of biofuels and bioproducts.

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    This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center)
    When “The Blob” Made It Hotter Under the Water
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

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    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

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    Ian Rambo, graduate student at UT-Austin, was a DOE Graduate Student Research Fellow at the JGI
    Virus-Microbe Interactions of Mud Island Mangroves
    Through the DOE Office of Science Graduate Student Research (SCGSR) program, Ian Rambo worked on part of his dissertation at the JGI. The chapter focuses on how viruses influence carbon cycling in coastal mangroves.

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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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    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

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    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

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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.

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    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

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    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

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    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

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    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

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    Integrating JGI Capabilities for Exploring Earth’s Secondary Metabolome
    Natural Prodcast podcast: Nigel Mouncey
    JGI Director Nigel Mouncey has a vision to build out an integrative genomics approach to looking at the interactions of organisms and environments. He also sees secondary metabolism analysis and research as a driver for novel technologies that can serve all JGI users.

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User Programs
Home › User Programs › User Support › Policies

Policies

  • JGI Data Policy
  • JGI Publication Policy
  • Acknowledgment of Federal Support
  • JGI Scientist Code of Conduct

JGI Data Policy

Data produced and released by the US Department of Energy (DOE) Joint Genome Institute (JGI) are subject to the following Data Policy. It is our mission to support open data and information sharing. We also recognize the need to have a limited and time-sensitive protection of certain types of data to support their use by those generating data.

The JGI Data Policy applies to research data and analysis products (referred to as “data” for the remainder of this policy) produced through all user projects accepted FY22 and later through the Community Science Program (CSP), Facilities Integrating Collaborations for User Science (FICUS) initiative, Director’s Science (DS), Biological and Environmental Research Support Science (BERSS), or Bioenergy Research Centers (BRCs).

For sequencing or metabolomics projects: data are subject to a one-year embargo. For each data or analysis product (raw or processed), the embargo starts at completion of standard deliverables as described in the product catalog. At the end of the embargo period data will be made publicly available on relevant JGI portals (i.e. JGI Genome/Data Portal, MycoCosm, PhycoCosom, Phytozome, or IMG) and outside repositories (e.g. NCBI SRA or GenBank) as described in the product catalog and are unrestricted for use.

For DNA synthesis projects: data are subject to a two-year embargo starting at construct or strain delivery. Detailed sequence information for constructs are made publicly available through the Inventory of Composable Elements (ICE) repository at the end of the embargo period.

During the embargo, proposal PIs, Co-PIs, and collaborators of any given proposal have full access to their data and may request full release to the public, ending the embargo at any point after data generation. The data will not be publicly available in JGI portals or outside repositories until the earliest of three points: (1) publication of the data (including, but not limited to, publication or citation of accession numbers in a peer-reviewed journal, or any public deposition of the data at outside repositories), (2) PI request to list data publicly, or (3) at the end of the embargo period. If data or analyses of the data are made publicly available in any format by the PI or collaborator during the embargo period, JGI will consider the embargo nullified. After the embargo period, JGI places no further restrictions on data availability or utilization except as outlined in the Publication Policy.

For questions about JGI policies, please contact Policy & Agreements Officer Grace Sprehn.

For a complete list of standard deliverables see the product catalog. All data are also subject to the Publication Policy below.

Legacy Data, Restricted Use, and Data Policy Transitions:

Previous JGI Data Release & Utilization Policies may be read in full here. The following is a summary and explanation of policies in place during the transition to the above JGI Data Policy.

Pre-FY22 proposals: Proposals accepted before FY22 are transitioning away from producing use-restricted data. JGI proposals typically include multiple projects of different types which can span several years. Projects are defined at proposal acceptance and may also be added during the proposal lifecycle based on scientific need. Proposals are considered complete when all agreed-upon projects are complete. This policy is applied at the project level to expedite the change in data policy. Data from projects for which JGI has not yet received samples as of Sep 30, 2021 are subject to a 2-year embargo to maintain the timeline for unrestricted data availability agreed to at proposal initiation. Data from projects that received samples before Sep 30, 2021 and are ongoing are subject to the 2-year use-restriction policy as described here. No single project has data under both use-restriction and embargo policies.

