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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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    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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    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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    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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    A Powerful Technique to Study Microbes, Now Easier
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    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)
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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)
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User Programs
Home › User Programs › User Program Info › Closed Calls › FICUS JGI-NERSC-KBase FY19

FICUS JGI-NERSC-KBase FY19

2019 FICUS JGI-NERSC-KBase Biological Data Science Call for Proposals (CLOSED)

The Biological Data Science call will enable users to perform state-of-the-art computational research to explore the wealth of genomic and metagenomic data generated worldwide and translate sequence information into biological discovery. Users will have access to resources and capabilities through two DOE Office of Science User Facilities, the Joint Genome Institute (JGI) and the National Energy Research Scientific Computing Center (NERSC), as well as the DOE Systems Biology Knowledgebase (KBase). The call aims to help users perform large-scale computational analyses of genomics and related omics data to solve problems relevant to the DOE missions in bioenergy and the environment.

Projects are encouraged that relate to:

  • Large-scale data mining for genes, genomes, metabolic and biosynthetic pathways, and regulatory motifs of interest
  • Large scale computations for large datasets exploring the power of High Performance Computing
  • Developing explainable scalable machine learning and artificial intelligence based methods for sequence classification, gene calling or gene functional annotation leveraging high performance computational tools such as HipMCL, MetaHipMer, etc.
  • Developing new analysis and/or visualization tools for Terabyte (TB)-sized multi-omics data that can be deployed in KBase, IMG, or MycoCosm
  • Distributing resulting data products through IMG/JGI portals or KBase

DOE JGI, NERSC and KBase core capabilities available through this call include:

  • Up to 2 million CPU hours on the Cori supercomputer (128GB memory per node, 32 cores)
  • Access of up to 100TB of high-performance storage on the NERSC parallel file system and burst buffer to overcome I/O bottlenecks
  • The expertise of DOE JGI, NERSC and KBase staff
  • The Integrated Microbial Genomes & Microbiomes (IMG/M) database, the largest publicly available integrated resource of assembled metagenomic sequences and isolate microbial genomes
  • The MycoCosm portal, the largest collection of fungal genomes
  • An integrated software and data platform, KBase, for metabolic modeling of microbes or microbial communities, custom processing of microbial and fungal genomes and metagenomes and state-of-the-art computational workflows, narratives, and pipelines
  • Comparative analyses (e.g. large or complex queries) of the IMG system that are not available through the web interface.
  • Gene/protein family-centric analysis of IMG or KBase data

Proposals will be reviewed for feasibility, scientific excellence and DOE mission relevance by scientific experts in microbial genomics and HPC. All relevant data must be available at the time of submission; proposals requesting sequencing will be rejected without peer review. Applications should be submitted at https://proposals.jgi.doe.gov.

General inquiries about the program should be directed to Susannah Tringe.

Technical inquiries related to JGI resources should be addressed to Nikos Kyrpides.

Technical inquiries related to NERSC resources should be directed to Deborah Bard.

Technical inquiries related to KBase should be directed to Shane Canon.

Proposal Schedule

2019 proposals will only be accepted electronically and should be submitted at https://proposals.jgi.doe.gov/ between August 20 and September 13, 2018.

The full schedule is below:

Calls for proposals issued August 17, 2018
Proposals received Sept 24, 2018
Technical and scientific review mid-Nov 2018
Approval and rejection notices sent December 3, 2018
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