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At least 1,225 records · Page 68

microMS: A Python Platform for Image-Guided Mass Spectrometry Profiling

Image-guided mass spectrometry (MS) profiling provides a facile framework for analyzing samples ranging from single cells to tissue sections. The fundamental workflow utilizes a whole-slide microscopy image to select targets of interest, determine their spatial locations, and subsequently perform MS analysis at those locations. Improving upon prior reported methodology, a software package was developed for working with microscopy images. microMS, for microscopy-guided mass spectrometry, allows the user to select and profile diverse samples using a variety of target patterns and mass analyzers. Written in Python, the program provides an intuitive graphical user interface to simplify image-guided MS for novice users. The class hierarchy of instrument interactions permits integration of new MS systems while retaining the feature-rich image analysis framework. microMS is a versatile platform for performing targeted profiling experiments using a series of mass spectrometers. The flexibility in mass analyzers greatly simplifies serial analyses of the same targets by different instruments. The current capabilities of microMS are presented, and its application for off-line analysis of single cells on three distinct instruments is demonstrated. The software has been made freely available for research purposes. .

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Dakota, a multilevel parallel object-oriented framework for design optimization, parameter estimation, uncertainty quantification, and sensitivity analysis version 6.0 theory manual

The Dakota (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides a exible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quanti cation with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a exible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a theoretical manual for selected algorithms implemented within the Dakota software. It is not intended as a comprehensive theoretical treatment, since a number of existing texts cover general optimization theory, statistical analysis, and other introductory topics. Rather, this manual is intended to summarize a set of Dakota-related research publications in the areas of surrogate-based optimization, uncertainty quanti cation, and optimization under uncertainty that provide the foundation for many of Dakota's iterative analysis capabilities.

97 MATHEMATICS AND COMPUTING↗

Dakota, a multilevel parallel object-oriented framework for design optimization, parameter estimation, uncertainty quantification, and sensitivity analysis :

The Dakota (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides a exible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quanti cation with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the Dakota toolkit provides a exible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a user's manual for the Dakota software and provides capability overviews and procedures for software execution, as well as a variety of example studies.

97 MATHEMATICS AND COMPUTING↗

Proceedings of the 1998 International Computational Accelerator Physics Conference

The 1998 International Computational Accelerator Physics Conference, ICAP’98, was held September 14-18, 1998, at the Monterey Convention Center in Monterey, California. The meeting continued the tradition of four earlier Computational Accelerator Physics conferences, held in La Jolla, California (1988), Los Alamos, New Mexico (1990), Pleasanton, California (1993), and Williamsburg, Virginia (1996). ICAP’98 was organized by the Stanford Linear Accelerator Center (SLAC), Los Alamos National Laboratory (LANL), and the National Energy Research Scientific Computing Center (NERSC), and received support from the U.S. Department of Energy. The aim of this conference series is to discuss recent advances in Computational Accelerator Physics and their applications to solving important problems related to present and future accelerators. The ICAP’98 program included plenary sessions on modeling challenges in next-generation accelerators, state-of-the art methods in computational accelerator physics, and a view of what high-end computing would be like in the 21st century. There were also focused sessions on accelerator design and control, modeling high intensity beam phenomena, electromagnetic modeling, advanced algorithms, software environments and libraries, visualization and graphic interfaces, modeling advanced accelerator concepts, modeling the beam-beam interaction, computing wakefields, and combined particle/field simulations. In addition to these oral sessions there was a poster session and a vendor display. Prior to the start of the technical program, a half-day tutorial on High Performance Computing was hosted by NERSC. The ICAP series recognizes that computing and, in particular, advanced computing, is playing an increasingly important role in the successful design and development of major accelerator facilities, and in research and development leading to advances in accelerator technology. We expect that this new emphasis on high-end computing will continue in future ICAP conferences.

