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At least 1,423 records · Page 79

Bioinformatic teaching resources - for educators, by educators - using KBase, a free, user-friendly, open source platform

Over the past year, biology educators and staff at the Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free and easily accessible data science platform that integrates many bioinformatics resources into a graphical user interface built upon reproducible analysis notebooks. KBase held conversations with college and high school instructors to understand how KBase could potentially support their educational goals. These conversations morphed into a working group of biological and data science instructors that adapted the KBase platform to their curriculum needs, specifically around concepts in Genomics, Metagenomics, Pangenomics, and Phylogenetics. The KBase Educators Working Group developed modular, adaptable, and customizable instructional units. Each instructional module contains teaching resources, publicly available data, analysis tools, and markdown capability to tailor instructions and learning goals for each class. The online user interface enables students to conduct hands-on data science research and analyses without requiring programming skills or their own computational resources (these are provided by KBase). Alongside these resources, KBase continues to work with instructors, supporting the development of additional curriculum modules. For anyone new to the platform, KBase, and the growing KBase Educators Organization, provides a community network, accompanied by community-sourced guidelines, instructional templates, and peer support to use KBase within a classroom whether virtual or in-person.

59 BASIC BIOLOGICAL SCIENCES↗

Architecture for Survivable System Processing (ASSP)

The Architecture for Survivable System Processing (ASSP) Program is a multi-phase effort to implement Department of Defense (DOD) and commercially developed high-tech hardware, software, and architectures for reliable space avionics and ground based systems. System configuration options provide processing capabilities to address Time Dependent Processing (TDP), Object Dependent Processing (ODP), and Mission Dependent Processing (MDP) requirements through Open System Architecture (OSA) alternatives that allow for the enhancement, incorporation, and capitalization of a broad range of development assets. High technology developments in hardware, software, and networking models, address technology challenges of long processor life times, fault tolerance, reliability, throughput, memories, radiation hardening, size, weight, power (SWAP) and security. Hardware and software design, development, and implementation focus on the interconnectivity/interoperability of an open system architecture and is being developed to apply new technology into practical OSA components. To insure for widely acceptable architecture capable of interfacing with various commercial and military components, this program provides for regular interactions with standardization working groups (e.g.) the International Standards Organization (ISO), American National Standards Institute (ANSI), Society of Automotive Engineers (SAE), and Institute of Electrical and Electronic Engineers (IEEE). Selection of a viable open architecture is based on the widely accepted standards that implement the ISO/OSI Reference Model.

Wood, Richard J.↗

The use of hypermedia to increase the productivity of software development teams

Rapid progress in low-cost commercial PC-class multimedia workstation technology will potentially have a dramatic impact on the productivity of distributed work groups of 50-100 software developers. Hypermedia/multimedia involves the seamless integration in a graphical user interface (GUI) of a wide variety of data structures, including high-resolution graphics, maps, images, voice, and full-motion video. Hypermedia will normally require the manipulation of large dynamic files for which relational data base technology and SQL servers are essential. Basic machine architecture, special-purpose video boards, video equipment, optical memory, software needed for animation, network technology, and the anticipated increase in productivity that will result for the introduction of hypermedia technology are covered. It is suggested that the cost of the hardware and software to support an individual multimedia workstation will be on the order of $10,000.

Coles, L. Stephen↗

NASA'S SERVIR Gulf of Mexico Project: The Gulf of Mexico Regional Collaborative (GoMRC)

The Gulf of Mexico Regional Collaborative (GoMRC) is a NASA-funded project that has as its goal to develop an integrated, working, prototype IT infrastructure for Earth science data, knowledge and models for the five Gulf U.S. states and Mexico, and to demonstrate its ability to help decision-makers better understand critical Gulf-scale issues. Within this preview, the mission of this project is to provide cross cutting solution network and rapid prototyping capability for the Gulf of Mexico region, in order to demonstrate substantial, collaborative, multi-agency research and transitional capabilities using unique NASA data sets and models to address regional problems. SERVIR Mesoamerica is seen as an excellent existing framework that can be used to integrate observational and GIs data bases, provide a sensor web interface, visualization and interactive analysis tools, archival functions, data dissemination and product generation within a Rapid Prototyping concept to assist decision-makers in better understanding Gulf-scale environmental issues.

