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DOE OSTI2020

Web of Registries Search (WoRS) v1.0.0

The Web of Registries Search (WoRs) is a web based software application that enables users to search for publicly available biological parts using keywords or sequence fragments. For the initial version (1.0.0) of the application, WoRS targets 10 sources of biological part data: the GenBank NIH genetic sequence database (https://www.ncbi.nlm.nih.gov/genbank/), the iGem parts registry (parts.igem.org), the Addgene plasmid repository (https://www.addgene.org/), and 7 Inventory of Composable Elements (ACS Synbio, JGI, JBEI, JBEI Public, ABF, SynBerc, ABF Public) registry instances. WoRs has built-in automated web scrapers which extract data from sources that do not have a public or well-defined application programming interface (API). They extract as much public data as they can find and create a searchable index to speed up searches. Included in the indexed information is the source of the information.

Plahar, Hector↗

DOE OSTI2023

In silico analyses of diversity and dissemination of antimicrobial resistance genes and mobile genetics elements, for plasmids of enteric pathogens

The antimicrobial resistance (AMR) mobilome plays a key role in the dissemination of resistance genes encoded by mobile genetics elements (MGEs) including plasmids, transposons (Tns), and insertion sequences (ISs). These MGEs contribute to the dissemination of multidrug resistance (MDR) in enteric bacterial pathogens which have been considered as a global public health risk. To further understand the diversity and distribution of AMR genes and MGEs across different plasmid types, we utilized multiple sequence-based computational approaches to evaluate AMR-associated plasmid genetics. A collection of 1,309 complete plasmid sequences from Gammaproteobacterial species, including 100 plasmids from each of the following 14 incompatibility (Inc) types: A/C, BO, FIA, FIB, FIC, FIIA, HI1, HI2, I1, K, M, N, P except W, where only 9 sequences were available, was extracted from the National Center for Biotechnology Information (NCBI) GenBank database using BLAST tools. The extracted FASTA files were analyzed using the AMRFinderPlus web-based tools to detect antimicrobial, disinfectant, biocide, and heavy metal resistance genes and ISFinder to identify IS/Tn MGEs within the plasmid sequences. In silico prediction based on plasmid replicon types showed that the resistance genes were diverse among plasmids, yet multiple genes were widely distributed across the plasmids from enteric bacterial species. These findings provide insights into the diversity of resistance genes and that MGEs mediate potential transmission of these genes across multiple plasmid replicon types. This notion was supported by the observation that many IS/Tn MGEs and resistance genes known to be associated with them were common across multiple different plasmid types. Our results provide critical insights about how the diverse population of resistance genes that are carried by the different plasmid types can allow for the dissemination of AMR across enteric bacteria. The results also highlight the value of computational-based approaches and in silico analyses for the assessment of AMR and MGEs, which are important elements of molecular epidemiology and public health outcomes.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2002

Non-Invasive, Quantitative, and Remote Detection of Early Radiation Cataracts for Applications in Bio-Astronautics and Bio-Informatics

Human exploration of Mars may be a possibility in the next twenty years. Maintaining good vision is an essential aspect of achieving a successful mission. Continuous radiation exposure is a risk factor for radiation-induced cataracts in astronauts. A compact device based on the technique of dynamic light scattering (DLS) is designed for monitoring an astronaut's ocular health during long-duration space travel. Preliminary data on the simulated effects of ionizing radiation exposure to the ocular tissues of nonhuman animals and results on the sensitivity of DLS over established clinical procedures in investigating cataracts are presented. This capability of early diagnosis, unmatched by any other clinical technique in use today, may enable prompt initiation of preventive/curative therapy. An internet web based system integrating photon correlation data and controlling the hardware to monitor cataract development in vivo at a remote site in real time (teleophthalmology) is currently being developed. Cataract studies on-board the International Space Station (ISS) will be helpful in designing better protective radiation shields for future space vehicles and space suits.

