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Final Report - Phylogenomic tools and web resources for the Systems Biology Knowledgebase

The major advance during this last reporting period (8/15/12 to present) is our release of data on the PhyloFacts website: phylogenetic trees, multiple sequence alignments and other data for protein families are now available for download from http://phylogenomics.berkeley.edu/data/. This project as a whole aimed to develop high-throughput functional annotation systems that exploit information from protein 3D structure and evolution to provide highly precise inferences of various aspects of gene function, including molecular function, biological process, pathway association, Pfam domains, cellular localization and so on. We accomplished these aims by developing and testing different systems on a database of protein family trees: the PhyloFacts Phylogenomic Encyclopedia (at http://phylogenomics.berkeley.edu/phylofacts/ ).

60 APPLIED LIFE SCIENCES↗

A Decision Theoretic Approach To Optimizing Machine Learning Decisions with Prediction Uncertainty

While the use of machine learning (ML) classifiers is widespread, their output is often not part of any follow-on decision-making process. To illustrate, consider the scenario where we have developed and trained an ML classifier to find malicious URL links. In this scenario, network administrators must decide whether to allow a computer user to visit a particular website, or to instead block access because the site is deemed malicious. It would be very beneficial if decisions such as these could be made automatically using a trained ML classifier. Unfortunately, due to a variety of reasons discussed herein, the output from these classifiers can be uncertain, rendering downstream decisions difficult. Herein, we provide a framework for: (1) quantifying and propagating uncertainty in ML classifiers; (2) formally linking ML outputs with the decision-making process; and (3) making optimal decisions for classification under uncertainty with single or multiple objectives.

97 MATHEMATICS AND COMPUTING↗

Precipitation links (PrecipLinks) - a prototype directory for precipitation information

This poster describes a web directory of research oriented precipitation links. In this era of sophisticated search engines and web agents, it might seem counterproductive to establish such a directory of links. However, entering precipitation into a search engine like google will yield over one million hits. To further exacerbate this situation many of the returned links are dead, duplicates of other links, incomplete, or only marginally related to research precipitation or even the broader precipitation area. Sometimes connecting the linked URL causes the browser to lose context and not be able to get back to the original page. Even using more sophisticated search engines query parameters or agents while reducing the overall return doesn't eliminate all of the other issues listed. As part of the development of the measurement-based Precipitation Processing System (PPS) that will support Tropical Rainfall Measuring Mission (TRMM) version 7 reprocessing and the Global Precipitation Measurement (GPM) mission a precipitation links (PrecipLinks) facility is being developed. PrecipLinks is intended to share locations of other sites that contain information or data pertaining to precipitation research. Potential contributors can log-on to the PrecipLinks website and register their site for inclusion in the directory. The price for inclusion is the requirement to place a link back to PrecipLinks on the webpage that is registered. This ensures that users will be able to easily get back to PrecipLinks regardless of any context issues that browsers might have. Perhaps more importantly users while visiting one site that they know can be referred to a location that has many others sites with which they might not be familiar. PrecipLinks is designed to have a very flat structure. This poster summarizes these categories (information, data, services) and the reasons for their selection. Providers may register multiple pages to which they wish to direct users. However, each page may be attached to only one of these categories. Each page to which they refer users will also have a return link to PrecipLinks. The poster describes the operation of the system both the automated and the human processes. It also provides images for the various steps in the registration and use.

Velanthapillia, Balendran↗

Market Survey 2020: Commercial Clinical Decision Support Systems and Wellness Tools

For long-duration, deep space exploration missions, current methods for managing and supporting crew health and medical conditions will be unsuitable. Communication and data transmission lags will necessitate the use of a sophisticated clinical decision support system (CDSS) that will tailor diagnosis and treatment guidance that is context-sensitive for anticipated astronaut health, wellness, and medical conditions. A variety of clinical decision support (CDS) and wellness tools (WT) are currently available in the commercial market and a broad-brush survey of this market can provide an initial impression of the current state of the art which, in turn, can inform the roadmap of NASA deep space CDSS development and associated requirements. Such a survey was undertaken during the first six months of 2020 using directed convenience sampling to obtain information provided by vendors on their websites; both commercially available CDS and WT (such as those used to track and monitor nutrition, exercise, and sleep) were included. Areas assessed were item type (e.g., software/application, device); primary purpose of the item (e.g., diagnostic support, nutrition tracking); additional purposes (if any); reported features, capabilities, and functionality; setting of use (e.g., inpatient, outpatient); intended user (e.g., clinician, patient); location and sources of data/information used or produced by the item; integration with patient electronic health record (EHR); compliance with interoperability ontologies and standards (e.g., Health Level 7 [HL7], Systematized Nomenclature of Medicine – Clinical Terminology [SNOMED-CT]); and whether the item is knowledge-based (derived from research findings) or non-knowledge-based (derived through artificial intelligence, machine learning, advanced probability and statistics), among others. Ninety-seven (97) vendor websites describing 196 CDS and 73 WT (269 total) were reviewed and coded. The primary purpose of the majority of CDS reviewed is diagnosis or diagnosis/treatment/drug decision support—targeted for clinician use— and the primary purpose of the majority of WT reviewed is the monitoring of different health metrics, most often through the use of a biosensor device (e.g., blood pressure)—targeted for patient use. Very few CDS or WT appear to comply with major international interoperability standards or can be integrated with a patient’s EHR data. None consider contextual factors, such as conditions of the physical environment (e.g., CO2 levels). The majority of CDS and WT reviewed are non-knowledge, cloud- or web-based applications or software. Forty-three (43) major findings were identified and the implications those findings have for NASA will be discussed. Example major findings include: CDS-WT capabilities range from diagnosis to treatment applications, CDS-WT may be wearable or non-wearable and are technologically advanced and only a few CDS-WT tools referenced compliance to ensure interoperability, among other findings. Recommendations will also be offered that will help to address ExMC Gap, Medical-701: Enhance medical capabilities within an exploration medical system.

