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At least 325 records · Page 18

Modern Computational Techniques for the HMMER Sequence Analysis

This paper focuses on the latest research and critical reviews on modern computing architectures, software and hardware accelerated algorithms for bioinformatics data analysis with an emphasis on one of the most important sequence analysis applications—hidden Markov models (HMM). We show the detailed performance comparison of sequence analysis tools on various computing platforms recently developed in the bioinformatics society. The characteristics of the sequence analysis, such as data and compute-intensive natures, make it very attractive to optimize and parallelize by using both traditional software approach and innovated hardware acceleration technologies.

59 BASIC BIOLOGICAL SCIENCES↗

The Stratospheric Aerosol and Gas Experiment (SAGE III) on the International Space Station (ISS) Mission

The Stratospheric Aerosol and Gas Experiment III on the International Space Station (SAGE III/ISS) mission will provide the science community with high-vertical resolution and nearly global observations of ozone, aerosols, water vapor, nitrogen dioxide, and other trace gas species in the stratosphere and upper-troposphere. SAGE III/ISS measurements will extend the long-term Stratospheric Aerosol Measurement (SAM) and SAGE data record begun in the 1970s. The multi-decadal SAGE ozone and aerosol data sets have undergone intense scrutiny and are considered the international standard for accuracy and stability. SAGE data have been used to monitor the effectiveness of the Montreal Protocol. Key objectives of the mission are to assess the state of the recovery in the distribution of ozone, to re-establish the aerosol measurements needed by both climate and ozone models, and to gain further insight into key processes contributing to ozone and aerosol variability. The space station mid-inclination orbit allows for a large range in latitude sampling and nearly continuous communications with payloads. The SAGE III instrument is the fifth in a series of instruments developed for monitoring atmospheric constituents with high vertical resolution. The SAGE III instrument is a moderate resolution spectrometer covering wavelengths from 290 nm to 1550 nm. Science data is collected in solar occultation mode, lunar occultation mode, and limb scatter measurement mode. A SpaceX Falcon 9 launch vehicle will provide access to space. Mounted in the unpressurized section of the Dragon trunk, SAGE III will be robotically removed from the Dragon and installed on the space station. SAGE III/ISS will be mounted to the ExPRESS Logistics Carrier-4 (ELC-4) location on the starboard side of the station. To facilitate a nadir view from this location, a Nadir Viewing Platform (NVP) payload was developed which mounts between the carrier and the SAGE III Instrument Payload (IP).

Cisewski, Michael↗

NASA Goddard Earth Sciences Graduate Student Program

The evolution of synoptic-scale dynamics associated with a middle and upper tropospheric cloud event that occurred on 26 November 1991 is examined. The case under consideration occurred during the FIRE CIRRUS-II Intensive Field Observing Period held in Coffeyville, KS during Nov. and Dec., 1991. Using data from the wind profiler demonstration network and a temporally and spatially augmented radiosonde array, emphasis is given to explaining the evolution of the kinematically-derived ageostrophic vertical circulations and correlating the circulation with the forcing of an extensively sampled cloud field. This is facilitated by decomposing the horizontal divergence into its component parts through a natural coordinate representation of the flow. Ageostrophic vertical circulations are inferred and compared to the circulation forcing arising from geostrophic confluence and shearing deformation derived from the Sawyer-Eliassen Equation. It is found that a thermodynamically indirect vertical circulation existed in association with a jet streak exit region. The circulation was displaced to the cyclonic side of the jet axis due to the orientation of the jet exit between a deepening diffluent trough and building ridge. The cloud line formed in the ascending branch of the vertical circulation with the most concentrated cloud development occurring in conjunction with the maximum large-scale vertical motion. The relationship between the large scale dynamics and the parameterization of middle and upper tropospheric clouds in large-scale models is discussed and an example of ice water contents derived from a parameterization forced by the diagnosed vertical motions and observed water vapor contents is presented.