Ansari, Rafat R.↗

DOE OSTI2023

Biofuels Information Center

The purpose of the Biofuels Information Center (BIC) task is to provide relevant data, information, reports, and web-based tools to all bioenergy stakeholders. The BIC task began in FY08 to meet the requirement under Title II, Sec. 229 of the Energy Independence and Security Act of 2007 (EISA) requires DOE to develop a "Biofuels and Biorefinery Information Center". The BIC task supports biofuels pages content on the EERE's most visited website - the Alternative Fuels Data Center (AFDC http://www.afdc.energy.gov) and the Bioenergy Atlas tools (currently archived) (previous address https://maps.nrel.gov). This task results in more than 1.7 million web pageviews (an instance of an internet user visiting a webpage) per year. In FY22, the task completed the final year of the 5 year USDA Biofuels Infrastructure Partnership (BIP). The USDA BIP expanded infrastructure for E15 and/or E85 to approximately 850 stations and NREL received and reviewed data for quality analyzed all infrastructure and sales data collected by USDA. Stations are privately held and previously it was difficult to ascertain infrastructure and sales data. This unique dataset allows insight into infrastructure data (number of pumps and tanks, costs to install new equipment) and sales data (price and volume for E10, E15, E85, and diesel by month). The 2021 USDA BIP National Summary Report is with DOE for review prior to publication. Future work will include the biannual Bioenergy Industry Status Report (4 previous versions have been published) . The task also supports the principal investigator's time to engage stakeholders on infrastructure and deployment of biofuels. This includes leading, membership, and participation in the following roles: member Board of Advisors at the Fuels Institute, voting member for multiple UL standards committees, Co-Chair of the Infrastructure team at Agriculture/Auto/Ethanol, Member of Coordination Research Council's ULSD Corrosion Committee. The Principal investigator routinely responds to industry inquires to assist in deployment of biofuels regularly.

biofuels↗

NASA NTRS2010

How to Boost Engineering Support Via Web 2.0 - Seeds for the Ares Project...and/or Yours?

The Mission Operations Laboratory (MOL) at Marshall Space Flight Center (MSFC) is responsible for Engineering Support capability for NASA s Ares launch system development. In pursuit of this, MOL is building the Ares Engineering and Operations Network (AEON), a web-based portal intended to provide a seamless interface to support and simplify two critical activities: a) Access and analyze Ares manufacturing, test, and flight performance data, with access to Shuttle data for comparison. b) Provide archive storage for engineering instrumentation data to support engineering design, development, and test. A mix of NASA-written and COTS software provides engineering analysis tools. A by-product of using a data portal to access and display data is access to collaborative tools inherent in a Web 2.0 environment. This paper discusses how Web 2.0 techniques, particularly social media, might be applied to the traditionally conservative and formal engineering support arena. A related paper by the author [1] considers use

Scott, David W.↗

NASA NTRS2007

Clinical Core Competency Training for NASA Flight Surgeons

Introduction: The cohort of NASA flight surgeons (FS) is a very accomplished group with varied clinical backgrounds; however, the NASA Flight Surgeon Office has identified that the extremely demanding schedule of this cohort prevents many of these physicians from practicing clinical medicine on a regular basis. In an effort to improve clinical competency, the NASA FS Office has dedicated one day a week for the FS to receive clinical training. Each week, an FS is assigned to one of five clinical settings, one being medical patient simulation. The Medical Operations Support Team (MOST) was tasked to develop curricula using medical patient simulation that would meet the clinical and operational needs of the NASA FS Office. Methods: The MOST met with the Lead FS and Training Lead FS to identify those core competencies most important to the FS cohort. The MOST presented core competency standards from the American Colleges of Emergency Medicine and Internal Medicine as a basis for developing the training. Results: The MOST identified those clinical areas that could be best demonstrated and taught using medical patient simulation, in particular, using high fidelity human patient simulators. Curricula are currently being developed and additional classes will be implemented to instruct the FS cohort. The curricula will incorporate several environments for instruction, including lab-based and simulated microgravity-based environments. Discussion: The response from the NASA FS cohort to the initial introductory class has been positive. As a result of this effort, the MOST has identified three types of training to meet the clinical needs of the FS Office; clinical core competency training, individual clinical refresher training, and just-in-time training (specific for post-ISS Expedition landings). The MOST is continuing to work with the FS Office to augment the clinical training for the FS cohort, including the integration of Web-based learning.