Ko, Kwok↗

Integration of design information

The overall concepts of the integrated programs for aerospace-vehicle design (IPAD) from the user's viewpoint are discussed. Also a top-level view of what the user requires from such a system is provided, and the interactions between the system and user are described. The four major components discussed are design process; data storage, management and manipulation; user interface; and project management. Although an outgrowth of aerospace production experience, the basic concepts discussed, and especially their emphasis on integration, are considered applicable to all problem solving. Thus, these concepts may offer a broad base for exploitation by industry in general. This is the first in a set of three papers, the other two being Future Integrated Design Process, by D. D. Mayer, and Requirements for Company-Wide Management of Engineering Information, by J. W. Southall. In addition to tying the three together, how project management can be handled in a computing environment and also the user interface needs are discussed in detail.

Anderton, G. L.↗

Evaluation of Fieldbus and OPC for Advanced Life Support

FOUNDATION(Tm) Fieldbus and OP(TM) (OLE(TM)for Process Control) technologies were integrated into an existing control system for a crop growth chamber at NASA Ames Research Center. FOUNDATION(TM) Fieldbus is a digital, bi-directional, multi-drop, serial communications network which functions essentially as a LAN for sensors. FOUNDATION(TM) Fieldbus is heterarchical, with publishers and subscribers of data performing complex control functions at low levels without centralized control and its associated overhead. OPC(TM) is a set of interfaces which replace proprietary drivers with a transparent means of exchanging data between the fieldbus and applications. The objectives were: (1) to integrate FOUNDATION(TM) Fieldbus into existing ALS hardware and determine its overall effectiveness and reliability and, (2) to quantify any savings produced by using fieldbus and OPC technologies. We encountered several problems with the FOUNDATION(TM) Fieldbus hardware chosen. Our hardware exposed 100 data for each channel of the fieldbus. The fieldbus configurator software used to program the fieldbus was simply not adequate. The fieldbus was also not inherently reliable. It lost its settings twice during our tests for unknown reasons. OPC also had issues. It did not function at all as supplied, requiring substitution of some of its components with those from other vendors. It would stop working after a fixed period of time. Certain database calls eventually lock the machine. Overall, we would not recommend FOUNDATION(TM) Fieldbus: it was too difficult to implement with little overall added value. It also seems unlikely that FOUNDATION(TM) Fieldbus will gain sufficient penetration into the laboratory instrument market to ever be cost effective for the ALS community. OPC had good reliability and performance once a stable installation was achieved. It allowed a rapid change to an alternative software strategy when our first strategy failed. It is a cost effective solution to distributed control systems development.

Boulanger, Richard P.↗

LinkWinds: An Approach to Visual Data Analysis

The Linked Windows Interactive Data System (LinkWinds) is a prototype visual data exploration and analysis system resulting from a NASA/JPL program of research into graphical methods for rapidly accessing, displaying and analyzing large multivariate multidisciplinary datasets. It is an integrated multi-application execution environment allowing the dynamic interconnection of multiple windows containing visual displays and/or controls through a data-linking paradigm. This paradigm, which results in a system much like a graphical spreadsheet, is not only a powerful method for organizing large amounts of data for analysis, but provides a highly intuitive, easy to learn user interface on top of the traditional graphical user interface.

Jacobson, Allan S.↗

OVERVIEW OF THE SAPHIRE PROBABILISTIC RISK ANALYSIS SOFTWARE

The Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE) is a software application developed for performing a complete probabilistic risk assessment (PRA) using a personal computer (PC) running the Microsoft Windows operating system. SAPHIRE Version 8 is funded by the U.S. Nuclear Regulatory Commission (NRC) and developed by the Idaho National Laboratory (INL). INL's primary role in this project is that of software developer and tester. However, INL also plays an important role in technology transfer by interfacing and supporting SAPHIRE users, who constitute a wide range of PRA practitioners from the NRC, national laboratories, the private sector, and foreign countries. In this paper, we provide an overview of the current technical capabilities found in SAPHIRE Version 8, including the user interface and enhanced solving algorithms.

