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Section 381: Earth Science Data Systems
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LinkWinds: The Application of Computer Graphics Methods to Interactive Science Data Analysis
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SAVS: A Space and Atmospheric Visualization Science system
The research environment faced by space and atmospheric scientists in the 1990s is characterized by unprecedented volumes of new data, by ever-increasing repositories of unexploited mission files, and by the widespread use of empirical and large-scale computational models needed for the synthesis of understanding across data sets and discipline boundaries. The effective analysis and interpretation of such massive amounts of information have become the subjects of legitimate concern. With SAVS (a Space and Atmospheric Visualization Science System), we address these issues by creating a 'push-button' software environment that mimics the logical scientific processes in data acquisition, reduction, and analysis without requiring a detailed understanding of the methods, networks, and modules that link the tools and effectively execute the functions. SAVS provides (1) a customizable framework for accessing a powerful set of visualization tools based on the popular AVS visualization software with hooks to PV-Wave and access to Khoros modules, (2) a set of mathematical and statistical tools, (3) an extensible library of discipline-specific functions and models (e.g., MSIS, IRI, Feldstein Oval, IGRF, satellite tracking with CADRE-3, etc.), and (4) capabilities for local and remote data base access. The system treats scalar, vector, and image data, and runs on most common Unix workstations. We present a description of SAVS and its components, followed by several applications based on generic research interests in interplanetary and magnetospheric physics (IMP/ISTP), active experiments in space (CRRES), and mission planning focused on the Earth's thermospheric, ionospheric, and mesospheric domains (TIMED).
Final Report Collaborative Project: Improving the Representation of Coastal and Estuarine Processes in Earth System Models
This project aimed to improve long term global climate simulations by resolving and enhancing the representation of the processes involved in the cycling of freshwater through estuaries and coastal regions. This was a collaborative multi-institution project consisting of physical oceanographers, climate model developers, and computational scientists. It specifically targeted the DOE objectives of advancing simulation and predictive capability of climate models through improvements in resolution and physical process representation.
The Need for Integrated Approaches in Metabolic Engineering
This review highlights state-of-the-art procedures for heterologous small-molecule biosynthesis, the associated bottlenecks, and new strategies that have the potential to accelerate future accomplishments in metabolic engineering. We emphasize that a combination of different approaches over multiple time and size scales must b e considered for successful pathway engineering in a heterologous host. We have classified these optimization procedures based on the "system" that is being manipulated: transcriptome, translatome, proteome, or reactome. By bridging multiple disciplines, including molecular biology, biochemistry, biophysics, and computational sciences, we can create an integral framework for the discovery and implementation of novel biosynthetic production routes.
UMT Pavilion Configs for Crossroads Acceptance [Slides]
Testing conducted to determine if requirements of a specifications are met. A python based framework to run and analyze tests for HPC systems.
SU-D-BRD-01: An Automated Physics Weekly Chart Checking System Supporting ARIA
Purpose: A software tool was developed in this study to perform automatic weekly physics chart check on the patient data in ARIA. The tool accesses the electronic patient data directly from ARIA server and checks the accuracy of treatment deliveries, and generates reports which summarize the delivery history and highlight the errors. Methods: The tool has four modules. 1) The database interface is designed to directly access treatment delivery data from the ARIA database before reorganizing the data into the patient chart tree (PCT). 2) PCT is a core data structure designed to store and organize the data in logical hierarchies, and to be passed among functions. 3) The treatment data check module analyzes the organized data in PCT and stores the checking results into PCT. 4) Report generation module generates reports containing the treatment delivery summary, chart checking results and plots of daily treatment setup parameters (couch table positions, shifts of image guidance). The errors that are found by the tool are highlighted with colors. Results: The weekly check tool has been implemented in MATLAB and clinically tested at two major cancer centers. Javascript, cascading style sheets (CSS) and dynamic HTML were employed to create the user-interactive reports. It takes 0.06 second to search the delivery records of one beam with PCT and compare the delivery records with beam plan. The reports, saved in the HTML files on shared network folder, can be accessed by web browser on computers and mobile devices. Conclusion: The presented weekly check tool is useful to check the electronic patient treatment data in Varian ARIA system. It could be more efficient and reliable than the manually check by physicists. The work was partially supported by a research grant from Varian Medical System.
