Intellectual Environment

Lawrence Berkeley National Laboratory (LBNL) is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science, and is charged with conducting unclassified research across a wide range of scientific disciplines. It is managed and operated by the University of California, and is located adjacent to the University of California, Berkeley campus. The research conducted at LBNL crosses a wide range of scientific disciplines, with key efforts in fundamental studies of the universe, quantitative biology, nanoscience, new energy systems and environmental solutions, and the use of integrated computing as a tool for discovery. Capabilities include state of the art equipment for microarray analysis, DNA sequencing, automated cell culture, multi-scale microscopy, nanotechnology, and large scale computing. LBNL employs approximately 4,200 scientists, engineers, support staff and students. It is supported by a current annual budget of $811 million. LBNL has a long history of scientific excellence. Thirteen Nobel prizes are associated with Berkeley Lab. Fifty-seven Lab scientists are members of the National Academy of Sciences (NAS), one of the highest honors for a scientist in the United States. Thirteen of our scientists have won the National Medal of Science, our nation's highest award for lifetime achievement in fields of scientific research. Eighteen of our engineers have been elected to the National Academy of Engineering, and three of our scientists have been elected into the Institute of Medicine. In addition, Berkeley Lab has trained thousands of university science and engineering students who are advancing technological innovations across the nation and around the world.

LBNL researchers participate actively in a variety of research forums with other groups at both LBNL and UC Berkeley. Interactive cross-departmental focus groups and formal seminars, including postdoctoral research seminars, biweekly journal clubs and a wide array of invited seminar speakers, are held to advance understanding of ongoing research and stimulate strategic collaborations. LBNL scientists are encouraged to attend and present their work at local, national, and international conferences. We also participate in ongoing, mutually beneficial interactions with UC Berkeley, UC San Francisco and Stanford scientists. Proximity to these campuses provides frequent opportunities for scientific collaborations with faculty from diverse departments and research units.

The diverse and collaborative environment described above provides researchers with a broad understanding of basic as well as applied research. It also provides access to cutting-edge, novel technologies and insights into technological developments that need to be achieved to answer the significant healthcare questions facing our society today. These unique features make LBNL an ideal site for the carrying out the research proposed in this application.

Animal Facility

The Animal Care Facility (ACF) at LBNL will house the mice involved in this research. The ACF is a state-of-the-art facility with a soft-wall design that is easy to modify as research needs change and with filtration design that creates individual clean rooms. This allows a controlled environment that permits continuous visibility of the individual environmental units through freestanding vinyl wall bio-Bubble transparent enclosures. Each bio-Bubble provides a separate enclosure for each specific animal colony, special projects, procedures and quarantine rooms. The LBNL ACF is accredited by the American Association for the Accreditation of Laboratory Animal Care International (AAALAC), and the animal laboratory staff at the ACF is devoted to full-time care of housed animals.

Cell Analyses Facility

The Cell Analyses Facility at LBNL has a BD FACSCalibur flow-cytometer and a BD FACSVantageSE cell sorter. For this project, the BD FACSVantage is most relevant. The Becton-Dickinson FACS Vantage SE DiVa is a high-speed multi-color multi-laser cell sorter equipped with a Coherent Enterprise laser with dual emission: UV (351 nm) and 488 nm wavelengths and a Spectra-Physics HeNe laser emitting at 633 nm. This machine is fitted with DiVa option which allows digital data acquisition and analysis. It can acquire data on a maximum of 7 colours in addition to forward and 90 degree light scatter measurements. The FACSVantage has a BD Macrosort system with interchangable nozzles ranging from 50 to 400 micrometers for  sorting a wide range of particle sizes. It is controlled by a PC running FACSDiVa software. Subsequent data analysis can be performed using any FCS 2.0 compatible software, including FACSDiVa, Cellquest, or FlowJo. Options are available for single cell deposition allowing a predefined number of cells to be sorted onto user-defined substrates, including slides or microtiter plates. 

The lab has state-of-art systems such as Affymetrix, Illumina Genotyping, Firefly, Cellomics, microarray spotting machine (Omnigrid), Axon scanner, FACS, Beckman GeneStream, Taqman, Tecan and Biotek robots, a custom-made automated tissue culture system (designed by LBNL engineering department). The facility has been using a state-of-the-art high throughput, high performance OmniGrid II arrayer from GeneMachine, Inc. (San Carlos, CA), which can accommodate 72 of the 384 well plates and 100 microarray substrates for each run.