97 MATHEMATICS AND COMPUTING↗

Merged Requests for Better Performance and Productivity in Multithreaded OpenSHMEM

A merged request is a handle representing a group of Remote Memory Access (RMA), Atomic or Collective operations. The merged request can be created either by combining multiple outstanding merged request handles or using the same merged request handle for additional operations. We show that introducing such simple yet powerful semantics in OpenSHMEM provides many productivity and performance advantages. In this paper, we first introduce the interfaces and semantics for creating and using merged request handles. Then, we demonstrate with a merge request that we can achieve better performance characteristics in multithreaded OpenSHMEM application. Particularly, we show one can achieve higher message rate, a higher bandwidth for smaller message, and better computation-communication overlap. Further, we use merged request to realize multithreaded collectives, where multiple threads co-operate to complete the collective operation. Our experimental results show that in a multithreaded OpenSHMEM program, the merged request based RMA operations achieve over 100 Million Messages Per Second (MMPS). It achieves over 10 MMPS compared to 4.5 MMPS with default RMA operations in a single threaded environment. Also, we achieve higher bandwidth for smaller message sizes, close to 100% overlap, and reduce the latency by 60%.

Gorentla Venkata, Manjunath↗

SU-G-TeP2-15: Feasibility Study of Fiber-Optic Cerenkov Radiation Sensors for in Vivo Measurement: Dosimetric Characterization and Clinical Application in Proton Beams

Purpose: To evaluate the possibility of a fiber-optic Cerenkov radiation sensor (FCRS) for in vivo dose verification in proton therapy. Methods: The Cerenkov radiation due to the proton beam was measured using a homemade phantom, consisting of a plastic optical fiber (POF, PGSCD1001-13-E, Toray, Tokyo, Japan) connected to each channel of a multianode photomultiplier tube (MAPMT:H7546, Hamamatsu Photonics, Shizuoka, Japan). Data were acquired using a multi-anode photomultiplier tube with the NI-DAQ system (National Instruments Texas, USA). The real-time monitoring graphic user interface was programmed using Labview. The FCRS was analyzed for its dosimetrics characteristic in proton beam. To determine the accuracy of the FCRS in proton dose measurements, we compared the ionization chamber dose measurements using a water phantom. We investigated the feasibility of the FCRS for the measurement of dose distributions near the superficial region for proton plans with a varying separation between the target volume and the surface of 3 patients using a humanoid phantom. Results: The dose-response has good linearity. Dose-rate and energy dependence were found to be within 1%. Depth-dose distributions in non-modulated proton beams obtained with the FCRS was in good agreement with the depth-dose measurements from the ionization chamber. To evaluate the dosimetric accuracy of the FCRS, the difference of isocenter dose between the delivery dose calculated by the treatment planning system and that measured by the FCRS was within 3%. With in vivo dosimetry using the humanoid phantom, the calculated surface doses overestimated measurements by 4%–8% using FCRS. Conclusion: In previous study, our results indicate that the performance of the array-type FCRS was comparable to that of the currently used a multi-layer ion chamber system. In this study, we also believe that the fiber-optic Cerenkov radiation sensor has considerable potential for use with in vivo patient proton dosimetry.

07 ISOTOPE AND RADIATION SOURCES↗

The cost benefits of the Spacelab system to scientific investigations and space applications

Cost advantages of the Spacelab system to scientific experiments in space and space operations are presented. The payload integration concepts developed for Spacelab are examined, and it is shown that Spacelab and Shuttle integration, communications and data processing, launch support requirements and flight operations will provide a considerable savings in the costs of space research relative to previous space systems. Spacelab modular design, incorporating features such as standard payload interfaces, optional mission dependent equipment and standard services, such as the Experiment Computer Operating System, is shown to offer the user a wider range of services than previous programs, also at significantly lower costs. It is concluded that the Spacelab system will greatly reduce the costs and broaden the opportunities for scientific investigation in space.