market survey↗

Toward Uncertainty Quantification for Supervised Classification

Our goal is to develop a general theoretical basis for quantifying uncertainty in supervised machine learning models. Current machine learning accuracy-based validation metrics indicate how well a classifier performs on a given data set as a whole. However, these metrics do not tell us a model's efficacy in predicting particular samples. We quantify uncertainty by constructing probability distributions of the predictions made by an ensemble of classifiers. This report details our initial investigations into uncertainty quantification for supervised machine learning. We apply an uncertainty analysis to the problem of malicious website detection. Machine learning models can be trained to find suspicious characteristics in the text of a website's Uniform Resource Locator (URL). However, given the vast numbers of URLs and the ever changing tactics of malicious actors, it will always be possible to find sets of websites which are outliers with respect to a model's hypothesis. Therefore, we seek to understand a model's per-sample reliability when classifying URL data. Acknowledgements This work was funded by the Sandia National Laboratories Laboratory Directed Research and Development (LDRD) program.

97 MATHEMATICS AND COMPUTING↗

PV Validation Hub

The Validation Hub will be a clearinghouse for the transfer of novel algorithms and software from the PV research community to industry. Potential algorithms tested in the Hub could include the estimation of various PV loss factors and the detection of various operational issues. The primary function of the Hub will be for developers to submit executable code which will run on hosted data sets. Developers will receive private reports on the accuracy and performance (e.g., run-time) of the submitted algorithms, and public high level summaries will be hosted. These summaries will indicate the organization who submitted the algorithm (e.g., links to GitHub pages, documentation websites, etc.), high-level accuracy metrics, and standardized performance metrics. These results will be stored in a publicly available database, accessible through the Hub, with the ability for users to sort and filter the results. In short, the Hub will be presented to public users as a collection of interactive leaderboards, organized around specific analysis tasks pertinent to the PV data science community. These tasks include things such as the estimation of various PV loss factors and the detection of various operational issues. We will present progress on the development of this hub, including preliminary results of comparative validation of PV data science algorithms and progress towards building the platform itself.

algorithm↗

Interactive Mobility Landscape App

This is the companion repository to NREL's Interactive Mobility Data Landscape (SEE: DOE Code ID 61284. NREL SWR-21-09). The landscapeapp is an upstream NPM module that supports building interactive landscape websites such as the CNCF Cloud Native Landscape (source) and the LF Artificial Intelligence Landscape (source). The application is managed by Dan Kohn of CNCF and is under active development by Andrey Kozlov (who did most of the development to date, 9/13/2021) and Jordi Noguera.

Shankari, Kalyanaraman↗

NSUF 2016 Annual Report

The Nuclear Science User Facilities (NSUF) and its partner facilities represent a prototype laboratory that utilizes a distributed partnership, with each facility bringing exceptional capabilities to the relationship including reactors, beamlines, state-of-the-art instruments, hot cells, and equally important, expertise. These capabilities and people together create a nationwide infrastructure that allows the best ideas to be tested using the most advanced capabilities. Through the NSUF, researchers and their collaborators are building on current knowledge to better understand the complex behavior of materials and fuels in a nuclear reactor. The NSUF’s partnership program in 2016 included eight universities, one research and education consortium, three national laboratories, and one industry partner. The avenues opened through these partnerships facilitate cooperative research across the country, matching people with capabilities and students with mentors. The NSUF in 2016 included Idaho National Laboratory (INL) and the following institutions: • Argonne National Laboratory • Center for Advanced Energy Studies (a research and education consortium between Boise State University, INL, Idaho State University, University of Idaho, and University of Wyoming) • Illinois Institute of Technology • Massachusetts Institute of Technology • North Carolina State University • Oak Ridge National Laboratory • Pacific Northwest National Laboratory • Purdue University • University of California, Berkeley • University of Michigan • University of Nevada, Las Vegas • University of Wisconsin • Westinghouse Materials Center of Excellence. This report contains details on new capabilities brought into the NSUF in 2016, the evidence of the increasing research facilitated by the NSUF, and new tools and activities to propel nuclear research and development forward to meet energy reliability and security needs. Learn about the NSUF Nuclear Fuels and Materials Library and the Nuclear Energy Infrastructure Database, and how the robust NSUF website continues to evolve to support new tools. Read about how the NSUF supports Department of Energy (DOE) missions through efforts like the 2016 NSUF Ion Beam Options Workshop, which led to a prioritiza-tion of ion beam facilities according to their ability to support Department of Energy Office of Nuclear Energy (DOE-NE) missions.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