Memory formation in matter
Memory formation in matter is a theme of broad intellectual relevance; it sits at the interdisciplinary crossroads of physics, biology, chemistry, and computer science. Memory connotes the ability to encode, access, and erase signatures of past history in the state of a system. Once the system has completely relaxed to thermal equilibrium, it is no longer able to recall aspects of its evolution. The memory of initial conditions or previous training protocols will be lost. Thus many forms of memory are intrinsically tied to far-from-equilibrium behavior and to transient response to a perturbation. This general behavior arises in diverse contexts in condensed-matter physics and materials, including phase change memory, shape memory, echoes, memory effects in glasses, return-point memory in disordered magnets, as well as related contexts in computer science. Yet, as opposed to the situation in biology, there is currently no common categorization and description of the memory behavior that appears to be prevalent throughout condensed-matter systems. Here the focus is on material memories. Here, the basic phenomenology of a few of the known behaviors that can be understood as constituting a memory will be described. The hope is that this will be a guide toward developing the unifying conceptual underpinnings for a broad understanding of memory effects that appear in materials.
Science at the Goddard Space Flight Center
The Sciences and Exploration Directorate of the NASA Goddard Space Flight Center (GSFC) is the largest Earth and space science research organization in the world. Its scientists advance understanding of the Earth and its life-sustaining environment, the Sun, the solar system, and the wider universe beyond. Researchers in the Sciences and Exploration Directorate work with engineers, computer programmers, technologists, and other team members to develop the cutting-edge technology needed for space-based research. Instruments are also deployed on aircraft, balloons, and Earth's surface. I will give an overview of the current research activities and programs at GSFC including the James Web Space Telescope (JWST), future Earth Observing programs, experiments that are exploring our solar system and studying the interaction of the Sun with the Earth's magnetosphere.
A Blockchain-Facilitated Secure Sensing Data Processing and Logging System
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Evolutionary Cell Computing: From Protocells to Self-Organized Computing
On the path from inanimate to animate matter, a key step was the self-organization of molecules into protocells - the earliest ancestors of contemporary cells. Studies of the properties of protocells and the mechanisms by which they maintained themselves and reproduced are an important part of astrobiology. These studies also have the potential to greatly impact research in nanotechnology and computer science. Previous studies of protocells have focussed on self-replication. In these systems, Darwinian evolution occurs through a series of small alterations to functional molecules whose identities are stored. Protocells, however, may have been incapable of such storage. We hypothesize that under such conditions, the replication of functions and their interrelationships, rather than the precise identities of the functional molecules, is sufficient for survival and evolution. This process is called non-genomic evolution. Recent breakthroughs in experimental protein chemistry have opened the gates for experimental tests of non-genomic evolution. On the basis of these achievements, we have developed a stochastic model for examining the evolutionary potential of non-genomic systems. In this model, the formation and destruction (hydrolysis) of bonds joining amino acids in proteins occur through catalyzed, albeit possibly inefficient, pathways. Each protein can act as a substrate for polymerization or hydrolysis, or as a catalyst of these chemical reactions. When a protein is hydrolyzed to form two new proteins, or two proteins are joined into a single protein, the catalytic abilities of the product proteins are related to the catalytic abilities of the reactants. We will demonstrate that the catalytic capabilities of such a system can increase. Its evolutionary potential is dependent upon the competition between the formation of bond-forming and bond-cutting catalysts. The degree to which hydrolysis preferentially affects bonds in less efficient, and therefore less well-ordered, peptides is also critical to evolution of a non-genomic system. Based on these results, a new computational object called a "molnet" is defined. Like a neural network, it is formed of interconnected units that send "signals" to each other. Like molecules, neural networks have a specific function once their structure is defined. The difference between a molnet and traditional neural networks, is that input to molnets is not simply passed along and processed from input to output units, but rather it is utilized to form and break connections(bonds), and thus to form new structures. Molnets represent a powerful tool that can be used to understand the conditions under which chemical systems can form large molecules, such as proteins, and display ever more complex functions. This has direct applications, for example to the design of smart,synthetic fabrics. Additional information is contained in the original.
Multi-scale Molecular Systems Biology: Reconstruction and Model Optimization (Final Report)
Within the Biological and Environmental Research program, the goal of the Genomic Science program is to achieve a predictive, systems-level understanding of plants, microbes, and biological communities to enable biobased solutions to DOE mission challenges in energy and environment. To achieve this goal, an ultimate objective is to develop the knowledgebase, computational infrastructure, and modeling capabilities to advance predictive understanding and manipulation of biological systems. Our project has increased the modeling capabilities and computational infrastructure required to advance predictive understanding and manipulation of biological systems. In particular, we have developed novel algorithms, for modelling biochemical reaction kinetics at genome-scale. These new algorithms have been publicly disseminated as open source software with extensive documentation and tutorials that enable widespread application of this advanced software to practical modelling scenarios. The technical effectiveness of all novel software has been conclusively demonstrated and the quality of this software is maintained by a dedicated continuous integration system. Ultimately, the results of this project will benefit the public because it will enable biologists to more accurately computationally model biological systems that need to be understood to address DOE challenges in energy and environment.