Quattrochi, Dale A.↗

Automated Cryocooler Monitor and Control System

A system was designed to automate cryogenically cooled low-noise amplifier systems used in the NASA Deep Space Network. It automates the entire operation of the system including cool-down, warm-up, and performance monitoring. The system is based on a single-board computer with custom software and hardware to monitor and control the cryogenic operation of the system. The system provides local display and control, and can be operated remotely via a Web interface. The system controller is based on a commercial single-board computer with onboard data acquisition capability. The commercial hardware includes a microprocessor, an LCD (liquid crystal display), seven LED (light emitting diode) displays, a seven-key keypad, an Ethernet interface, 40 digital I/O (input/output) ports, 11 A/D (analog to digital) inputs, four D/A (digital to analog) outputs, and an external relay board to control the high-current devices. The temperature sensors used are commercial silicon diode devices that provide a non-linear voltage output proportional to temperature. The devices are excited with a 10-microamp bias current. The system is capable of monitoring and displaying three temperatures. The vacuum sensors are commercial thermistor devices. The output of the sensors is a non-linear voltage proportional to vacuum pressure in the 1-Torr to 1-millitorr range. Two sensors are used. One measures the vacuum pressure in the cryocooler and the other the pressure at the input to the vacuum pump. The helium pressure sensor is a commercial device that provides a linear voltage output from 1 to 5 volts, corresponding to a gas pressure from 0 to 3.5 MPa (approx. = 500 psig). Control of the vacuum process is accomplished with a commercial electrically operated solenoid valve. A commercial motor starter is used to control the input power of the compressor. The warm-up heaters are commercial power resistors sized to provide the appropriate power for the thermal mass of the particular system, and typically provide 50 watts of heat. There are four basic operating modes. "Cool " mode commands the system to cool to normal operating temperature. "Heat " mode is used to warm the device to a set temperature near room temperature. "Pump " mode is a maintenance function that allows the vacuum system to be operated alone to remove accumulated contaminants from the vacuum area. In "Off " mode, no power is applied to the system.

Britcliffe, Michael J.↗

Molecular Dynamics Investigation of the Structural and Mechanical Properties of Off-Stoichiometric Epoxy Resins

Molecular dynamic (MD) simulations were performed to compute the mechanical properties of off-stoichiometric epoxy resins as a function of hardener/epoxy mixture ratio (r). Properties were characterized in relation to their microscopic structures. Such resins have been used recently for adhesive-free bonding of large-scale composite structures using the co-curing-ply method. In this process, two partially precured composite panels with hardener-poor (HP) off-stoichiometric resins are coupled with ply(ies) of complementary hardener-rich (HR) formulations and then cured simultaneously. This bonding process has the potential to produce reliable and certifiable composite joints without the need for additional fasteners, which are often required for many conventional bonding methods because even small amounts of contamination can cause a weak bond. The reflow and mixing of the HP/HR resin in this bonding process result in a joint with no discernable interface that should not be susceptible to surface contamination. However, incomplete mixing of the two offset resins may result in chemical heterogeneity of the cured polymeric joint. Thus, different r values may be obtained across the joint. Classical MD simulations were performed to compute the Young’s modulus of polymers with different r values and correlate their properties to network structures. High stiffness was associated with molecular packing due to chemical crosslinking, leading to a single network structure. Moreover, the networks became denser as the ratio approached the stoichiometric value r = 1. Thus, the r = 1 systems were single clusters, with high stiffness, high molecular weight, and a high degree of crosslinking. Structural properties such as radius of gyration and mean square displacement were determined to investigate the variation in the stiffness with respect to r. This MD simulation study was validated with experimental measurements.

Chang Woon Jang↗

Computational Approaches for Clean Energy Materials

Currently, 80% of the global final energy consumption occurs in form of fuels and only 20% as electricity. On the other hand, renewable energy additions come almost exclusively in the form of electricity (dominantly photovoltaics and wind). Thus, a successful energy transition will require enormous growth in renewables, sufficient to convert excess electricity into fuels, as well as the development of non-electricity based solar fuel technologies. As much as photovoltaic capacities have grown over the past 20 years, it is far from clear that current technologies and materials are up to the task to grow from here by yet another factor 100 until 2050. Therefore, sustained research efforts on emerging inorganic semiconductors for solar electricity and fuels are essential for facing the double challenge of climate change and energy security. Computational materials science can make important contributions, guiding and supporting research activities through both materials search and discovery and through detailed studies that help to develop a mechanistic understanding of materials performance and bottlenecks. This presentation will highlight three recent computational projects with relevance for photovoltaics and solar fuels (1) Defect graph neural networks (dGNN) for materials discovery in solar thermochemical hydrogen (STCH) [1]. The dGNN approach facilitates broad and fast materials screening for defect properties. (2) Modeling highly off-stoichiometric systems by evaluating the free energy of defect interaction [2]. This approach allows quantitative prediction of H2 production in complex STCH oxides. (3) First-principles atomic structure prediction for interfaces [3]. This work showed how an atomically thin CdCl2 interlayer phase enables in principle ideal electron transport across the incommensurate SnO2/CdTe interface. [1] M.D. Witman, A. Goyal, T. Ogitsu, A.H. McDaniel, S. Lany, Nat. Comput. Sci. (2023). https://doi.org/10.1038/s43588-023-00495-2. [2] A. Goyal, M.D. Sanders, R.P. O'Hayre, S. Lany, PRX Energy 3, 013008 (2024). https://doi.org/10.1103/PRXEnergy.3.013008. [3] A. Sharan, M. Nardone, D. Krasikov, N. Singh, S. Lany, Appl. Phys. Rev. 9, 041411 (2022). https://doi.org/10.1063/5.0104008.