National Wind Technology Center-Characterization of Atmospheric Conditions

Data provided by the instrumentation located at the National Wind Technology Center (NWTC) is compiled below for the purposes of characterizing the atmospheric operating conditions at the National Renewable Energy Laboratories (NREL) wind site. Conditions are presented conditioned on month of the year to show seasonal variation, and based on characteristic quantities seen in the atmospheric flow including, bulk wind speed, direction, and atmospheric stability. All data reported and analyzed in the following document were collected from instrumentation mounted on the 135 m-tall masts erected at the NWTC near Boulder, Colorado. Each of the two met-masts (named M4 and M5) were sited specifically to measure the inflow wind to several of the utility-scale turbines at the NWTC. The construction, operation, and maintenance of the masts has been supported since their commissioning in 2011 by the Department of Energy, Office of Energy Efficiency and Renewable Energy, Wind and Water Power Program. Data from the masts are publicly available for download or basic visualization, hosted on NREL's website (https://nwtc.nrel.gov/135mData). Data from the masts have been used in the past for a wide range of projects including wind turbine power performance measurements, high fidelity model development and validation, and atmospheric science research. An interactive visualization platform has been developed on NREL's Open Energy Information platform and can be used to reproduce many of the graphics included in the current work. This report describes in detail the atmospheric conditions recorded by M5, the inflow mast for the DOE-owned GE 1.5 MW wind turbine. The report focuses on data recorded from August 2012 to May 2018 and includes: an introduction to the wind climate at the NWTC; a physical description of the met masts; a review of installed instrumentation; and data collection, processing, and quality control methods. In addition to a concise description of the instrumentation from the met masts and the data channels they provide, this report characterizes the behavior of the atmospheric resource first in a cumulative sense, discussing mainly the distributions wind speeds, flow directions and thermodynamic properties at several heights along the towers. Periodicity in atmospheric conditions is then detailed through analysis of diurnal and annual cycles of the data streams. Periods of both low turbulence and extreme atmospheric events that are of interest in terms of wind turbine operation and wind energy research are detailed in the final chapter of this report. Low turbulence events are somewhat rare at the NWTC and are of interest from the perspective of validating the operation of new wind turbine and blade designs. Similarly, the NTWC is known for a relatively higher rate of occurrence of extreme weather events.

17 WIND ENERGY↗

U.S. Hydropower Market Report 2023

This is the fourth complete edition of the U.S. Hydropower Market Report (the previous editions, published in 2015, 2018, and 2021, are available here). In intervening years between publishing the full report, updated data are also summarized and released and can be found at the Oak Ridge National Laboratory HydroSource website. This report combines data from public and commercial sources and research findings from other U.S. Department of Energy (DOE) R&D projects to provide a comprehensive picture of developments in the U.S. hydropower and pumped storage hydropower (PSH) fleet and industry trends. Prior to the first Hydropower Market Report being published, there was a noted lack of publicly available and easily accessible information about hydropower in the United States and other important trends affecting this important sector of the energy industry. New and valuable types of information are constantly being developed as part of DOE research activities and, in a rapidly evolving energy industry, it is important that these data be made available in a predictable and consistent manner for use by all different types of stakeholders and decision-makers.