Ackerman, Thomas P.↗

Real-Time Analysis and Signal Optimization for Charge Detection Mass Spectrometry

Charge detection mass spectrometry (CDMS) is an important tool for measuring mass distributions for high mass samples and heterogeneous mixtures. In CDMS, single ions are trapped and their m/z and charge are measured simultaneously. As a single particle technique, the average signal must be optimized to maximize the number of single ion trapping events. If the average signal is too small, most of the trapping events will be empty, and if the average signal is too large, most of the trapping events will contain multiple ions. In recent embodiments, the time domain signal from the trapped ion is analyzed by fast Fourier transforms. The analysis time is much longer that the data collection time which precludes real-time optimization of the experimental conditions. In this paper, we describe the implementation of CDMS with real-time analysis. Processing the data in real time allows the average signal intensities to be dynamically optimized to maximize the number of single ion trapping events. Real-time analysis also allows the experimental settings to be optimized in a timely manner to target specific mass regimes to maximize the useful information content of the measurements. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Distributed non-negative matrix factorization with determination of the number of latent features

The holistic analysis and understanding of the latent (that is, not directly observable) variables and patterns buried in large datasets is crucial for data-driven science, decision making and emergency response. Such exploratory analyses require devising unsupervised learning methods for data mining and extraction of the latent features, and non-negative matrix factorization (NMF) is one of the prominent such methods. NMF is based on compute-intense non-convex constrained minimization, which, for large datasets requires fast and distributed algorithms. However, current parallel implementations of NMF fail to estimate the number of latent features. In practice, identifying these features is both difficult and significant for pattern recognition and latent feature analysis, especially for large dense matrices. Here, we introduce a distributed NMF algorithm coupled with distributed custom clustering followed by a stability analysis on dense data, which we call DnMFk, to determine the number of latent variables. The results on synthetic data and the classical Swimmer data set demonstrate the accuracy of model determination while scaling nearly linearly across multiple processors for large data. Further, we employ DnMFk to determine the number of hidden features from a terabyte matrix.

97 MATHEMATICS AND COMPUTING↗

In-flight scale/distortion calibration of the Hubble Space Telescope fixed-head star trackers

This paper describes an in-flight scale and distortion calibration procedure that has been developed for the Ball Aerospace Systems Division Fixed-Head Star Trackers (FHST's) used on the Hubble Space Telescope (HST). The FHST is a magnetically focused and deflected imaging sensor that is designed to track stars as faint as m(sub v) = 5.7 over an 8 degree by 8 degree field of view. Raw FHST position measurements are accurate to approximately 200 arcseconds, but this can be improved to 10-15 arcseconds by processing the raw measurements through calibration polynomials that correct for flat field, temperature intensity, and magnetic field effects. The coefficients for these polynomials were initially determined using ground test data. On HST the use of three FHST's is an integral part of the preliminary attitude update procedures required before the acquisition of guide stars for science observations. To this end, FHST-based attitude determination having single-axis errors no worse than 22 arcseconds (1 sigma) is required. In early 1991 it became evident that one of the HST FHST's was experiencing a significant change in its optical scale. By mid-1993 the size of this error had grown to a point that, if not corrected, it would correspond to a maximum position error on the order of 100 arcseconds. Subsequent investigations demonstrated that substantial, uncompensated cubic distortion effects had also developed, the maximum contribution to position errors from the cubic terms being on the order of 30 arcseconds. To ensure accurate FHST-based attitude updates, procedures have been developed to redetermine the FHST scale and distortion calibration coefficients based on in-flight data gathered during normal HST operations. These scale and distortion calibrations have proven very effective operationally, and procedures are in place to monitor FHST calibration changes on a continuing basis.