Jean, O. C.↗

Hardware Interface Description for the Integrated Power, Avionics, and Software (iPAS) Space Telecommunications Radio Ssystem (STRS) Radio

The Space Telecommunications Radio System (STRS) provides a common, consistent framework for software defined radios (SDRs) to abstract the application software from the radio platform hardware. The STRS standard aims to reduce the cost and risk of using complex, configurable and reprogrammable radio systems across NASA missions. To promote the use of the STRS architecture for future NASA advanced exploration missions, NASA Glenn Research Center (GRC) developed an STRS-compliant SDR on a radio platform used by the Advance Exploration System program at the Johnson Space Center (JSC) in their Integrated Power, Avionics, and Software (iPAS) laboratory. The iPAS STRS Radio was implemented on the Reconfigurable, Intelligently-Adaptive Communication System (RIACS) platform, currently being used for radio development at JSC. The platform consists of a Xilinx ML605 Virtex-6 FPGA board, an Analog Devices FMCOMMS1-EBZ RF transceiver board, and an Embedded PC (Axiomtek eBox 620-110-FL) running the Ubuntu 12.4 operating system. Figure 1 shows the RIACS platform hardware. The result of this development is a very low cost STRS compliant platform that can be used for waveform developments for multiple applications.The purpose of this document is to describe how to develop a new waveform using the RIACS platform and the Very High Speed Integrated Circuits (VHSIC) Hardware Description Language (VHDL) FPGA wrapper code and the STRS implementation on the Axiomtek processor.

Flight Computer↗

Multimode scanning X-ray diffraction microscopy for diamond anvil cell experiments

We have designed and implemented a new experimental system for fast mapping of crystal structures and other structural features of materials under high pressure at the High Pressure Collaborative Access Team, Sector 16 of the Advanced Photon Source. The system utilizes scanning X-ray diffraction microscopy (SXDM) and is optimized for use with diamond anvil cell devices. In SXDM, the X-ray diffraction (XRD) is collected in a forward scattering geometry from points on a two-dimensional grid by fly-scanning the sample with respect to a micro-focused X-ray beam. The recording of XRD is made during the continuous motion of the sample using a fast (millisecond) X-ray area detector in synchrony with the sample positioners, resulting in a highly efficient data collection for SXDM. A new computer program, X-ray Diffractive Imaging (XDI), has been developed with the SXDM system. The XDI program provides a graphical interface for constructing and displaying the SXDM images in several modes: (1) phase mapping based on structural information, (2) pressure visualization based on the equation of state, (3) microstructural features mapping based on peak shape parameters, and (4) grain size and preferred-orientation based on peak shape parameters. The XDI is a standalone program and can be generally used for displaying SXDM images. Two examples of iron and zirconium samples under high pressure are presented to demonstrate the applications of SXDM. Published under license by AIP Publishing.

47 OTHER INSTRUMENTATION↗

Coolant Channel Design for Additively Manufactured Reactor Cores

Additive manufacturing (AM) methods are currently being explored for applications in nuclear reactors to make advanced reactors more efficient, safe, and reliable. The Transformational Challenge Reactor (TCR) program has explored AM for nuclear by designing a high-temperature gas reactor (HTGR) using an AM silicon carbide fuel form with uranium nitride–tristructural isotropic fuel. In this study, we detail the design process for the TCR fuel form’s coolant channels using computational fluid dynamics models with conjugate heat transfer. Additionally, this work discusses how these models were interfaced with other design teams, project milestones, and the agile design method used to mature the reactor design. The methodology deployed was able to create a channel design with lower maximum fuel temperatures and thermal stresses in the fuel form over traditional channel designs that can be manufactured subtractively. These results were achieved with only small manufacturing penalties. Results are discussed and presented on lessons learned for designing AM components for nuclear reactors. Finally, areas of opportunity are discussed for advanced design tools to further automate design activities and optimize reactors with fewer built-in assumptions.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Experiment module concepts study. Volume 2: Experiments and mission operations