density functional theory↗

Enabling modern data discovery for atmospheric measurements

The Atmospheric Radiation Measurement (ARM) user facility is a US Department of Energy Office of Science user facility that is managed and operated through a collaborative effort led by nine US Department of Energy national laboratories. The ARM Data Center, located at Oak Ridge National Laboratory, is responsible for the timely collection, processing, and delivery of data products to the scientific community. The ARM Data Center holds more than 11,000 data products, including metadata collected from field campaigns, instruments, value-added products, and principal investigator–contributed data. These data sets are checked for successful transfer (for most data, this transfer is carried out automatically via the network; however, some of the largest data sets and some of the most remote sites require manual shipping of hard disks) and both the data and metadata are processed to a standard format, which is an ARM-standardized structure, via the Network Common Data Form. The Network Common Data Form is a self-describing binary format with many compatible software tools. Once processed, the data are cataloged, stored in the ARM Data Archive, and made discoverable through association with an array of metadata-characterizing information, such as location and measurement classification. These metadata enable powerful search capabilities through the ARM Data Center Data Discovery interface. This paper discusses the workflow of how the new discovery system has been redesigned from user requirements and how the data are distributed to the scientific community.

54 ENVIRONMENTAL SCIENCES↗

Development of machine learning framework for interface force closures based on bubble tracking data

Interfacial force closures in the two-fluid model play a critical role for the predictive capabilities of void fraction distribution. However, the practices of interfacial force modeling have long been challenged by the inherent physical complexity of the two-phase flows. The rapidly expanding computational capabilities in the recent years have made high-fidelity data from the interface-captured direct numerical simulation become more available, and hence potential for data-driven interfacial force modeling has prevailed. In this work, we established a data-driven modeling framework integrated to the HZDR multiphase Eulerian-Eulerian framework for computational fluid dynamics simulations. The data-driven framework is verified in a benchmark problem, where a feedforward neural network managed to capture the non-linear mapping between bubble Reynolds number and drag coefficient and reproduce the void distribution resulting from the baseline model in the test case. The second focus is on utilizing the bubble tracking data set to form a closure for the bubble drag in the turbulent bubbly flow, in which the drag coefficient is set to be correlated with the bubble Reynolds number and the Eötvös number. Pseudo-steady state filtering in the Frenet Frame was carried out to obtain the drag coefficient from the turbulent bubbly flow data. The performance of the data-driven drag model is also examined through a case study, where improvement of model’s prediction near-wall is regarded necessary. In conclusion, discussion and further plans of investigation are provided.

42 ENGINEERING↗

Organic Matrix Derived from Host–Microbe Interplay Contributes to Pathological Renal Biomineralization

Matrix stones are a rare form of kidney stones. They feature a high percentage of hydrogel-like organic matter, and their formation is closely associated with urinary tract infections. Herein, comprehensive materials and biochemical approaches were taken to map the organic-inorganic interface and gather insights into the host-microbe interplay in pathological renal biomineralization. Surgically extracted soft and slimy matrix stones were examined using micro-X-ray computed tomography and various microspectroscopy techniques. Higher-mineral-density laminae were positive for calcium-bound Alizarin red. Lower-mineral-density laminae revealed periodic acid-Schiff-positive organic filamentous networks of varied thickness. These organic filamentous networks, which featured a high polysaccharide content, were enriched with zinc, carbon, and sulfur elements. Neutrophil extracellular traps (NETs) along with immune response-related proteins, including calprotectin, myeloperoxidase, CD63, and CD86, also were identified in the filamentous networks. Expressions of NETs and upregulation of polysaccharide-rich mucin secretion are proposed as a part of the host immune defense to "trap" pathogens. These host-microbe derived organic matrices can facilitate heterogeneous nucleation and precipitation of inorganic particulates, resulting in macroscale aggregates known as "matrix stones". These insights into the plausible aggregation of constituents through host-microbe interplay underscore the unique "double-edged sword" effect of the host immune response to pathogens and the resulting renal biominerals.

