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At least 235 records · Page 13

Optimal expression evaluation for data parallel architectures

A data parallel machine represents an array or other composits data structure by allocating one processor per data item. A pointwise operation can be performed between two such arrays in unit time, provided their corresponding elements are allocated in the same processors. If the arrays are not aligned in this fashion, the cost of moving one or both of them is part of the cost of operation. The choice of where to perform the operation then affects this cost. If an expression with several operands is to be evaluated, there may be many choices of where to perform the intermediate operations. An efficient algorithm is given to find the minimum cost way to evaluate an expression, for several different data parallel architectures. The algorithm applies to any architecture in which the metric describing the cost of moving an array has a property called robustness. This encompasses most of the common data parallel communication architectures, including meshes of arbitrary dimension and hypercubes.

Gilbert, John R.↗

Measurement and Analysis of Failures in Computer Systems

This thesis presents a study of software failures spanning several different releases of Tandem's NonStop-UX operating system running on Tandem Integrity S2(TMR) systems. NonStop-UX is based on UNIX System V and is fully compliant with industry standards, such as the X/Open Portability Guide, the IEEE POSIX standards, and the System V Interface Definition (SVID) extensions. In addition to providing a general UNIX interface to the hardware, the operating system has built-in recovery mechanisms and audit routines that check the consistency of the kernel data structures. The analysis is based on data on software failures and repairs collected from Tandem's product report (TPR) logs for a period exceeding three years. A TPR log is created when a customer or an internal developer observes a failure in a Tandem Integrity system. This study concentrates primarily on those TPRs that report a UNIX panic that subsequently crashes the system. Approximately 200 of the TPRs fall into this category. Approximately 50% of the failures reported are from field systems, and the rest are from the testing and development sites. It has been observed by Tandem developers that fewer cases are encountered from the field than from the test centers. Thus, the data selection mechanism has introduced a slight skew.

Thakur, Anshuman↗

Evolution of International Space Station Program Safety Review Processes and Tools

The International Space Station Program at NASA is constantly seeking to improve the processes and systems that support safe space operations. To that end, the ISS Program decided to upgrade their Safety and Hazard data systems with 3 goals: make safety and hazard data more accessible; better support the interconnection of different types of safety data; and increase the efficiency (and compliance) of safety-related processes. These goals are accomplished by moving data into a web-based structured data system that includes strong process support and supports integration with other information systems. Along with the data systems, ISS is evolving its submission requirements and safety process requirements to support the improved model. In contrast to existing operations (where paper processes and electronic file repositories are used for safety data management) the web-based solution provides the program with dramatically faster access to records, the ability to search for and reference specific data within records, reduced workload for hazard updates and approval, and process support including digital signatures and controlled record workflow. In addition, integration with other key data systems provides assistance with assessments of flight readiness, more efficient review and approval of operational controls and better tracking of international safety certifications. This approach will also provide new opportunities to streamline the sharing of data with ISS international partners while maintaining compliance with applicable laws and respecting restrictions on proprietary data. One goal of this paper is to outline the approach taken by the ISS Progrm to determine requirements for the new system and to devise a practical and efficient implementation strategy. From conception through implementation, ISS and NASA partners utilized a user-centered software development approach focused on user research and iterative design methods. The user-centered approach used on the new ISS hazard system utilized focused user research and iterative design methods employed by the Human Computer Interaction Group at NASA Ames Research Center. Particularly, the approach emphasized the reduction of workload associated with document and data management activities so more resources can be allocated to the operational use of data in problem solving, safety analysis, and recurrence control. The methods and techniques used to understand existing processes and systems, to recognize opportunities for improvement, and to design and review improvements are described with the intent that similar techniques can be employed elsewhere in safety operations. A second goal of this paper is to provide and overview of the web-based data system implemented by ISS. The software selected for the ISS hazard systemMission Assurance System (MAS)is a NASA-customized vairant of the open source software project Bugzilla. The origin and history of MAS as a NASA software project and the rationale for (and advantages of) using open-source software are documented elsewhere (Green, et al., 2009).