An Efficient Bayesian Method for Advancing the Application of Deep Learning in Earth Science
Despite their wide and successful applications, deep learning (DL) models are prone to overfitting for small training datasets, produce a poor predictive performance for uncertain data, and provide point estimations without any indication of the accuracy and credibility. These limitations of the deterministic DL models hinder their effective application in Earth system science where the labelled data are sparse, noisy and incomplete with large uncertainty and where the predictive uncertainty quantification is needed for scientific understanding and policy decision making. Integration of Bayesian inference into DL models adds an estimate of uncertainty and regularization in the predictions. However, traditional Bayesian methods are computationally unaffordable and inflexible for high-dimensional problems, which limits their application to DL systems that typically have millions of model parameters. In this effort, we propose an efficient and general-purpose Bayesian inference method to advance DL model optimization and uncertainty quantification, so as to facilitate the adoption of DL in Earth sciences. In a demonstration, we integrate the proposed Bayesian method with a feedforward neural network (NN) to build a fast-to-evaluate surrogate of the complex Energy Exascale Earth System Land Model for efficient modeling. The formulated Bayesian NN, using a small number of training data, produces an accurate prediction with high credibility, whereas with the same small training size, the deterministic NN cannot yield a reasonable estimation and does not provide confidence information. The proposed Bayesian method is computationally efficient and flexible, capable of integration with diverse network variants such as convolutional NNs and recurrent NNs to advance the application of DL in Earth sciences.
A Long Range Science Rover For Future Mars Missions
This paper describes the design and implementation currently underway at the Jet Propulsion Laboratory of a long range science rover for future missions to Mars. The small rover prototype, called Rocky 7, is capable of long traverse. autonomous navigation. and science instrument control, carries three science instruments, and can be commanded from any computer platform and any location using the World Wide Web. In this paper we describe the mobility system, the sampling system, the sensor suite, navigation and control, onboard science instruments. and the ground command and control system.
Computer Science Research Institute (CSRI) Summer Proceedings 2013
The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia National Laboratories for focused collaborative research on computer science, computational science, and mathematics problems that are critical to the mission of the laboratories, the Department of Energy, and the United States. The CSRI provides a mechanism by which university researchers learn about and impact national— and global—scale problems while simultaneously bringing new ideas from the academic research community to bear on these important problems. A key component of CSRI programs over the last decade has been an active and productive summer program where students from around the country conduct internships at CSRI. Each student is paired with a Sandia staff member who serves as technical advisor and mentor. The goals of the summer program are to expose the students to research in mathematical and computer sciences at Sandia and to conduct a meaningful and impactful summer research project with their Sandia mentor. Every effort is made to align summer projects with the student's research objectives and all work is coordinated with the ongoing research activities of the Sandia mentor in alignment with Sandia technical thrusts. For the 2013 CSRI Proceedings, research articles have been organized into the following broad technical focus areas — Computational Mathematics and Algorithms, Combinatorial Algorithms and Visualization, Advanced Architectures and Systems Software, Computational Applications — which are well aligned with Sandia's strategic thrusts in computer and information sciences.
Phase fluctuation spectra: New radio science information to become available in the DSN tracking system Mark III-77
An algorithm was developed for the continuous and automatic computation of Doppler noise concurrently at four sample rate intervals, evenly spanning three orders of magnitude. Average temporal Doppler phase fluctuation spectra will be routinely available in the DSN tracking system Mark III-77 and require little additional processing. The basic (noise) data will be extracted from the archival tracking data file (ATDF) of the tracking data management system.
McIDAS III - A modern interactive data access and analysis system
A powerful facility for meteorological analysis called the Man Computer Interactive Data Access System (McIDAS) was designed and implemented in the early 1970's at the Space Science and Engineering Center of the University of Wisconsin-Madison. Hardware and software experience gained via extensive use of that facility and its derivatives have led to a newer implementation of McIDAS on a larger computer with significant enhancements to the supporting McIDAS software. McIDAS allows remote and local access to a wide range of data from satellites and conventional observations, time lapse displays of imagery data, overlaid graphics, and current and past meteorological data. Available software allows one to perform analysis of a wide range of digital images as well as temperature and moisture sounding data obtained from satellites. McIDAS can generate multicolor composites of conventional and satellite weather data, radar and forecast data in a wide variety of two- and three-dimensional displays as well as time lapse movies of these analyses. These and other capabilities are described in this paper.