Microscopy Facility

The Biosciences Advanced Microscopy facility provides to all researchers in the Biosciences Division a variety of microscopes with a range of experimental capabilities including live-cell microscopy, multicolor quantitative CCD digital imaging, multispectral imaging, and multicolor 3D confocal microscope imaging. For wide-field fluorescence imaging two Zeiss upright and inverted epifluorescence microscopes equipped with high-resolution megapixel CCD cameras microscope automation (scanning stage, filterwheels and shutters) are controlled by AxioVision software for semi-automated quantitative imaging and analysis. Computer workstations for automated data acquisition, image analysis, data archiving are provided. For confocal microscopy, the facility provides two top-of-the-line Zeiss LSM 710 Laser Scanning Confocal Microscopes and a Solamere spinning disk live cell confocal microscope. Each of the LSM 710 setups is comprised of a Zeiss AxioObserver (inverted) fluorescence microscope for conventional epifluorescence and laser scanning confocal (3D) operation. Laser lines excite fluorochromes at 405, 457, 488, 514, 561, and 633 nm. Fluorescence emission is detected by a 34-channel spectral detector for quantitative multicolor 3D imaging. It is equipped with a computer-controlled XY stage enabling complete automation of the image acquisition procedure and full or partial CO2, heat, and humidity incubation for live cell imaging. The Zeiss ZEN software supports multi-location, multi-timepoint, multi-channel acquisition as well as FRAP, FRET, RICS, and photo-activation manipulation. The Solamere spinning disk system consists of an inverted fluorescence Zeiss Axiovert 200 microscope with an environmental chamber with heat, CO2, and humidity incubation capabilities, which is coupled with a Yokogawa CSU10 spinning disk confocal attachment and a Stanford Photonics 10-bit intensified CCD camera. A combination of a solid state and Ar-Ion lasers provide 405, 457, 488, 514, 561, and 638 nm excitation light for all common fluorescent proteins and fluorochromes. A large selection of objectives is available ranging from 2.5X to 100X oil-immersion. QED Imaging InVivo and MicroManager software controls all aspects of time-lapse, 3D, multi-color and/or multi-location fluorescence and transmitted light image acquisition and the system is integrated into the computer network for data storage and analysis. All these instruments allow for high resolution confocal analysis of live cells. A dedicated multispectral microscope based on a Cambridge Research Inc. (Cri) Nuance camera and a Zeiss Axioskop2 upright microscope allows imaging and analysis of complex multi-label and strongly autofluorescent tissue samples and quantitatively separate the different fluorescent species.  This facility also offers access to a Cellomics Arrayscan VTI high-content imaging microscope. In August 2012, the facility will receive a GE/Applied Precision OMX super-resolution microscope with both Structured Illumination (SI) imaging and also TIRF imaging for PALM/STORM localization microscopy. The system having 405, 488, and 561 lasers, 2 EM-CCD cameras, and in SI mode uses a high-speed electro-optical pattern generator will drastically increase our capacity for multiplex detection of molecules in single cells by using super-resolution microscopy in combination with combinatorial labeling (Lubeck & Cai ‘Single-cell systems biology by super-resolution imaging and combinatorial labeling’, Nature Methods 9:743-748, 2012).

Supercomputing Facility

Lawrencium is a 198-node, 1584 processor Linux cluster equipped with a high performance, low latency Infiniband interconnect that is suitable for providing a stable, high performing resource for running wide diversity of scientific applications. Currently, it is coupled with a BlueArc high performance NFS storage server that provides a total of 48TB home and 9TB scratch shared filesystem space to users. Lawrencium is currently ranked at number 500 on the November 2008 Top500 list of the world's fastest supercomputers. All data and software are routinely backed by High Performance Storage System (HPSS) at NERSC.

The NERSC facility, at Lawrence Berkeley Laboratory, is now hosting Magellan cloud computing. Magellan is built on the IBM iDataplex chassis using 5,760 processor cores for a theoretical peak of 61.5 teraflop per second. The NERSC supercomputing center has a GPU cluster named DIRC, which is a 50 GPU node cluster connected with QDR IB.  Each GPU node also contains 2 Intel 5530 2.4 GHz, 8MB cache, 5.86GT/sec QPI Quad core Nehalem processors (8 cores per node) and 24GB DDR3-1066 Reg ECC memory.

  • 44 nodes:  1 NVIDIA Tesla C2050 (code named Fermi) GPU with 3GB of memory and 448 parallel CUDA processor cores. 
  • 4 nodes:  1 C1060 NVIDIA Tesla GPU with 4GB of memory and 240 parallel CUDA processor cores.
  • 1 node:  4 NVIDIA Tesla C2050 (Fermi) GPU's, each with 3GB of memory and 448 parallel CUDA processor cores.
  • 1 node:  4 C1060 Nvidia Tesla GPU's, each with 4GB of memory and 240 parallel CUDA processor cores.