Ratterman, Christian D.↗

Improving NASA Earth Science Data and Information Access Through Natural Language Processing Based Data Analysis and Visualization

NASA: The Research Access initiative is part of the agency's framework for increasing public access to scientific publications and digital scientific data. The initiative follows the release of White House Office of Science and Technology Policy's (OSTP) memorandum "Increasing Access to the Results of Federally Funded Research," to ensure federally funded research is available to the public within one year of publication. NASA answered the mandate by creating an agency plan entitled "NASA Plan for Increasing Access to the Results of Scientific Research" and associated policy, NPD 2230.1, Research Data and Publication Access. Principles in NASA SMD Strategic Plan for Scientific Data and Computing: Continued free and open access to scientific data for any use. Improved ease of use and discoverability. Enhanced science applications and new use cases. Incorporates best practices and "state of the art" through partnerships. Earth Data and Systems are Evolving: Increasing archive and file sizes. More complicated data structures. More user-friendly and data services. What is the future direction?

Liu, Zhong↗

Systems Development, Datamining and Knowledge Discovery Abstract

This summer, 2020, during my NASA internship I worked with my mentor, Ali Shaykhian, as well as a group of four other interns: Javel Gramling, Janelisse Morales, Tristian Running Crane, and Zulmarie Jiménez. Our research and projects all differ but work together to solve datamining unstructured data into an easy to read format. Turning unstructured data into something easier to follow is important for helping quickly pull data out of larger documents, so that one doesn’t have to go through multiple pages to find certain data points. By being able to structure data pulled from a document, it can be usedto collect data from mass amounts of forms and arrange it in an easy to glance at table instead of multiple forms. I chose to focus mainly on creating form templates with both Microsoft Word and Excel and getting used to the types of data that can be collected; as well as learning where both programs differed. After I was familiar with what could be gathered, I worked towards taking data collected by a Word form and importing it into an Excel spreadsheet. By being able to transfer data from a Word document to an Excel document, there is an added layer of functionality to the datamining. Moving data around between Excel sheets isn’t that complex of a process, but when you try to import from a Word document a lot of formatting and readability can be lost. The purpose of my research is to reduce that loss by using Visual Basic scripts to clean and arrange imported data.

Makayla Amber Renfro↗

Gravity survey of the Mt. Toondina impact structure, South Australia

The Mt. Toondina impact structure is located in northern South Australia, about 45 km south of the town of Oodnadatta. Only the central uplift is exposed. The outcrops at Mt. Toondina reveal a remarkable structural anomaly surrounded by a broad expanse of nearly flat-lying beds of the Bulldog Shale of Early Cretaceous age. A gravity survey was undertaken in 1989 to determine the diameter of the impact structure, define the form of the central uplift, and understand the local crustal structure. Data were collected along two orthogonal lines across the structure. In addition to the profiles, a significant number of measurements were made on and around the central uplift. The 1989 gravity data combined with 1963 gravity data and the seismic reflection data provide an excellent data base to interpret the subsurface structure of the Mt. Toondina feature.

Plescia, J. B.↗

The nature of chemisorbed oxygen on Ni(100) and Cu(100)

Model calculations indicate two low-lying states for the interaction of O with Ni and Cu(100). The oxide state is approximately 1 eV more stable and its R(perpendicular) for Ni(100) is consistent with the experimental value for Ni(100), indicating only one type of stable chemisorption bond. This agrees with XPS (X-ray photoemission spectroscopy) and EXAFS (extended X-ray absorption fine structure) data for the observed LEED (low energy electron diffraction) structures. Interpretations of EELS (electron energy loss spectroscopy) data in terms of a radical state forthe p(2x2) and the oxide state for the c(2x2) structure must be seriously questioned.

Bauschlicher, C. W., Jr.↗

Dynamic Server-Based KML Code Generator Method for Level-of-Detail Traversal of Geospatial Data