Mccutcheon, R.↗

Einstein@Home All-Sky Search for Periodic Gravitational Waves in LIGO S5 Data

This paper presents results of an all-sky search for periodic gravitational waves in the frequency range [50, 1 190] Hzand and with frequency derivative range of approx. [-20,1.1] x 10(exp-10) H(sub 0)z s(exp-1) for the fifth LIGO science run (S5). The search uses a noncoherent Hough-transform method to combine the information from coherent searches on time scales of about one day. Because these searches are very computationally intensive, they have been carried out with the Einstein@Home volunteer distributed computing project. Postprocessing identifies eight candidate signals; deeper follow-up studies rule them out. Hence, since no gravitational wave signals have been found, we report upper limits on the intrinsic gravitational wave strain amplitude ho. For example, in the 0.5 Hz-wide band at 152.5 Hz, we can exclude the presence of signals with h(exp 0) greater than 7.6 x 10(exp-25) at a 90% confidence level. This search is about a factor 3 more sensitive than the previous Einstein@Home search of early S5 LIGO data.

J Aasi↗

Space life sciences perspectives for Space Station Freedom

It is now generally acknowledged that the life science discipline will be the primary beneficiary of Space Station Freedom. The unique facility will permit advances in understanding the consequences of long duration exposure to weightlessness and evaluation of the effectiveness of countermeasures. It will also provide an unprecedented opportunity for basic gravitational biology, on plants and animals as well as human subjects. The major advantages of SSF are the long duration exposure and the availability of sufficient crew to serve as subjects and operators. In order to fully benefit from the SSF, life sciences will need both sufficient crew time and communication abilities. Unlike many physical science experiments, the life science investigations are largely exploratory, and frequently bring unexpected results and opportunities for study of newly discovered phenomena. They are typically crew-time intensive, and require a high degree of specialized training to be able to react in real time to various unexpected problems or potentially exciting findings. Because of the long duration tours and the large number of experiments, it will be more difficult than with Spacelab to maintain astronaut proficiency on all experiments. This places more of a burden on adequate communication and data links to the ground, and suggests the use of AI expert system technology to assist in astronaut management of the experiment. Typical life science experiments, including those flown on Spacelab Life Sciences 1, will be described from the point of view of the demands on the astronaut. A new expert system, 'PI in a Box,' will be introduced for SLS-2, and its applicability to other SSF experiments discussed. (This paper consists on an abstract and ten viewgraphs.)

Young, Laurence R.↗

In situ observations of reacting Al/Fe 2 O 3 thermite: Relating dynamic particle size to macroscopic burn time

Time-resolved x-ray imaging is used to capture high-resolution images of the Al/Fe 2 O 3 thermite reaction as it proceeds in an extended burn tube. The observed thermite reaction products are generally large, multi-phase composite particles. Image processing algorithms are developed to extract a continuous record of composite particle size as a function of time and distance from the ignition point. Small particles are observed immediately after ignition, followed by a rapid increase in particle size and a gradual decline toward late times. Correlating the dynamic particle size with visible light emission from the reaction, we propose a two-stage mechanism where the combination of early ignition and delayed expansion causes the material closest to the ignition point to undergo substantial coalescence before it begins moving down the tube. We also identify two mechanisms that may contribute to particle size refinement at late times, both based on the collapse of large gas bubbles that are observed preferentially in particles at earlier times. A new approach to extracting burn times from luminous intensity data is explored, and we find that a more nuanced analysis of burn time and luminous intensity may help to improve reactivity assessments when data from in situ studies is unavailable.