Polk, J. D.↗

NASA NTRS2011

NASA Human Research Wiki - An Online Collaboration Tool

In preparation for exploration-class missions, the Exploration Medical Capability (ExMC) element of NASA's Human Research Program (HRP) has compiled a large evidence base, which previously was available only to persons within the NASA community. The evidence base is comprised of several types of data, for example: information on more than 80 medical conditions which could occur during space flight, derived from several sources (including data on incidence and potential outcomes of these medical conditions, as captured in the Integrated Medical Model's Clinical Finding Forms). In addition, approximately 35 gap reports are included in the evidence base, identifying current understanding of the medical challenges for exploration, as well as any gaps in knowledge and/or technology that would need to be addressed in order to provide adequate medical support for these novel missions. In an effort to make the ExMC information available to the general public and increase collaboration with subject matter experts within and outside of NASA, ExMC has developed an online collaboration tool, very similar to a wiki, titled the NASA Human Research Wiki. The platform chosen for this data sharing, and the potential collaboration it could generate, is a MediaWiki-based application that would house the evidence, allow "read only" access to all visitors to the website, and editorial access to credentialed subject matter experts who have been approved by the Wiki's editorial board. Although traditional wikis allow users to edit information in real time, the NASA Human Research Wiki includes a peer review process to ensure quality and validity of information. The wiki is also intended to be a pathfinder project for other HRP elements that may want to use this type of web-based tool. The wiki website will be released with a subset of the data described and will continue to be populated throughout the year.

Barr, Y. R.↗

NASA NTRS2006

Recommendations from NASA's Operational and Research Musculoskeletal Summit

Introduction: Continuously evolving medical standards of care, limited crew training time, and the inherent constraints of space flight necessitate regular revisions of the mission medical support infrastructure and methodology. A three-day Operational and Research Musculoskeletal Summit was held to review NASA s current strategy for preflight health maintenance and injury screening, risk mitigation for musculoskeletal injuries or syndromes, treatment methods during flight, and research topics to mitigate risks to astronaut health. The Summit also undertook consideration of the best evidence-based terrestrial musculoskeletal practices to recommend their adaptation for use in space. Methods: The types and frequencies of musculoskeletal injuries sustained by short- and long-duration astronauts were obtained from the Longitudinal Study of Astronaut Health. The Summit panel was comprised of experts from the clinical and research communities, as well as representatives from NASA Headquarters, the Astronaut corps, and the offices of JSC Medical Operations, JSC Human Adaptation and Countermeasures, Glenn Research Center Human Research, and Astronaut Strength Conditioning and Rehabilitation. Before the summit, panelists participated in a Web-based review of NASA s Space Medical Conditions List (SMCL). Results: The Summit generated seventy-five operational and research recommendations to the NASA Office of Space Medicine, including changes to the SMCL and to the musculoskeletal section of the ISS debrief questionnaire. From these recommendations, seven were assigned highest value and priority, and could be immediately adopted for the exploration architecture. Discussion: Optimized exercise and conditioning to improve performance and forestall musculoskeletal damage on orbit were the primary area of focus. Special attention was paid to exercise timing and muscle group specificity. The panel s recommendations are currently in various stages of consideration or integration into the ISS and Exploration programs. This effort serves to enhance the on-orbit system so comprehensive treatment can be delivered in a more effective and standardized manner.

Jones, J. A.↗

NASA NTRS2007

Design and Data Management System

The Design and Data Management System (DDMS) was developed to automate the NASA Engineering Order (EO) and Engineering Change Request (ECR) processes at the Propulsion Test Facilities at Stennis Space Center for efficient and effective Configuration Management (CM). Prior to the development of DDMS, the CM system was a manual, paper-based system that required an EO or ECR submitter to walk the changes through the acceptance process to obtain necessary approval signatures. This approval process could take up to two weeks, and was subject to a variety of human errors. The process also requires that the CM office make copies and distribute them to the Configuration Control Board members for review prior to meetings. At any point, there was a potential for an error or loss of the change records, meaning the configuration of record was not accurate. The new Web-based DDMS eliminates unnecessary copies, reduces the time needed to distribute the paperwork, reduces time to gain the necessary signatures, and prevents the variety of errors inherent in the previous manual system. After implementation of the DDMS, all EOs and ECRs can be automatically checked prior to submittal to ensure that the documentation is complete and accurate. Much of the configuration information can be documented in the DDMS through pull-down forms to ensure consistent entries by the engineers and technicians in the field. The software also can electronically route the documents through the signature process to obtain the necessary approvals needed for work authorization. The workflow of the system allows for backups and timestamps that determine the correct routing and completion of all required authorizations in a more timely manner, as well as assuring the quality and accuracy of the configuration documents.