Web-based geospatial client applications such as Google Earth and NASA World Wind must listen to data requests, access appropriate stored data, and compile a data response to the requesting client application. This process occurs repeatedly to support multiple client requests and application instances. Newer Web-based geospatial clients also provide user-interactive functionality that is dependent on fast and efficient server responses. With massively large datasets, server-client interaction can become severely impeded because the server must determine the best way to assemble data to meet the client applications request. In client applications such as Google Earth, the user interactively wanders through the data using visually guided panning and zooming actions. With these actions, the client application is continually issuing data requests to the server without knowledge of the server s data structure or extraction/assembly paradigm. A method for efficiently controlling the networked access of a Web-based geospatial browser to server-based datasets in particular, massively sized datasets has been developed. The method specifically uses the Keyhole Markup Language (KML), an Open Geospatial Consortium (OGS) standard used by Google Earth and other KML-compliant geospatial client applications. The innovation is based on establishing a dynamic cascading KML strategy that is initiated by a KML launch file provided by a data server host to a Google Earth or similar KMLcompliant geospatial client application user. Upon execution, the launch KML code issues a request for image data covering an initial geographic region. The server responds with the requested data along with subsequent dynamically generated KML code that directs the client application to make follow-on requests for higher level of detail (LOD) imagery to replace the initial imagery as the user navigates into the dataset. The approach provides an efficient data traversal path and mechanism that can be flexibly established for any dataset regardless of size or other characteristics. The method yields significant improvements in userinteractive geospatial client and data server interaction and associated network bandwidth requirements. The innovation uses a C- or PHP-code-like grammar that provides a high degree of processing flexibility. A set of language lexer and parser elements is provided that offers a complete language grammar for writing and executing language directives. A script is wrapped and passed to the geospatial data server by a client application as a component of a standard KML-compliant statement. The approach provides an efficient means for a geospatial client application to request server preprocessing of data prior to client delivery. Data is structured in a quadtree format. As the user zooms into the dataset, geographic regions are subdivided into four child regions. Conversely, as the user zooms out, four child regions collapse into a single, lower-LOD region. The approach provides an efficient data traversal path and mechanism that can be flexibly established for any dataset regardless of size or other characteristics.

Baxes, Gregory↗

Structure analysis of the telomere resolvase from the Lyme disease spirochete Borrelia garinii reveals functional divergence of its C-terminal domain

Borrelia spirochetes are the causative agents of Lyme disease and relapsing fever, two of the most common tick-borne illnesses. A characteristic feature of these spirochetes is their highly segmented genomes which consists of a linear chromosome and a mixture of up to approximately 24 linear and circular extrachromosomal plasmids. The complexity of this genomic arrangement requires multiple strategies for efficient replication and partitioning during cell division, including the generation of hairpin ends found on linear replicons mediated by the essential enzyme ResT, a telomere resolvase. Using an integrative structural biology approach employing advanced modelling, circular dichroism, X-ray crystallography and small-angle X-ray scattering, we have generated high resolution structural data on ResT from B. garinii. Our data provides the first high-resolution structures of ResT from Borrelia spirochetes and revealed active site positioning in the catalytic domain. We also demonstrate that the C-terminal domain of ResT is required for both transesterification steps of telomere resolution, and is a requirement for DNA binding, distinguishing ResT from other telomere resolvases from phage and bacteria. These results advance our understanding of the molecular function of this essential enzyme involved in genome maintenance in Borrelia pathogens.

59 BASIC BIOLOGICAL SCIENCES↗

Myna

The additive manufacturing (AM) community has been developing digital factory tools over the past decade to better leverage the multi-modal process data coming out of the advanced manufacturing process. As a result, numerous databases of additive manufacturing process data exist in the literature and in the archival storage of disparate research groups. While some efforts have been made to create a standard ontology for storing and sharing AM data, in practice a variety of data structures are used to store AM build data, even within a single institution. This causes many problems for maintainability and extensibility when attempting to integrate computational modeling tools with experimental data to either validate models or to provide further insight into results and trends. Myna is a Python-based framework that aims to decrease the effort needed to connect individual computational models to the variety of AM process data that exist in different research groups and institutions. This type of software is sometimes referred to as "middleware" or “glueware,” in that it connects disparate databases and applications into a single computational ecosystem. Instead of maintaining unique interfaces between each application and each database, developers can create a single interface from each application to Myna and thereby gain access to the implemented database connections. Similarly, developing a database connection in Myna provides access to the developed simulation applications. This framework greatly simplifies the maintainability of model applications that rely on experimental data. Using external simulation tools, users will also be able to run pre-configured workflows using the built-in workflow manager. Several examples of input files are provided with Myna for different workflows, including melt pool geometry predictions and detailed melt pool and solidification microstructure predictions.

Knapp, GerryL. [Oak Ridge National Laboratory (ORN↗

The application of remote sensing techniques to inter and intra urban analysis

This is an effort to assess the applicability of air and spaceborne photography toward providing data inputs to urban and regional planning, management, and research. Through evaluation of remote sensing inputs to urban change detection systems, analyzing an effort to replicate an existing urban land use data file using remotely sensed data, estimating population and dwelling units from imagery, and by identifying and evaluating a system of urban places ultilizing space photography, it was determined that remote sensing can provide data concerning land use, changes in commercial structure, data for transportation planning, housing quality, residential dynamics, and population density.