36 MATERIALS SCIENCE↗

Line-shape study of self-broadened O{sub 2} transitions measured by Pound-Drever-Hall-locked frequency-stabilized cavity ring-down spectroscopy

We present high-sensitivity and high-spectral-resolution line-shape and line-intensity measurements of self-broadened O{sub 2} b {sup 1}{Sigma}{sub g}{sup +}(v=1)(leftarrow)X {sup 3}{Sigma}{sub g}{sup -}(v=0) band transitions measured using the Pound-Drever-Hall-locked frequency-stabilized cavity ring-down spectroscopy technique. We give collisional broadening parameters and take into account the line-narrowing effects described by Dicke narrowing or the speed dependence of collisional broadening. We compare line intensities measured with relative uncertainties below 0.4% to data available in the HITRAN spectroscopic database.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

PAL Experimental Report Form

We constructed the first simultaneous dark- and bright-field X-ray microscope in this experiment, coupling it to simultaneous measurements of the wide-angle Xray diffraction, and the XFEL pulse intensity and energy spectrum on each shot. This experiment established proof of concept for this new advanced measurement technique and demonstrated DFXM at an XFEL for the first time. Within this complex experiment, we also acquired data that advanced our research goals within materials science and mathematics. These included: A preliminary study of how local effects reduce the X-ray damage threshold in diamond; A preliminary study of how X-ray radiation imparts heat into materials based on irreversible phase transitions that occur in boric acid with increasing temperature (based on hydration); A study of X-ray radiation damage from ultrafast thermal cycling and nonthermal melting in bismuth selenide; We also began developing software to automate alignment of compound refractive lenses (CRLs) using stochastic Nelder-Mead optimization methods. This work will expedite and improve the accuracy of alignments for many future experiments using CRLs.

36 MATERIALS SCIENCE↗

Cyber-Infrastructure for Data-Intensive Geospatial Computing

With the recent advent of heterogeneous High-performance Computing (HPC) to handle EO “Big Data” workloads, there is a need for a unified Cyber-infrastructure (CI) platform that can bridge the best of many HPC worlds. In this chapter, we discuss such a CI platform being developed at Geographic Information Science and Technology (GIST) group using novel and innovative techniques, and emerging technologies that are scalable to large-scale supercomputers. The CI platform utilizes a wide variety of computing such as GPGPU, distributed, real-time and cluster computing, which are being brought together architecturally to enable data-driven analysis, scientific understanding of earth system models, and research collaboration. This development addresses the need for close integration of EO and other geospatial information in the face of growing volumes of the data, and facilitates spatio-temporal analysis of disparate and dynamic data streams. Horizontal scalability and linear throughput are supported in the heart of the platform itself. It is being used to support very broad application areas, ranging from high-resolution settlement mapping, national bioenergy infrastructure to urban information and mobility systems. The platform provides spatio-temporal decision support capabilities in planning, policy and operational missions for US federal agencies. Also, the platform is designed to be functionally and technologically sustainable for continued support of the US energy and environment mission for the coming decades.

Karthik, Rajasekar↗

Real-Time Science Decisioning During High Tempo-High Intensity Mission Operations and the Role of Analogs