The baseline experiment program is concerned with future space experiments and cover the scientific disciplines of astronomy, space physics, space biology, biomedicine and biotechnology, earth applications, materials science, and advanced technology. The experiments within each discipline are grouped into functional program elements according to experiments that support a particular area of research or investigation and experiments that impose similar or related demand on space station support systems. The experiment requirements on module subsystems, experiment operating modes and time profiles, and the role of the astronaut are discussed. Launch and rendezvous with the space station, disposal, and on-orbit operations are delineated. The operational interfaces between module and other system elements are presented and include space station and logistic system interfaces. Preliminary launch and on-orbit environmental criteria and requirements are discussed, and experiment equipment weights by functional program elements are tabulated.

Macdonald, J. M.↗

Investigations of high power problems in space shuttle antenna designs

A study program is discussed which includes a survey of industry and government laboratories and was undertaken to determine the state of the art in dealing with problems of high power levels in reentry antenna design. A laboratory program to develop techniques for testing dielectric materials for effects on RF transmission is also considered, with emphasis on high power applications in space and reentry flights. The study program resulted in a set of guidelines for avoiding breakdown in antenna design. A discussion of temperature effects on dielectric breakdown is also given. From the laboratory program, a description is presented of techniques for (1) heating with a carbon arc image furnace, (2) temperature measurement (using thermocouples and an infrared pyrometer), (3) mass spectrometric monitoring of outgassing, (4) testing for RF breakdown in both heated dielectrics and the dielectric/air and dielectric/plasma interfaces. Data and observations are reported from technique development using candidate shuttle materials falling into three categories: (1) lightweight refractory foams, (2) dense RF window materials, and (3) ablative materials.

Taylor, W. C.↗

NASA research in teleoperation and robotics

Increased automation is necessary in future NASA missions. Drivers for automation include constrained funding and physical resources as well as mission capabilities not achievable through conventional means. The application of emerging technology in manipulators and machine intelligence will enable the development of robotic devices remotely commanded by human operators to increase man's productivity in space. The Office of Aeronautics and Space Technology (OAST) has established a program for research in teleoperation and robotics. The program's near-term focus is a Remote Orbital Servicing System (ROSS). The longer range goals include: (1) basic research in autonomous operations, (2) human factors research on the man-machine interface to remote systems, and (3) system integration and analysis of advanced concepts. This paper reviews the current NASA research and technology and considers future work needed to meet the OAST goals.

Meintel, A. J., Jr.↗

Adaptation of a Control Center Development Environment for Industrial Process Control

In the control center, raw telemetry data is received for storage, display, and analysis. This raw data must be combined and manipulated in various ways by mathematical computations to facilitate analysis, provide diversified fault detection mechanisms, and enhance display readability. A development tool called the Graphical Computation Builder (GCB) has been implemented which provides flight controllers with the capability to implement computations for use in the control center. The GCB provides a language that contains both general programming constructs and language elements specifically tailored for the control center environment. The GCB concept allows staff who are not skilled in computer programming to author and maintain computer programs. The GCB user is isolated from the details of external subsystem interfaces and has access to high-level functions such as matrix operators, trigonometric functions, and unit conversion macros. The GCB provides a high level of feedback during computation development that improves upon the often cryptic errors produced by computer language compilers. An equivalent need can be identified in the industrial data acquisition and process control domain: that of an integrated graphical development tool tailored to the application to hide the operating system, computer language, and data acquisition interface details. The GCB features a modular design which makes it suitable for technology transfer without significant rework. Control center-specific language elements can be replaced by elements specific to industrial process control.

Killough, Ronnie L.↗