Messer, Elizabeth↗

NASA NTRS2016

IN13B-1660: Analytics and Visualization Pipelines for Big Data on the NASA Earth Exchange (NEX) and OpenNEX

We are developing capabilities for an integrated petabyte-scale Earth science collaborative analysis and visualization environment. The ultimate goal is to deploy this environment within the NASA Earth Exchange (NEX) and OpenNEX in order to enhance existing science data production pipelines in both high-performance computing (HPC) and cloud environments. Bridging of HPC and cloud is a fairly new concept under active research and this system significantly enhances the ability of the scientific community to accelerate analysis and visualization of Earth science data from NASA missions, model outputs and other sources. We have developed a web-based system that seamlessly interfaces with both high-performance computing (HPC) and cloud environments, providing tools that enable science teams to develop and deploy large-scale analysis, visualization and QA pipelines of both the production process and the data products, and enable sharing results with the community. Our project is developed in several stages each addressing separate challenge - workflow integration, parallel execution in either cloud or HPC environments and big-data analytics or visualization. This work benefits a number of existing and upcoming projects supported by NEX, such as the Web Enabled Landsat Data (WELD), where we are developing a new QA pipeline for the 25PB system.

visualization↗

NASA NTRS2012

The NASA Tournament Laboratory (NTL): Improving Data Access at PDS while Spreading Joy and Engaging Students through 16 Micro-Contests

NASA PDS hosts terabytes of valuable data from hundreds of data sources and spans decades of research. Data is stored on flat-file systems regulated through careful meta dictionaries. PDS's data is available to the public through its website which supports data searches through drill-down navigation. While the system returns data quickly, result sets in response to identical input differ depending on the drill-down path a user follows. To correct this Issue, to allow custom searching, and to improve general accessibility, PDS sought to create a new data structure and API, and to use them to build applications that are a joy to use and showcase the value of the data to students, teachers and citizens. PDS engaged TopCoder and Harvard Business School through the NTL to pursue these objectives in a pilot effort. Scope was limited to Small Bodies Node data. NTL analyzed data, proposed a solution, and implemented it through a series of micro-contests. Contest focused on different segments of the problem; conceptualization, architectural design, implementation, testing, etc. To demonstrate the utility of the completed solution, NTL developed web-based and mobile applications that can compare targets, regardless of mission. To further explore the potential of the solution NTL hosted "Mash-up" challenges that integrated the API with other publically available assets, to produce consumer and teaching applications, including an Augmented Reality iPad tool. Two contests were also posted to middle and high school students via the NoNameSite.com platform, and as a result of these contests, PDS/SBN has initiated a Facebook program. These contests defined and implemented a data warehouse with the necessary migration tools to transform legacy data, produced a public web interface for the new search, developed a public API, and produced four mobile applications that we expect to appeal to users both within and, without the academic community.

LaMora, Andy↗

NASA NTRSDate not supplied

Radiation Data Portal: Connection of Radiation Measurements on Airplane Flights with Observations of Solar-Terrestrial Environment

The impact of solar radiation dramatically increases at high altitudes in the Earth’s atmosphere and in space. Therefore, continuous monitoring of the radiation environment is critical for the safety of aircraft and spacecraft crews and passengers. Addressing the problem requires a complex approach of integration of different data sources and enhancement of the visualization and search capabilities. The Radiation Portal Database represents an interactive web-based application for convenient search and visualization of in-flight radiation measurements and exploration of various properties related to the radiation environment. The primary element of the Radiation Portal back-end is a MySQL relational database that currently contains the radiation measurements obtained from the Automated Radiation Measurements for Aerospace Safety (ARMAS)device, and soft X-ray and proton fluxes from Geostationary Orbiting Environmental Satellite (GOES). The developed Application Programming Interface (API) and related Python routines allow a user to retrieve the database records directly and efficiently, without interaction with the web interface. As a use case of the Radiation Portal, we examine the properties of the ARMAS flights taken during the enhanced Solar Proton (SP) fluxes and compare them to the flights of similar time and location taken during SP-quiet periods.