Introduction: NASA’s VIPER mission presents a unique operational paradigm within the history of robotic spaceflight. The proximity of the Moon to the Earth and the terrain elements (surface characteristics, light/shadow dynamics, communication links) of the lunar South Polar landing site create unprecedented operational conditions between these two planetary bodies. Apollo era lunar science and exploration included humans in situ to operate instruments and assimilate observational inputs in real-time. Previous lunar orbital missions have worked to operational timescales, e.g., decisional timelines and communication exchanges, that were weeks in length. Mars rover missions have worked to operational timescales, e.g., decisional timelines and communication exchanges between Mars and Earth, that were hours, days, and weeks in length. In the case of the VIPER mission, our operational decisioning for rover driving and instrument commanding will be compressed to minute-scale timeframes. These operational conditions directly impact the manner and speed with which the VIPER Science Team (VST) is required to synthesize and analyze data and produce timely science-driven decisions throughout surface mission operations. The VST shall provide mission enhancing scientific input to guide rover traverse planning and drill site confirmation and selection throughout surface operations. Further, the VST input will be of vital importance to the mission’s ability to maximize science return and to meet broader NASA objectives for future lunar in-situ resource utilization (ISRU)and exploration activities. The VST co-located in the Mission Science Center (MSC) will be responsive to the tactical operational cadence of the Mission Operations Center (MOC) and will provide further strategic and Long-Term Planning (LTP) guidance to the mission. The VIPER Science Operations & Integration(SO&I)team has developed an architecture that is focused on the infusion of science-decisioning into the operational framework and execution cadence of VIPER. NASA analog research has played a significant role in the construction of the VIPER science operations systems. As an example, the SO&I team has led analog missions that have focused on bringing together expertise in the sciences (natural, applied and social) and in operations in service of learning how to build and hold together interdisciplinary work environments and what tools are needed to support high tempo, high intensity integrated decisioning. These experiences have provided an essential foundation of knowledge to the VIPER team. Those analogs that specifically influenced the VIPER science operations construct were identified through a process of comparative analysis to prioritize those that offered relevance in whole or in part, and those that did not. The analog research output that provided extensibility to the VIPER science operations architecture included remote teams of humans and robots in cooperation (synchronous and asynchronous) with simulated earthbound systems, engineering and science teams, and the integrated assembly of tools that supported scientific analysis and data synthesis and provided infrastructure for the remote testing framework. Analogs which included real-time data monitoring, synthesis, visualization and access in a democratized and operationalized manner were of particular interest to the development of the VIPER MSC toolset both in terms of the technology and the processes used to develop the supporting infrastructure. We anticipate that each subsequent mission to the lunar south pole, whether with robots or humans, will be able to optimize science and exploration return by evolving strategies to infuse real-time collaborative science-decisioning. Furthermore, these efforts will result in a foundation for science operations development in support of human-robotic exploration of deep space and Mars. NASA analogs can continue to provide the opportunity to prepare, test and iterate on the operational concepts and tools that will support these ever-expanding space exploration efforts. Our presentation will include an overview of the VIPER Science Operations & Integration development process and specifics on what aspects of analog research have had a significant impact on our work systems.

D S S Lim↗

A statistical approach for isolating fossil fuel emissions in atmospheric inverse problems

We study independent verification and quantification of fossil fuel (FF) emissions that constitutes a considerable scientific challenge. By coupling atmospheric observations of CO 2 with models of atmospheric transport, inverse models offer the possibility of overcoming this challenge. However, disaggregating the biospheric and FF flux components of terrestrial fluxes from CO 2 concentration measurements has proven to be difficult, due to observational and modeling limitations. In this study, we propose a statistical inverse modeling scheme for disaggregating winter time fluxes on the basis of their unique error covariances and covariates, where these covariances and covariates are representative of the underlying processes affecting FF and biospheric fluxes. The application of the method is demonstrated with one synthetic and two real data prototypical inversions by using in situ CO 2 measurements over North America. Also, inversions are performed only for the month of January, as predominance of biospheric CO 2 signal relative to FF CO 2 signal and observational limitations preclude disaggregation of the fluxes in other months. The quality of disaggregation is assessed primarily through examination of a posteriori covariance between disaggregated FF and biospheric fluxes at regional scales. Findings indicate that the proposed method is able to robustly disaggregate fluxes regionally at monthly temporal resolution with a posteriori cross covariance lower than 0.15 µmol m -2 s -1 between FF and biospheric fluxes. Error covariance models and covariates based on temporally varying FF inventory data provide a more robust disaggregation over static proxies (e.g., nightlight intensity and population density). However, the synthetic data case study shows that disaggregation is possible even in absence of detailed temporally varying FF inventory data.