59 BASIC BIOLOGICAL SCIENCES↗

A Sparse Distributed Gigascale Resolution Material Point Method

In this paper, we present a four-layer distributed simulation system and its adaptation to the Material Point Method (MPM). The system is built upon a performance portable C++ programming model targeting major High-Performance-Computing (HPC) platforms. A key ingredient of our system is a hierarchical block-tile-cell sparse grid data structure that is distributable to an arbitrary number of Message Passing Interface (MPI) ranks. We additionally propose strategies for efficient dynamic load balance optimization to maximize the efficiency of MPI tasks. Our simulation pipeline can easily switch among backend programming models, including OpenMP and CUDA, and can be effortlessly dispatched onto supercomputers and the cloud. Finally, we construct benchmark experiments and ablation studies on supercomputers and consumer workstations in a local network to evaluate the scalability and load balancing criteria. We demonstrate massively parallel, highly scalable, and gigascale resolution MPM simulations of up to 1.01 billion particles for less than 323.25 seconds per frame with 8 OpenSSH-connected workstations.

97 MATHEMATICS AND COMPUTING↗

eCounter: Inline Per-IP Network Monitoring at Millisecond Resolution via eBPF

Scientific data acquisition (SciDAQ) systems are shifting from archive-based workflows to streaming paradigms, where real-time, fine-grained network monitoring becomes essential. While P4-enabled devices offer per-packet in-band observability, they require specialized switches and routers. Host-side tools like Prometheus exporters lack sufficient temporal granularity. To bridge this gap, we present eCounter, a lightweight, hardware-agnostic, inline telemetry agent built on extended Berkeley Packet Filter (eBPF). eCounter captures per-interface ingress and egress traffic, categorized by IP address and protocol, at millisecond to sub-millisecond resolution. In a 100 Gbps environment, it continuously exports up to 3,257 time-series bins per second with only 4% CPU utilization at a 35¿KiB/s data rate. We evaluate eCounter across diverse NIC MTU settings, hook types, CPU architectures and operating systems, and observed negligible impact on concurrent high-throughput streaming applications. Complexity analysis confirms that it can be readily scaled to distributed SciDAQ deployments.

Mei, Xinxin [Computational Sciences and Technology↗

Intelligent systems technology infrastructure for integrated systems

Significant advances have occurred during the last decade in intelligent systems technologies (a.k.a. knowledge-based systems, KBS) including research, feasibility demonstrations, and technology implementations in operational environments. Evaluation and simulation data obtained to date in real-time operational environments suggest that cost-effective utilization of intelligent systems technologies can be realized for Automated Rendezvous and Capture applications. The successful implementation of these technologies involve a complex system infrastructure integrating the requirements of transportation, vehicle checkout and health management, and communication systems without compromise to systems reliability and performance. The resources that must be invoked to accomplish these tasks include remote ground operations and control, built-in system fault management and control, and intelligent robotics. To ensure long-term evolution and integration of new validated technologies over the lifetime of the vehicle, system interfaces must also be addressed and integrated into the overall system interface requirements. An approach for defining and evaluating the system infrastructures including the testbed currently being used to support the on-going evaluations for the evolutionary Space Station Freedom Data Management System is presented and discussed. Intelligent system technologies discussed include artificial intelligence (real-time replanning and scheduling), high performance computational elements (parallel processors, photonic processors, and neural networks), real-time fault management and control, and system software development tools for rapid prototyping capabilities.

Lum, Henry, Jr.↗

Upgrade of the Thermal Vacuum Data System at NASA/GSFC

The Goddard Space Flight Center's new thermal vacuum data acquisition system is a networked client-sever application that enables lab operations crews to monitor all tests from a central location. The GSFC thermal vacuum lab consists of eleven chambers in Building 7 and one chamber in Building 10. The new data system was implemented for several reasons. These included the need for centralized data collection, more flexible and easier to use operator interface, greater data accessibility, a reduction in testing time and cost, and increased payload and personnel safety. Additionally, a new data system was needed for year-2000 compliance. This paper discusses the incorporation of the Thermal Vacuum Data System (TVDS) within the thermal vacuum lab at GSFC, its features and capabilities and lessons learned in its implementation. Additional topics include off-center (Internet) capability for remote monitoring and the role of TVDS in the efforts to automate thermal vacuum chamber operations.