SMD↗

DOE OSTI2024

Resources, Training, and Education Under the Heliostat Consortium: Industry Gap Analysis and Building a Resource Database

Concentrating solar power is not a widely deployed or known technology area, and the heliostat workforce community in the United States is currently small, with knowledge and expertise not widely available. The resource, training, and education (RTE) topic within the Heliostat Consortium (HelioCon) was established to address this. RTE encompasses resources, practices, and programs to ensure that (1) newcomers to the heliostat development community have an adequate knowledge base and training to conduct R&D efforts, (2) outsiders to the field are provided with resources and opportunities to join the workforce, and (3) the workforce community is a productive, healthy, and fulfilling environment for all workers. In the first year of the project, a roadmap study was conducted, in which the major gaps in RTE were identified by consulting experts in the industry, with the top gap being the lack of public accessibility to concentrating solar-thermal power (CSP) knowledge. Here, to address this, the HelioCon team has been developing a centralized web-based resource database, containing a reference library, educational videos, lists of components suppliers and software/metrology tools, a power tower plant database, and information on existing standards/guidelines.

14 SOLAR ENERGY↗

NASA NTRS2010

Update on PISCES

An updated version of the Platform Independent Software Components for the Exploration of Space (PISCES) software library is available. A previous version was reported in Library for Developing Spacecraft-Mission-Planning Software (MSC-22983), NASA Tech Briefs, Vol. 25, No. 7 (July 2001), page 52. To recapitulate: This software provides for Web-based, collaborative development of computer programs for planning trajectories and trajectory- related aspects of spacecraft-mission design. The library was built using state-of-the-art object-oriented concepts and software-development methodologies. The components of PISCES include Java-language application programs arranged in a hierarchy of classes that facilitates the reuse of the components. As its full name suggests, the PISCES library affords platform-independence: The Java language makes it possible to use the classes and application programs with a Java virtual machine, which is available in most Web-browser programs. Another advantage is expandability: Object orientation facilitates expansion of the library through creation of a new class. Improvements in the library since the previous version include development of orbital-maneuver- planning and rendezvous-launch-window application programs, enhancement of capabilities for propagation of orbits, and development of a desktop user interface.

Pearson, Don↗

NASA NTRS1997

Providing the Persistent Data Storage in a Software Engineering Environment Using Java/COBRA and a DBMS

An investigation was undertaken to build the software foundation for the WHERE (Web-based Hyper-text Environment for Requirements Engineering) project. The TCM (Toolkit for Conceptual Modeling) was chosen as the foundation software for the WHERE project which aims to provide an environment for facilitating collaboration among geographically distributed people involved in the Requirements Engineering process. The TCM is a collection of diagram and table editors and has been implemented in the C++ programming language. The C++ implementation of the TCM was translated into Java in order to allow the editors to be used for building various functionality of the WHERE project; the WHERE project intends to use the Web as its communication back- bone. One of the limitations of the translated software (TcmJava), which militated against its use in the WHERE project, was persistent data management mechanisms which it inherited from the original TCM; it was designed to be used in standalone applications. Before TcmJava editors could be used as a part of the multi-user, geographically distributed applications of the WHERE project, a persistent storage mechanism must be built which would allow data communication over the Internet, using the capabilities of the Web. An approach involving features of Java, CORBA (Common Object Request Broker), the Web, a middle-ware (Java Relational Binding (JRB)), and a database server was used to build the persistent data management infrastructure for the WHERE project. The developed infrastructure allows a TcmJava editor to be downloaded and run from a network host by using a JDK 1.1 (Java Developer's Kit) compatible Web-browser. The aforementioned editor establishes connection with a server by using the ORB (Object Request Broker) software and stores/retrieves data in/from the server. The server consists of a CORBA object or objects depending upon whether the data is to be made persistent on a single server or multiple servers. The CORBA object providing the persistent data server is implemented using the Java progranu-ning language. It uses the JRB to store/retrieve data in/from a relational database server. The persistent data management system provides transaction and user management facilities which allow multi-user, distributed access to the stored data in a secure manner.