Horton, F. E.↗

DecisionMaker software and extracting fuzzy rules under uncertainty

Knowledge acquisition under uncertainty is examined. Theories proposed in deKorvin's paper 'Extracting Fuzzy Rules Under Uncertainty and Measuring Definability Using Rough Sets' are discussed as they relate to rule calculation algorithms. A data structure for holding an arbitrary number of data fields is described. Limitations of Pascal for loops in the generation of combinations are also discussed. Finally, recursive algorithms for generating all possible combination of attributes and for calculating the intersection of an arbitrary number of fuzzy sets are presented.

Walker, Kevin B.↗

Complexities in Subsetting Level 2 Data

Satellite Level 2 data presents unique challenges for tools and services. From nonlinear spatial geometry to inhomogeneous file data structure to inconsistent temporal variables to complex data variable dimensionality to multiple file formats, there are many difficulties in creating general tools for Level 2 data support. At NASA Goddard Earth Sciences Data and Information Services Center (GES DISC), we are implementing a general Level 2 Subsetting service for Level 2 data to a user-specified spatio-temporal region of interest (ROI). In this presentation, we will unravel some of the challenges faced in creating this service and the strategies we used to surmount them.

Data acces↗

Interfacing with Legacy using Remote Method Invocation

The assignment described was enough to make a neophyte Java developer bolt for the door: provide a remote method for use by an applet which invokes a native method that wraps a function in an existing legacy library. The purpose of the remote method is to return an instance of a class object whose contents reflect the data structure returned by the legacy function. While embroiled in implementation, I would have spent the time wading through their JNI use group archive as well, but I couldn't seem to locate one. Subsequently, I made the decision to try to document my findings in order to assist others. Before we start on the class design, let's look at what the existing legacy code does. The C function to be called, Get-Legacy-Data, consists of two steps: an ASII file is read from the local disk and its contents are parsed into a Legacy_Type structure whose address is passed as an argument by the caller. The legacy code was compiled into a shared object library, legacy. so, using the IRIX 6.2 compiler and then loaded onto the Web server, a Silicon Graphics Indy station loaded with the IRIX 6.4 operating system. As far as the class design is concerned, the first thing required is a class to act as a template for the data structure returned by the legacy function. This class, JLegacy, declares a series of public instance variables which correspond to the members of Legacy_Type and provides a parameterless constructor. This constructor is never called, not even by the native method which allocates the object for return to the remote method. Next, the remote interface declaration for the remote object must be defined. In order for JLegacyRO to implement getJLegacy, JLegacyRO must interface with the existing legacy code through a native method, getn. getn is declared in the JLegacyRO class but implemented in C, just like the legacy code. getn returns a JLegacy instance and is declared static since its implementation is the same for all instances of the JLegacyRO class.

Howard, Scott M.↗

rcsb-api : Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.

FAIR principles↗

Automatic Data Distribution for CFD Applications on Structured Grids

Data distribution is an important step in implementation of any parallel algorithm. The data distribution determines data traffic, utilization of the interconnection network and affects the overall code efficiency. In recent years a number data distribution methods have been developed and used in real programs for improving data traffic. We use some of the methods for translating data dependence and affinity relations into data distribution directives. We describe an automatic data alignment and placement tool (ADAPT) which implements these methods and show it results for some CFD codes (NPB and ARC3D). Algorithms for program analysis and derivation of data distribution implemented in ADAPT are efficient three pass algorithms. Most algorithms have linear complexity with the exception of some graph algorithms having complexity O(n(sup 4)) in the worst case.

Frumkin, Michael↗

Automatic Data Distribution for CFD Applications on Structured Grids

Data distribution is an important step in implementation of any parallel algorithm. The data distribution determines data traffic, utilization of the interconnection network and affects the overall code efficiency. In recent years a number data distribution methods have been developed and used in real programs for improving data traffic. We use some of the methods for translating data dependence and affinity relations into data distribution directives. We describe an automatic data alignment and placement tool (ADAFT) which implements these methods and show it results for some CFD codes (NPB and ARC3D). Algorithms for program analysis and derivation of data distribution implemented in ADAFT are efficient three pass algorithms. Most algorithms have linear complexity with the exception of some graph algorithms having complexity O(n(sup 4)) in the worst case.

Frumkin, Michael↗

Directory interchange format manual, version 3.0

The Directory Interchange Format (DIF) is a data structure used to exchange directory level information about data sets among information systems. The format consists of a number of fields that describe the attributes of a directory entry and text blocks that contain a descriptive summary of and references for the directory entry. All fields and the summary are preceded by labels identifying their contents. All values are ASCII character strings. The structure is intended to be flexible, allowing for future changes in the contents of directory entries.

Source record↗