13 HYDRO ENERGY↗

Echo the Bat and the Pigeon Adventure

A multimedia, CD ROM to teach 2nd graders about remote sensing was created and developed into a web site. Distribution was expanded for Grades K-4 or 5-8. The idea was to have a story introduction, interactive story and a teacher's website. Interactive Multimedia Adventures in Grade School Education using Remote Sensing (I.M.A.G.E.R.S.) was created. The lessons are easy to use, readily available and aligned with national standards. This resource combines hands-on activities with an interactive web site

Butcher, Ginger↗

NASA GSFC Flood Mapping System (In beta testing)

The authors are developing the NASA GSFC Flood Mapping System, designed to provide near real time, on-demand satellite-based products to disaster management practitioners for requests provided through a website interface. The initial version of the system, which only provides products based on Planetscope data provided by Planet Labs to NASA through the NASA CSDA Program, is currently being beta tested in partnership with the disaster management community and interested research partners. Products include images, NDWI maps, NDVI maps, and water extent maps for flood scenes of interest, the same four products for a specified reference scene, and water extent change maps based on the flood scenes and reference scenes. The team’s vision for the system includes adding products based on all appropriate sources of data that are available at no cost to the project (Landsat, Sentinel-1, Sentinel-2), and obtaining funding for commercial SAR data to provide products in the case where none of the “no-cost” data meets end-user needs. We provide an overview of the system, and discuss the products offered, lessons learned from initial testing, and plans to evolve the system in accordance with our overall vision and the lessons learned.

F. Policelli↗

BSV Gateway Description

Los Alamos National Laboratory (LANL) is part of that worldwide team and has been developing state of the art information systems to aid the global health community. For instance, in 2014 LANL announced the release of the LANL Biosurveillance (BSV) Gateway. The site provides information about ongoing biosurveillance research projects and capabilities at LANL, and provides access to a host of LANL-developed biosurveillance tools and resources. We are seeking feedback on this gateway and would like to ask interested folk to offer comments and suggestions after they have perused the BSV website.

60 APPLIED LIFE SCIENCES↗

Responder Technology Alert Monthly (December 2014)

As part of technology foraging for the Responder Technology Alliance, established by the Department of Homeland Science and Technologies First Responders Group, this report summarizes technologies that are relevant in the area of “wearables,” with the potential for use by first responders. The content was collected over the previous month(s) and reproduced from a general Internet search using the term wearables. Additional information is available at the websites provided. This report is not meant to be an exhaustive list nor an endorsement of any technology described herein. Rather, it is meant to provide useful information about current developments in the areas wearable technology.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Responder Technology Alert Monthly (January 2015)

As part of technology foraging for the Responder Technology Alliance, established by the Department of Homeland Science and Technologies First Responders Group, this report summarizes technologies that are relevant in the area of “wearables,” with the potential for use by first responders. The content was collected over the previous month(s) and reproduced from a general Internet search using the term wearables. Additional information is available at the websites provided. This report is not meant to be an exhaustive list nor an endorsement of any technology described herein. Rather, it is meant to provide useful information about current developments in the areas wearable technology.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Responder Technology Alert Monthly (Oct-Nov 2014)

As part of technology foraging for the Responder Technology Alliance, established by the Department of Homeland Science and Technologies First Responders Group, this report summarizes technologies that are relevant in the area of “wearables,” with the potential for use by first responders. The content was collected over the previous month(s) and reproduced from a general Internet search using the term wearables. Additional information is available at the websites provided. This report is not meant to be an exhaustive list nor an endorsement of any technology described herein. Rather, it is meant to provide useful information about current developments in the areas wearable technology. The content is organized by technology function including: Sensors – Devices that detect physiological, particle, and chemical activity; Displays – Heads-up and body-worn visual displays; Power – Wearable power systems including chargers, batteries, self-powering or harvesting technologies, and power supplies; Integrated Communications – Voice and data communications systems utilizing Bluetooth, wireless, hands-free, ergonomically optimized systems, noise-filtering digital speakers or microphones, etc.; Exoskeletons – Whole or partial body suit that enhances mobility and physical performance; Wearable Computers – Body-worn data processing devices; General – Miscellaneous technologies as well as emerging trends or recent advances in the field of wearables.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Responder Technology Alert (February 2015)

As part of technology foraging for the Responder Technology Alliance, established by the Department of Homeland Science and Technologies First Responders Group, this report summarizes technologies that are relevant in the area of “wearables,” with the potential for use by first responders. The content was collected over the previous month(s) and reproduced from a general Internet search using the term wearables. Additional information is available at the websites provided. This report is not meant to be an exhaustive list nor an endorsement of any technology described herein. Rather, it is meant to provide useful information about current developments in the areas wearable technology.

99 GENERAL AND MISCELLANEOUS↗

BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data

Abstract BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models and computational chemistry methods development. This update reports significant growth and enhancements since our last review in 2016. Of note, the database now contains 2.9 million binding measurements spanning 1.3 million compounds and thousands of protein targets. This growth is largely attributable to our unique focus on curating data from US patents, which has yielded a substantial influx of novel binding data. Recent improvements include a remake of the website following responsive web design principles, enhanced search and filtering capabilities, new data download options and webservices and establishment of a long-term data archive replicated across dispersed sites. We also discuss BindingDB’s positioning relative to related resources, its open data sharing policies, insights gleaned from the dataset and plans for future growth and development.

Liu, Tiqing↗