Use-restricted data: In past data policies, data were publicly visible in JGI systems only but use-restricted until publication by PIs or at a set time (most recently, two years after release to JGI portals). JGI will no longer produce use-restricted data except in already active projects as described above, but JGI portals will still host use-restricted data until the period of use-restriction expires. All use-restricted data have an associated date of use-restriction expiration. Use-restrictions are also lifted at publication of the data. In short, those users not involved with the proposal under which the data were generated who wish to include use-restricted data in publications, or who wish to redistribute data in any way are required to contact the proposal PI and receive permission for their planned work. It is the responsibility of the user to ensure they have taken all appropriate steps before publishing or otherwise making publicly available use-restricted data.

JGI Publication Policy

The JGI has a strong interest in seeing that the data produced by the facility result in scientific publications. JGI users and collaborators have the right to produce manuscripts for publication and the responsibility for leading the efforts to do so, and JGI expects acknowledgment (see Auspice Statement below) for the generation of sequence or metabolomic data, DNA synthesized, and any other contributions, such as assembly, analysis, annotation, verification, creation of genome browsers, etc.

The users, collaborators and JGI together aim to publish the first analysis of data produced at the facility, provided this is done in a timely fashion. The publications resulting from such efforts should specify the collaborative nature of the project, and authorship is expected to include all those contributing significantly to the work.

The JGI has significant experience and capabilities in the analysis, annotation, comparative analysis, and interpretation of sequence, metabolomics, and functional genomics data types as well as in advanced assembly and engineering strategies for DNA synthesis applications. If JGI personnel contribute substantially to data generation and analysis or DNA synthesis and engineering work in a way that goes beyond the deliverables for JGI standard products  and/or make substantial intellectual contributions to the production of a manuscript, it is best practice to credit those individuals as authors on the publication for their contributions. Authorship arrangements should reflect the respective contributions of collaborators and users. For example if, by agreement with the collaborator, JGI staff take a lead role in the analysis, planning, writing, and editing of the manuscript, it is best practice for those individuals to appear as first and/or senior authors of the paper.

Auspice Statements

Including appropriate tracking numbers is critical to facilitating the tracking of publications and allowing connections between all systems to maximize the impact of user research. The crucial elements are proposal Award DOI(s), JGI’s ROR ID number, and DOE contract numbers.

Please include the appropriate Auspice Statement in any external publications, and include proposal Award DOIs following these guidelines:

  • If you use data from 3 or fewer JGI proposals, include those DOIs in the auspice statement where indicated.
  • If you use data from 4 or more proposals, include those DOIs in a data availability section.
  • If it is impossible (for word limits or other reasons) to include all of the DOIs for proposals you accessed in the data availability section, include those DOIs in the supplemental materials for your publication.

Any external publication using data from the “Facilities Integrating Collaborations for User Science” (FICUS) JGI-EMSL program should contain the following Auspice Statement in the acknowledgments:

“(A portion of) This research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program (proposal: INSERT PROPOSAL AWARD DOI(S) HERE) and used resources at the DOE Joint Genome Institute (https://ror.org/04xm1d337) and the Environmental Molecular Sciences Laboratory (https://ror.org/04rc0xn13), which are DOE Office of Science User Facilities operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL).”

Any external publication using data from the “Facilities Integrating Collaborations for User Science” (FICUS) JGI-NERSC program should contain the following Auspice Statement in the acknowledgments:

“(A portion of) This research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program (proposal: INSERT PROPOSAL AWARD DOI(S) HERE) and used resources at the DOE Joint Genome Institute (JGI) (https://ror.org/04xm1d337) and the National Energy Research Scientific Computing Center (NERSC) (https://ror.org/05v3mvq14), which are DOE Office of Science User Facilities operated under Contract No. DE-AC02-05CH11231.”

All other external publications using JGI data produced under a specific proposal(s) and authored by that proposals PIs, Co-PIs, and collaborator(s), or any JGI-led publication without user data should contain the following Auspice Statement in the acknowledgments:

“The work (proposal: INSERT PROPOSAL AWARD DOI(S) HERE) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.”

Any external publication using JGI data that is not associated with a specific JGI proposal, and/or by authors other than PIs, Co-PIs, and collaborators of a JGI proposal should contain the following Auspice Statement in the acknowledgments: 

“(A portion of) These data were produced by the US Department of Energy Joint Genome Institute (https://ror.org/04xm1d337; operated under Contract No. DE-AC02-05CH11231) in collaboration with the user community.”

Acknowledgment of Federal Support

DOE Funding Acknowledgment: please follow the DOE Office of Science guidelines for news releases: https://science.osti.gov/Funding-Opportunities/Acknowledgements

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