Dhaliwal, Swarn S.↗

NASA NTRS2012

Linked Open Data in the Global Change Information System (GCIS)

The U.S. Global Change Research Program (http://globalchange.gov) coordinates and integrates federal research on changes in the global environment and their implications for society. The USGCRP is developing a Global Change Information System (GCIS) that will centralize access to data and information related to global change across the U.S. federal government. The first implementation will focus on the 2013 National Climate Assessment (NCA) . (http://assessment.globalchange.gov) The NCA integrates, evaluates, and interprets the findings of the USGCRP; analyzes the effects of global change on the natural environment, agriculture, energy production and use, land and water resources, transportation, human health and welfare, human social systems, and biological diversity; and analyzes current trends in global change, both human-induced and natural, and projects major trends for the subsequent 25 to 100 years. The NCA has received over 500 distinct technical inputs to the process, many of which are reports distilling and synthesizing even more information, coming from thousands of individuals around the federal, state and local governments, academic institutions and non-governmental organizations. The GCIS will present a web-based version of the NCA including annotations linking the findings and content of the NCA with the scientific research, datasets, models, observations, etc. that led to its conclusions. It will use semantic tagging and a linked data approach, assigning globally unique, persistent, resolvable identifiers to all of the related entities and capturing and presenting the relationships between them, both internally and referencing out to other linked data sources and back to agency data centers. The developing W3C PROV Data Model and ontology will be used to capture the provenance trail and present it in both human readable web pages and machine readable formats such as RDF and SPARQL. This will improve visibility into the assessment process, increase understanding and reproducibility, and ultimately increase credibility and trust of the resulting report. Building on the foundation of the NCA, longer term plans for the GCIS include extending these capabilities throughout the U.S. Global Change Research Program, centralizing access to global change data and information across the thirteen agencies that comprise the program.

Tilmes, Curt A.↗

DOE OSTI2021

NeuralCubes: Deep Representations for Visual Data Exploration

Visual exploration of large multi-dimensional datasets has seen tremendous progress in recent years, allowing users to express rich data queries that produce informative visual summaries, all in real time. Techniques based on data cubes are some of the most promising approaches. However, these techniques usually require a large memory footprint for large datasets. To tackle this problem, we present NeuralCubes: neural networks that predict results for aggregate queries, similar to data cubes. NeuralCubes learns a function that takes as input a given query, for instance, a geographic region and temporal interval, and outputs the result of the query. The learned function serves as a real-time, low-memory approximator for aggregation queries. Our models are small enough to be sent to the client side (e.g. the web browser for a web-based application) for evaluation, enabling data exploration of large datasets without database/network connection. Here, we demonstrate the effectiveness of NeuralCubes through extensive experiments on a variety of datasets and discuss how NeuralCubes opens up opportunities for new types of visualization and interaction.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Color Transformations of Photometric Measurements of Galaxies in Optical and Near-infrared Wide-field Imaging Surveys*

Abstract Over the past 2 decades, wide-field photometric surveys in optical and infrared domains reached a nearly all-sky coverage thanks to numerous observational facilities operating in both hemispheres. However, subtle differences among exact realizations of Johnson and SDSS photometric systems require one to convert photometric measurements into the same system prior to analysis of composite data sets originating from multiple surveys. It turns out that the published photometric transformations lead to substantial biases when applied to integrated photometry of galaxies from the corresponding catalogs. Here we present photometric transformations based on piece-wise linear approximations of integrated photometry of galaxies in the optical surveys SDSS, DECaLS, BASS, MzLS, DES, DELVE, KiDS, VST ATLAS, and the near-infrared surveys UKIDSS, UHS, VHS, and VIKING. We validate our transformations by constructing k -corrected color–magnitude diagrams of non-active galaxies and measuring the position and tightness of the “red sequence.” We also provide transformations for aperture magnitudes and show how they are affected by the image quality difference among the surveys. We present the implementation of the derived transformations in python and idl and also a web-based color transformation calculator for galaxies. By comparing DECaLS and DES, we identified systematic issues in DECaLS photometry for extended galaxies, which we attribute to the photometric software package used by DECaLS. As an application of our method, we compiled two multi-wavelength photometric catalogs for over 200,000 low- and intermediate-redshift galaxies originating from CfA FAST and Hectospec spectral archives.

Astronomy & Astrophysics↗