Advanced architectures can deliver dramatically increased throughput for genomics and proteomics applications, reducing time-to-completion in some cases from days to minutes. One such architecture, hybrid-core computing, marries a traditional x86 environment with a reconfigurable coprocessor, based on field programmable gate array (FPGA) technology. In addition to higher throughput, increased performance can fundamentally improve research quality by allowing more accurate, previously impractical approaches. We will discuss the approach used by Convey?s de Bruijn graph constructor for short-read, de-novo assembly. Bioinformatics applications that have random access patterns to large memory spaces, such as graph-based algorithms, experience memory performance limitations on cache-based x86 servers. Convey?s highly parallel memory subsystem allows application-specific logic to simultaneously access 8192 individual words in memory, significantly increasing effective memory bandwidth over cache-based memory systems. Many algorithms, such as Velvet and other de Bruijn graph based, short-read, de-novo assemblers, can greatly benefit from this type of memory architecture. Furthermore, small data type operations (four nucleotides can be represented in two bits) make more efficient use of logic gates than the data types dictated by conventional programming models.JGI is comparing the performance of Convey?s graph constructor and Velvet on both synthetic and real data. We will present preliminary results on …

Activities leading to the incident were: (1) RCRA Class 2 Permit Modification granted on July 25, 2007 to install a walk-in fume hood in room 1025; (2) USQ-695-07-148 to do the work approved on 9/17; (3) ducting removed early October done by Facility Personnel under IWS 10331.09; (4) ducting swiped for 'free release' radioactivity only by team 1 personnel on 10/16; (5) all ducting and valves remained in building 695 room 1025 except for one piece delivered to building 391 (MMED shop); (6) material delivered by facility personnel to MMED shope B391 on about 10/19; (7) MMED personnel took a duct piece to B511 shop and removed the flange which went to salvage; (8) MMED personnel took the duct piece back to B391 shop and welded on a cap; (9) RHWM personnel picked up the welded duct from B391 around 10/26 and returned ti to B695 room 1025; and (10) the analysis report receive don 12/3 indicated that beryllium swipes take on 11/16, in B695 room 1025, and on ducting that did not leave the room where personnel worked, were above the release level for beryllium.

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Energy efficiency resource standards (EERS) are a prominent strategy to potentially achieve rapid and aggressive energy savings goals in the U.S. As of December 2010, twenty-six U.S. states had some form of an EERS with savings goals applicable to energy efficiency (EE) programs paid for by utility customers. The European Union has initiated a similar type of savings goal, the Energy End-use Efficiency and Energy Services Directive, where it is being implemented in some countries through direct partnership with regulated electric utilities. U.S. utilities face significant financial disincentives under traditional regulation which affects the interest of shareholders and managers in aggressively pursuing cost-effective energy efficiency. Regulators are considering some combination of mandated goals ('sticks') and alternative utility business model components ('carrots' such as performance incentives) to align the utility's business and financial interests with state and federal energy efficiency public policy goals. European countries that have directed their utilities to administer EE programs have generally relied on non-binding mandates and targets; in the U.S., most state regulators have increasingly viewed 'carrots' as a necessary condition for successful achievement of energy efficiency goals and targets. In this paper, we analyze the financial impacts of an EERS on a large electric utility …

A series of laser wake field accelerator experiments leading to electron energy exceeding 1 GeV are described. Theoretical concepts and experimental methods developed while conducting experiments using the 10 TW Ti:Sapphire laser at UCLA were implemented and transferred successfully to the 100 TW Callisto Laser System at the Jupiter Laser Facility at LLNL. To reach electron energies greater than 1 GeV with current laser systems, it is necessary to inject and trap electrons into the wake and to guide the laser for more than 1 cm of plasma. Using the 10 TW laser, the physics of self-guiding and the limitations in regards to pump depletion over cm-scale plasmas were demonstrated. Furthermore, a novel injection mechanism was explored which allows injection by ionization at conditions necessary for generating electron energies greater than a GeV. The 10 TW results were followed by self-guiding at the 100 TW scale over cm plasma lengths. The energy of the self-injected electrons, at 3 x 10{sup 18} cm{sup -3} plasma density, was limited by dephasing to 720 MeV. Implementation of ionization injection allowed extending the acceleration well beyond a centimeter and 1.4 GeV electrons were measured.

This report summarizes code requirements and energy savings of commercial buildings in climate zone 4 built to the 2009 IECC when compared to the 2006 IECC. In general, the 2009 IECC has higher insulation requirements for exterior walls, roof, and windows and have higher efficiency requirements for HVAC equipment (HVAC equipment efficiency requirements are governed by National Appliance Conversion Act of 1987 (NAECA), and are applicable irrespective of the IECC version adopted). The energy analysis results show that residential and nonresidential commercial buildings meeting the 2009 IECC requirements save between 6.1% and 9.0% site energy, and between 6.4% and 7.7% energy cost when compared to 2006 IECC. Analysis also shows that semiheated buildings have energy and cost savings of 3.9% and 5.6%.

