DOE Joint Genome Institute

  • About Us
  • Phone Book
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Products
    • Science Highlights
    • Scientists
    Serpula lacrymans var. lacrymans, an aggressive decomposer of the built environment, attacking this dresser. (Inger Skrede)
    The fungus that made itself at home
    Due to its aggressive capacity to damage the wood in homes, bioenergy researchers have been interested in harnessing the brown rot Serpula lacrymans towards breaking down plant mass for conversion to sustainable, alternative biofuels and bioproducts. In The ISME Journal, insights on how the fungus has responded to manmade changes in its ecological habitat, adapting to thrive in built environments.

    Read more

    Sexual reproduction in Rhizopus microspores: (a) Successful mating between fungi harboring bacteria; (b) Lack of sex between mates cured of endobacteria. (Stephen Mondo)
    An Addiction Crucial to a Fungus’ Reproduction
    In the absence of the Burkholderia endobacteria, the Rhizopus fungus cannot act as a plant pathogen, and researchers have now discovered that endobacteria also regulate its sexual reproduction. The work sheds light on a poorly understood group of oleaginous or oil-producing fungi, and the impact this mutualistic interaction has on these potential large-scale biodiesel producing fungi.

    Read more

    In Nature Communications, researchers sequenced and analyzed the genome of Kalanchoe fedtschenkoi (lavender scallops) to better understand how this plant transitioned from C3 to CAM photosynthesis. (Forest and Kim Starr, Flickr CC BY 2.0)
    Succulent Genes for Water Use Efficiency
    To understand how many plant lineages have independently transitioned from C3 to CAM photosynthesis, researchers sequenced and analyzed the genome of Kalanchoë fedtschenkoi (lavender scallops). As the first CAM eudicot to have its genome sequenced, Kalanchoë offers researchers a reference to trace the evolution of CAM photosynthesis in this group.

    Read more

  • Our Projects
    • Search JGI Project List
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    Morphological diversity of Xylariaceous endophytes. (J.M. U'Ren)
    Comparative and Population Genomics of Xylariaceae
    A genomic survey of the Xylariaceae, one of the largest and most diverse families of fungi made up of endophytic, pathogenic, and saprotrophic (including wood degrading) species.

    Read more

    Virus-infected Brachypodium (Courtesy of Kranthi Mandadi)
    Gene Atlases of Grass-Microbe Interactions
    This proposal seeks to build comprehensive gene atlas maps for diverse bioenergy grass-microbe interactions, including pathogenic and beneficial interactions in two grass models, Brachypodium and Setaria.

    Read more

    Yellowstone National Park, Octopus hot spring biofilms (Courtesy of Devaki Bhaya)
    Quantifying Cyanobacteria Interactions
    The long term objective is to quantify dynamic interactions between phototrophs and their virus predators. This will help to build quantitative, dynamic and predictive models of host-viral interactions and the effect on carbon and nutrient cycling.

    Read more

  • Data & Tools
    • IMG
    • Genome Portal
    • MycoCosm
    • Phytozome
    • GOLD
    DOE JGI BOOST logo
    New Software Tools Streamline DNA Sequence Design-and-Build Process
    Researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows.

    Read more

    This graphic depicts the geographic distribution of GOLD biosamples and organisms. Organism location of isolation is marked in pink while Biosample location of collection is denoted with blue dots. Updates to the Genomes OnLine Database (GOLD) are reported in the upcoming Database issue of Nucleic Acids Research. (Image from Supratim Mukherjee et al. Nucl. Acids Res. 2016;nar.gkw992)
    DOE JGI Database of DNA viruses and retroviruses debuts on IMG platform
    In a series of four articles published in the Database issue of the Nucleic Acids Research journal, DOE JGI researchers report on the latest updates to several publicly accessible databases and computational tools that benefit the global community of microbial researchers.

    Read more

    Sakinaw Lake UBC
    Benchmark Study for Improving Microbial Community Profiling
    Researchers used synthetic and natural microbial lake communities to compare the microbial community profiles generated from high throughput short-read sequencing and high throughput long-read sequencing approaches.

    Read more

  • User Program Info
    • Calls for User Proposals
    • Special Programs
    • User Support
    • Submit a Proposal
    Tobias Erb, MPI Marburg (Courtesy of Tobias Erb)
    Meet a JGI User: Tobias Erb
    "The JGI has been crucial for our research because it has provided the scientific community with a tremendous amount of gene sequences over the last couple of years. These gene sequences have become a true treasure grove for synthetic biologists like us."

    Read more

    Colleen Hansel, WHOI
    Meet a JGI User: Colleen Hansel
    "We have been working on genomic and transcriptome studies of a unique group of manganese (Mn) oxidizing Ascomycete fungi that were isolated from coal mine drainage treatment systems and metal-laden freshwater ponds. The staff and facilities at the JGI were critical for conducting this research. "

    Read more

    J. Chris Pires, University of Missouri
    Meet a JGI User: J. Chris Pires
    "My mission is to train the next generation of scientists by doing high impact, interdisciplinary science in a collaborative atmosphere. JGI is an important partner in this team science effort in cross-training students and postdoctoral researchers."

    Read more

  • News & Publications
    • News Releases
    • Blog
    • Publications
    • Scientific Posters
    • Newsletter
    • Logos
    • Photos
    Freedom and Flexibility: Thinking Outside the Cell for Functional Genomics
    The latest proposal approved through the JGI’s Emerging Technologies Opportunity Program (ETOP) aims to develop an optimized cell-free platform that will enable researchers to speed up the “build” and “test” portion of the design-build-test-analyze cycle in synthetic biology.

