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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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    (PXFuel)
    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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    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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    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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    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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    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

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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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User Programs
Home › User Programs › User Support › Policies › Legacy Data Policies

Legacy Data Policies

JGI Data Release Policy

The JGI Standard Data Release Policy for sequencing and metabolomics is immediate public release for all user projects accepted through the Community Science Program (CSP), Facilities Integrating Collaborations for User Science (FICUS) initiative, Bioenergy Research Centers (BRCs) program or as Director’s Science projects. The data released includes the following:

  • Raw sequence data: fastq or other file formats as appropriate are deposited to NCBI’s Sequence Read Archive (SRA) after completion of standard analysis as described in the product catalog.
  • Genome projects: assemblies and annotations are posted to JGI portals as soon as each genome project is complete. Microbial sequences (raw data and assembled contigs) are released after assembly and annotation in IMG. Fungal and plant sequences are released after assembly and annotation with RNA-seq data in Mycocosm and Phytozome, respectively.
  • Functional genomics data (e.g. resequencing and transcriptomes): analysis files, including alignments to reference genomes, are released upon completion of standard deliverables as described in the product catalog.
  • Improved assemblies and annotations and associated data will be publicly released as soon as complete.
  • Metabolomics projects: raw data will be released on the JGI Genome Portal upon completion of standard deliverables

The JGI Standard Release Policy for DNA synthesis projects requires that detailed sequence information for constructs be made publicly available through the Inventory of Composable Elements (ICE) repository two years after construct delivery for all user projects accepted through the Community Science Program (CSP), Facilities Integrating Collaborations for User Science (FICUS) initiative, Bioenergy Research Centers (BRCs) program or as Director’s Discretion projects.

This JGI Standard Data Release policy is effective for all user proposals/projects approved January 1, 2019 and later. All data are subject to the data usage policies described below and at http://genome.jgi.doe.gov/pages/data-usage-policy.jsf.

JGI Data Utilization Policy

Data produced and released to the public by the JGI is subject to a Data Usage Policy.

As a public service, the data from sequencing projects are made available to the community by the Department of Energy Joint Genome Institute (JGI) before their publication in the scientific literature. The purpose of this policy is to balance the imperative of DOE and JGI that the data from its sequencing projects be made available to the scientific community as soon as possible with the reasonable expectation that the principal investigators will publish the primary report without concerns about preemption by other groups that did not participate in the effort.

The Data Usage Policy for data generated under proposals accepted before November 2018 is:

Update May 20, 2021

In support of open science and as part of DOE’s ongoing effort to harmonize data policies, data and analysis products generated under proposals accepted before November 30th 2018 are now required to be public without use-restrictions at the latest two years from now, by May 31st, 2023. Use-restrictions will lift earlier than May 2023 if the data is published, or at the written request of a PI. When data is unrestricted it will be available without use-restrictions on JGI portals and will be publicly released to appropriate community repositories including NCBI (SRA, GenBank).

For proposals that are not yet completed and for which data generation is ongoing, data and analysis products that are generated after May 31st, 2021 will be subject to the JGI Data Utilization Policy below that was previously only applied to data from proposals accepted after November 2018. This means that this data will be use-restricted for two years after public release of the individual data or analysis product to JGI portal(s), until publication by the data-generating PI, or at the written request of a PI, whichever comes first. See below for complete policy terms.

Original Utilization Policy

By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data prior to publication by the principal investigators of its comprehensive analysis without the consent of project’s principal investigator. These restrictions will be lifted on the publication of the whole genome or comparable description. Scientists must contact the principal investigator and JGI about their intentions to include any data from this project in a publication prior to publication of principal investigator’s primary report in order to ensure that their publication does not compete directly with planned publications (e.g. reserved analyses) of the JGI and collaborators.

The principal investigator, listed on the relevant portal page, is the point of contact and arbiter regarding publication plans. Reserved analyses include but are not limited to the identification and analysis of complete (whole genome) sets of genomic features such as genes and gene expression levels, gene families, gene clusters, regulatory elements, repeat structures, GC content, etc., and whole-genome comparisons of regions of evolutionary conservation or change. Manually annotated genes within the Genome Portal are also reserved. Studies of any type on the reserved data sets that are not in direct competition with those planned by the JGI and its collaborators may also be undertaken after an agreement with principal investigator and JGI. Interested parties must contact the principal collaborator and JGI to discuss such possibilities.

If these data are used for publication, the following acknowledgment should be included: “These sequence data were produced by the US Department of Energy Joint Genome Institute http://www.jgi.doe.gov/ in collaboration with the user community.” We request that you notify us upon publication so that this information can be included in the final annotation.

The data may be freely downloaded and used by all who respect the restrictions in the previous paragraphs. While still in waiting period, the assembly and raw sequence reads should not be redistributed or repackaged without permission from the JGI. When such permission has been obtained, any redistribution of the data during this period should carry this notice: “The Joint Genome Institute provides these data in good faith, but makes no warranty, expressed or implied, nor assumes any legal liability or responsibility for any purpose for which the data are used.” and users should be directed to this release policy page. Once moved to unreserved status, the data are freely available for any subsequent use.

The Data Usage Policy for data generated under proposals accepted after November 2018 is:

By accessing JGI data, you agree not to publish any articles containing analyses of genes or genomic data prior to publication by the principal investigators of its comprehensive analysis without the consent of the project’s principal investigator(s). These restrictions will be lifted upon publication(s) of the dataset or two years after the public release of this data, whichever is first. Scientists are expected to contact the principal investigator about their intentions to include any data from this project in a publication prior to publication of the primary report in order to ensure that their publication does not compete directly with planned publications (e.g. reserved analyses) of the principal investigators.

The principal investigator, listed on the relevant portal page, is the point of contact regarding publication plans. Reserved analyses include but are not limited to the identification and analysis of complete (whole genome) sets of genomic features such as genes and gene expression levels, gene families, gene clusters, regulatory elements, repeat structures, etc., and whole-genome comparisons of regions of evolutionary conservation or change. Studies of any type on the reserved data sets that are not in direct competition with those planned by the principal investigators may also be undertaken after agreement with the principal investigator. Interested parties must contact the principal investigator (or JGI if the PI cannot be reached) to discuss such possibilities.

If these data are used for publication, the following acknowledgment should be included: ‘These sequence data were produced by the US Department of Energy Joint Genome Institute http://www.jgi.doe.gov/ in collaboration with the user community.’ We also request that you appropriately cite any JGI resources used for analysis (such as IMG, Phytozome or Mycocosm) and that you notify us upon publication.

The data may be freely downloaded and used by all who respect the restrictions in the previous paragraphs, and the same restrictions apply to internal use by JGI staff and affiliates. Prior to full data release, the assembly and raw sequence reads must not be redistributed or repackaged without permission from the JGI. When such permission has been obtained, any redistribution of the data during this period must carry this notice: ‘The Joint Genome Institute provides these data in good faith, but makes no warranty, expressed or implied, nor assumes any legal liability or responsibility for any purpose for which the data are used.’ and users should be directed to this release policy page. Once moved to unreserved status (after publication or two years after public data release), the data are freely available for any subsequent use, but the source must still be cited.

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