A premier applied-science laboratory, Lawrence Livermore National Laboratory (LLNL) has at its core a primary national security mission - to ensure the safety, security, and reliability of the nation's nuclear weapons stockpile without nuclear testing, and to prevent and counter the spread and use of weapons of mass destruction: nuclear, chemical, and biological. The Laboratory uses the scientific and engineering expertise and facilities developed for its primary mission to pursue advanced technologies to meet other important national security needs - homeland defense, military operations, and missile defense, for example - that evolve in response to emerging threats. For broader national needs, LLNL executes programs in energy security, climate change and long-term energy needs, environmental assessment and management, bioscience and technology to improve human health, and for breakthroughs in fundamental science and technology. With this multidisciplinary expertise, the Laboratory serves as a science and technology resource to the U.S. government and as a partner with industry and academia. This annual report discusses the following topics: (1) Advanced Sensors and Instrumentation; (2) Biological Sciences; (3) Chemistry; (4) Earth and Space Sciences; (5) Energy Supply and Use; (6) Engineering and Manufacturing Processes; (7) Materials Science and Technology; Mathematics and Computing Science; (8) Nuclear …

Next Generation sequencing is producing ever larger data sizes with a growth rate outpacing Moore's Law. The data deluge has made many of the current sequenceanalysis tools obsolete because they do not scale with data. Here we present BioPig, a collection of cloud computing tools to scale data analysis and management. Pig is aflexible data scripting language that uses Apache's Hadoop data structure and map reduce framework to process very large data files in parallel and combine the results.BioPig extends Pig with capability with sequence analysis. We will show the performance of BioPig on a variety of bioinformatics tasks, including screeningsequence contaminants, Illumina QA/QC, and gene discovery from metagenome data sets using the Rumen metagenome as an example.

Residential customers in California's Pacific Gas and Electric (PG&E) territory have seen several electricity rate structure changes in the past decade. A relatively simple two-tiered pricing system (charges by usage under/over baseline for the home's climate zone) was replaced in the summer of 2001 by a more complicated five-tiered system (usage below baseline and up to 30percent, 100percent, 200percent, and 300percent+ over baseline). In 2009, PG&E began the process of upgrading its residential customers to Smart Meters and laying the groundwork for time of use pricing, due to start in 2011. This paper examines the history of the tiered pricing system, discusses the problems the utility encountered with its Smart Meter roll out, and evaluates the proposed dynamic pricing incentive structures. Scenario analyses of example PG&E customer bills will also be presented. What would these residential customers pay if they were still operating under a tiered structure, and/or if they participated in peak hour reductions?

The Long Baseline Neutrino Experiment (LBNE) will utilize a neutrino beamline facility located at Fermilab. The facility is designed to aim a beam of neutrinos toward a detector placed at the Deep Underground Science and Engineering Laboratory (DUSEL) in South Dakota. The neutrinos are produced in a three-step process. First, protons from the Main Injector hit a solid target and produce mesons. Then, the charged mesons are focused by a set of focusing horns into the decay pipe, towards the far detector. Finally, the mesons that enter the decay pipe decay into neutrinos. The parameters of the facility were determined by an amalgam of the physics goals, the Monte Carlo modeling of the facility, and the experience gained by operating the NuMI facility at Fermilab. The initial beam power is expected to be {approx}700 kW, however some of the parameters were chosen to be able to deal with a beam power of 2.3 MW.

We describe a modification of the treatment of photon sources in the IMC algorithm. We describe this modified algorithm in the context of thermal emission in an infinite medium test problem at equilibrium and show that it completely eliminates statistical noise.

The shallow ocean environment is ever changing mostly due to temperature variations in its upper layers (< 100m) directly affecting sound propagation throughout. The need to develop processors that are capable of tracking these changes implies a stochastic as well as an 'adaptive' design. The stochastic requirement follows directly from the multitude of variations created by uncertain parameters and noise. Some work has been accomplished in this area, but the stochastic nature was constrained to Gaussian uncertainties. It has been clear for a long time that this constraint was not particularly realistic leading a Bayesian approach that enables the representation of any uncertainty distribution. Sequential Bayesian techniques enable a class of processors capable of performing in an uncertain, nonstationary (varying statistics), non-Gaussian, variable shallow ocean. In this paper adaptive processors providing enhanced signals for acoustic hydrophonemeasurements on a vertical array as well as enhanced modal function estimates are developed. Synthetic data is provided to demonstrate that this approach is viable.

Babel is an open-source language interoperability framework tailored to the needs of high-performance scientific computing. As an integral element of the Common Component Architecture (CCA) it is used in a wide range of research projects. In this paper we describe how we extended Babel to support interoperable tuple data types (structs). Structs are a common idiom in scientific APIs; they are an efficient way to pass tuples of nonuniform data between functions, and are supported natively by most programming languages. Using our extended version of Babel, developers of scientific code can now pass structs as arguments between functions implemented in any of the supported languages. In C, C++ and Fortran 2003, structs can be passed without the overhead of data marshaling or copying, providing language interoperability at minimal cost. Other supported languages are Fortran 77, Fortran 90, Java and Python. We will show how we designed a struct implementation that is interoperable with all of the supported languages and present benchmark data compare the performance of all language bindings, highlighting the differences between languages that offer native struct support and an object-oriented interface with getter/setter methods.