Palmer, John↗

Upgrade of The Thermal Vacuum Data System at NASA/GSFC

The Goddard Space Flight Center's new thermal vacuum data acquisition system is a networked client-sever application that enables lab operations crews to monitor all tests from a central location. The GSFC thermal vacuum lab consists of eleven chambers in Building 7 and one chamber in Building 10. The new data system was implemented for several reasons. These included the need for centralized data collection, more flexible and easier to use operator interface, greater data accessibility, a reduction in testing time and cost, and increased payload and personnel safety. Additionally, a new data system was needed for year-2000 compliance. This paper discusses the incorporation of the Thermal Vacuum Data System (TVDS) within the thermal vacuum lab at GSFC, its features and capabilities and lessons learned in its implementation. Additional topics include off-center (Internet) capability for remote monitoring and the role of TVDS in the efforts to automate thermal vacuum chamber operations.

Palmer, John↗

Time Analyzer for Time Synchronization and Monitor of the Deep Space Network

A software package has been developed to measure, monitor, and archive the performance of timing signals distributed in the NASA Deep Space Network. Timing signals are generated from a central master clock and distributed to over 100 users at distances up to 30 kilometers. The time offset due to internal distribution delays and time jitter with respect to the central master clock are critical for successful spacecraft navigation, radio science, and very long baseline interferometry (VLBI) applications. The instrument controller and operator interface software is written in LabView and runs on the Linux operating system. The software controls a commercial multiplexer to switch 120 separate timing signals to measure offset and jitter with a time-interval counter referenced to the master clock. The offset of each channel is displayed in histogram form, and "out of specification" alarms are sent to a central complex monitor and control system. At any time, the measurement cycle of 120 signals can be interrupted for diagnostic tests on an individual channel. The instrument also routinely monitors and archives the long-term stability of all frequency standards or any other 1-pps source compared against the master clock. All data is stored and made available for

Cole, Steven↗

ISTP CDF Skeleton Editor

Basic Common Data Format (CDF) tools (e.g., cdfedit) provide no specific support for creating International Solar-Terrestrial Physics/Space Physics Data Facility (ISTP/SPDF) standard files. While it is possible for someone who is familiar with the ISTP/SPDF metadata guidelines to create compliant files using just the basic tools, the process is error-prone and unreasonable for someone without ISTP/SPDF expertise. The key problem is the lack of a tool with specific support for creating files that comply with the ISTP/SPDF guidelines. There are basic CDF tools such as cdfedit and skeletoncdf for creating CDF files, but these have no specific support for creating ISTP/ SPDF compliant files. The SPDF ISTP CDF skeleton editor is a cross-platform, Java-based GUI editor program that allows someone with only a basic understanding of the ISTP/SPDF guidelines to easily create compliant files. The editor is a simple graphical user interface (GUI) application for creating and editing ISTP/SPDF guideline-compliant skeleton CDF files. The SPDF ISTP CDF skeleton editor consists of the following components: A swing-based Java GUI program, JavaHelp-based manual/ tutorial, Image/Icon files, and HTML Web page for distribution. The editor is available as a traditional Java desktop application as well as a Java Network Launching Protocol (JNLP) application. Once started, it functions like a typical Java GUI file editor application for creating/editing application-unique files.

Chimiak, Reine↗

SpaceOps 2012 Plus 2: Social Tools to Simplify ISS Flight Control Communications and Log Keeping

A paper written for the SpaceOps 2012 Conference (Simplify ISS Flight Control Communications and Log Keeping via Social Tools and Techniques) identified three innovative concepts for real time flight control communications tools based on social mechanisms: a) Console Log Tool (CoLT) - A log keeping application at Marshall Space Flight Center's (MSFC) Payload Operations Integration Center (POIC) that provides "anywhere" access, comment and notifications features similar to those found in Social Networking Systems (SNS), b) Cross-Log Communication via Social Techniques - A concept from Johnsson Space Center's (JSC) Mission Control Center Houston (MCC-H) that would use microblogging's @tag and #tag protocols to make information/requests visible and/or discoverable in logs owned by @Destination addressees, and c) Communications Dashboard (CommDash) - A MSFC concept for a Facebook-like interface to visually integrate and manage basic console log content, text chat streams analogous to voice loops, text chat streams dedicated to particular conversations, generic and position-specific status displays/streams, and a graphically based hailing display. CoLT was deployed operationally at nearly the same time as SpaceOps 2012, the Cross- Log Communications idea is currently waiting for a champion to carry it forward, and CommDash was approved as a NASA Iinformation Technoloby (IT) Labs project. This paper discusses lessons learned from two years of actual CoLT operations, updates CommDash prototype development status, and discusses potential for using Cross-Log Communications in both MCC-H and/or POIC environments, and considers other ways for synergizing console applcations.

Cowart, Hugh S.↗