    Read more

    Depiction of rumen microbiome. (Ella Maru studio, www.scientific-illustrations.com)
    A Reference Catalog for the Rumen Microbiome
    In Nature Biotechnology, an international team presents one of the largest targeted cultivation and sequencing projects to date: a reference catalog of rumen microbial genomes and isolates cultivated and sequenced from the Hungate1000 collection produced through the coordinated efforts of rumen microbiology researchers worldwide.

    Read more

    https://jgi.doe.gov/tracking-microbial-diversity-through-terrestrial-subsurface/
    Tracking Microbial Diversity Through the Terrestrial Subsurface
    In Nature Microbiology, JGI researchers collaborated with a team led by longtime collaborator Jill Banfield of the University of California, Berkeley and Cathy Ryan of the University of Calgary in Canada, investigating samples collected at Utah's Crystal Geyser over one of the its complex, five-day eruption cycles.

    Read more

For JGI Staff

Emergency Operations Information

Emergency Numbers

  • Dial 911 in an emergency
  • From a JGI land line dial 9-911 in an emergency.
  • Dial 1-925-935-6400 to call 911 from a cell phone in Walnut Creek.

JGI Emergency Status Announcements

1-925-927-2911

LBNL Emergency Status Announcements

1-800-445-5830

LBNL Emergency Preparedness
1-510-486-6999

After Hours Non-emergency

LBNL Security/ Blackberry Gate
1-510-486-4050

Key Contacts

JGI Operations Manager
Ray Turner 1-925-296-5804

JGI Facilities Manager
Greg Stanley 1-925-296-5788

JGI Safety Coordinator
Stephen Franaszek 1-925-296-5807

Health Services

LBNL Health Services
1-510-486-6266

LLNL Health Services
1-925-422-7459

John Muir Medical Emergency Room
1-925-939-5800

More Emergency Web Links

LBNL Emergency Status Web site

LBNL Pandemic Flu Info

LBNL EH&S Emergency Preparedness

LBNL Ops Emergency Action Guide

LBNL Remote Access Info

LBNL Our Safety

CDC Seasonal Flu

FLU.gov

Where to Get JGI Emergency Info

This page is meant for DOE JGI employees and staff as a resource in the event of an emergency, and for emergency preparedness. In the event of a real emergency, information and updates will be communicated in several ways including:

  • on this web site
  • site-wide email messages
  • JGI emergency status phone number 1-925-927-2911
  • departmental phone trees — emergency updates from your supervisor

In the event of an emergency on-site at JGI, dial 9-911 from JGI phone, or 911 from your cell.

JGI Operational Status

The current operational status is: NORMAL OPERATIONS

  • Normal Operations
  • Reduced Operations 
    Remote work authorized. Continue production/research.
  • Essential Operations
    Limited JGI personnel on-site: Facilities Mgr, IT staff, Shipping & Receiving, Emergency Mgmt Team.

Employee Preparedness Measures

Flu Shots

Call LBNL Health Services 1-510-486-6266 to make an appointment. Otherwise, please contact your physician to get your annual influenza and pneumonia vaccinations. More information about the flu.

Plan for Web Outages — Alternate Emergency Info Sources

Write down or enter in your cell phone the JGI Emergency Contact number (1-925-927-2911) and other essential numbers and information, including the LBL Emergency Status Announcements number 1-800-445-5830.

 

Keep Your Emergency Contact Info Up-to-Date

Update your LBNL Emergency Contact Info. Ask your supervisor for contact information and for an alternate contact should he or she not be available in the event of an emergency.

JGI Emergency Phone Number — Get Updates by Phone

JGI Emergency Status Announcements 1-925-927-2911
In the event of an emergency communication messages will be posted on this line. Please keep a copy of this number on hand in the event this web site should go down.

LBNL Paycheck Direct Deposits — Get Paid Off-site

Make sure you get your paycheck while off-site by signing up for direct deposit (LBNL payroll forms.)

Be Prepared to Work From Home

Make sure you are prepared to work remotely: check that your home computer is set up for remote access. You will need to set this up in advance, possibly with help from the System Operations Group.

Working Off-site

Computer Access

To gain remote access to your desktop computer and the JGI network, you will need to plan ahead. Make sure your system is set up for access using either a Virtual Private Network (VPN), the JGI proxy server, or set up a remote desktop on your machine. You may need assistance from the JGI Systems Operations group to get set up with the proxy server or other connection. You can request their help through JIRA. More information about configuring the JGI proxy server is available on the JGI intranet page (internal only), and from the System Operations group.

Gain access to the JGI network by connecting using a Virtual Private Network (VPN.) Detailed information about installing VPN on your home system (LBNL password required to access this page) and access to download VPN software is available from LBNL Services Group.

Voicemail

To log in to your CallPilot mailbox, you need the CallPilot mailbox number and password. Call your own phone line and follow instructions to get your voicemail (e.g. dial 1-925-296-5670)

For specific instructions see, Voicemail User Guide and Telephone User Guide.

Payroll & Time cards

LETS time card system is available off-site (login with your LDAP password.) Ensure your paycheck is available to you off site by signing up for direct deposit (LBNL payroll forms.)

  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Facebook
  • Flickr
  • Google+
  • Instagram
  • Linkedin
  • RSS
  • 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

© 1997-2018 The Regents of the University of California