54 ENVIRONMENTAL SCIENCES↗

Autonomous Rovers for Mars Exploration

Rovers will play a critical role in the exploration of Mars. Near-term mission plans call for long traverses over unknown terrain, robust navigation and instrument placement, and reliable operations for extended periods of time. Longer-term missions may visit multiple science sites in a single day and perform opportunistic science data collection, as well as complex scouting, construction, and maintenance tasks in preparation for an eventual human presence. The Pathfinder mission demonstrated the potential for robotic Mars exploration but at the same time indicated the need for more rover autonomy. The highly ground-intensive control with infrequent communication and high latency limited the effectiveness of the Sojourner rover. When failures occurred, Sojourner often sat idle for extended periods of time, awaiting further commands from earth. In future missions, the tasks will be more complex and extended; hence there will be even more situations where things do not go exactly as planned. Significant advances in rover autonomy are needed to cope with increasing task complexity and greater execution uncertainty. Towards this end, we have designed an on-board executive architecture that incorporates robust operation, resource utilization, and failure recovery. In addition, we have designed ground tools to produce and refine contingent schedules that take advantage of the on-board architecture's flexible execution characteristics. Together, the on-board executive and the ground tools constitute an integrated rover autonomy architecture. This work draws from our experience with the Deep Space One autonomy experiment, with enhancements to ensure robust operation in the face of the unpredictable, complex environment that the rover will encounter on Mars. The rover autonomy architecture is currently being developed and deployed on the Marsokhod rover platform at NASA Ames Research Center. The capabilities of the rover autonomy architecture to support autonomous operations will be demonstrated concretely in upcoming field tests.

Anderson, Corin↗

TOF-SIMS Analysis of Hydrogen in Niobium, From 160 deg. K to 475 deg. K

Niobium (Nb) is the material of choice for superconducting radio frequency (SRF) cavities due to its high critical temperature and critical magnetic field. Interstitial impurity elements such as H directly influence the efficiency of these cavities. Quantification of H in Nb is difficult since H is extremely mobile in Nb with a very high diffusion coefficient even at room temperature. In the presented work, Time of Flight Secondary Ion Mass Spectrometry (TOF-SIMS) was used to characterize H in Nb over a wide temperature range (160°K to 475°K) in situ to check for changes in mobility. Multiple experiments showed that as the specimen temperature is decreased below 300 °K, the H/Nb intensity changes by first increasing and then decreasing drastically at temperatures below 200°K. As specimen temperature is increased from 300°K to 450°K, the H/Nb intensity decreases. Remarkably, the H intensity with respect to Nb increases with time at 475°K (approximately 200°C). Correlation between this data and the H-Nb phase diagram appears to account for the H behaviour.

36 MATERIALS SCIENCE↗

The Living With a Star CDAW on the Solar and Geospace Connections of Solar Energetic Particles

The Living With a Star Program is sponsoring its first CDAW (Coordinated Data Analysis Workshop) to be held July 23-26, 2002 at a conference support location near the NASA Goddard Space Flight Center. This CDAW's topic is Solar Energetic Particle events. The topic was chosen due to the breadth of the impact of SEP's on the space environment and terrestrial climate. General goals of the LWS CDAW are a) Stimulate LWS Science on the near term, b) Facilitate cross-disciplinary interaction between the LWS scientific and space environment communities, c) Produce science products for all potential users, and d) Assist in the development of the LWS data system. The workshop will proceed similar to a previous CDAW held in 1999 on Interplanetary Type 11 Shocks. A list of target events has been compiled, which can be found at the workshop home page. The page lists all of the SEP events from 1996 January to 2001 December with energy > 10 MeV particle intensities exceeding 10 PFU. Preparation for the workshop consists of identifying relevant data from a wide variety of sources (solar, interplanetary, magnetospheric and climatary), accumulating the data (frequently this consists of both raw data, processed data and plots to ease perusal during the workshop) and gathering the software tools. Participants in the workshop are expected to complete their contributions of data or models prior to arriving at the workshop. Most of the CDAW consists of joint analysis of this data; only a few introductory talks are given at the beginning of the workshop, with the rest of the time being devoted to producing scientific results. Additional symposia may be scheduled at a later date, which will allow a venue for scientific talks on the CDAW results and associated science. The poster will list the scientific goals of the workshop, as well as a scientific discussion of the data which has been accumulated thus far.

Thompson, Barbara J.↗