Results for “readability” — Page 33

NASA NTRSDate not supplied

NASA Open Science Data Repository: Biomedical FAIR Data, Analysis Tools, User Communities, and Discoveries for Deep Space Missions

Increased biomedical risks and challenges associated with deep space missions require new knowledge discovery, new health countermeasures, and development of novel ecosystems, life support, crop production, and biomedical support capabilities. To meet NASA’s Moon to Mars strategic program goals for Human and Biological Sciences, findable, accessible, interoperable, reusable (FAIR), and maximally open-access data is going to be required to enable humanity to thrive in deep space. Indeed, this cornerstone perspective on FAIR and maximally open access data was also recommended in the recent 2023-2032 Decadal Survey from the National Academies of Sciences, Engineering, and Medicine. The NASA Open Science Data Repository (OSDR) is a maximally open access and FAIR database, and meets various scientific, technical, and operational spaceflight needs. It offers public users and submitters the ability to upload, download, search, share, analyze, and visualize data across ‘omics, physiological, phenotypic, behavioral, bioimaging, video, and environmental monitoring telemetry datasets. OSDR includes NASA GeneLab, NASA Ames Life Sciences Data Archive, and the NASA Biological Institutional Scientific Collection. OSDR has >455 studies with datasets from model organisms and non-NASA human astronauts. There are ~12 datasets from the Inspiration 4 (I4) mission, spanning metagenomics, comprehensive metabolic panels, clonal hematopoiesis, spatial transcriptomics, proteomics, and cytokine panels. In the interest of data privacy, two I4 datasets have raw FASTQ and FASTA files relating to the epitranscriptome, and a new request feature is live in OSDR (with a backend review process established) which was developed based on industry norms. OSDR also recently began a collaboration with the European Space Agency (ESA) to scientifically curate and make available >200 terabytes of human and model organism space-relevant data. The OSDR submission portal is designed to ingest and curate ~25 ‘omics assay data types, and ~50 physiological-phenotypic-imaging assay data types, spanning ultrasonography, micro-computed tomography, histology, morphometric photography, rebound tonometry, gait analysis, optical coherence tomography, novel object recognition, flow cytometry, and immunohistochemistry. A suite of analysis tools are available for OSDR users including: 1) an Environmental Data Application to compare radiation, CO2, relative humidity, temperature, and other telemetry across missions and subjects, 2) the RadLab database, a collaboration between NASA, ESA, the German and Italian Space Agencies, and the Bulgarian Academy of Sciences, which compiles radiation measurements relevant to human spaceflight and provides tools for accessing and manipulating the data, and 3) a Multi-study visualization tool which enables users to look across and combine GeneLab’s omics datasets across different experiments and missions. There are ~600 volunteer OSDR Analysis Working Group (AWG) members who: 1) provide feedback on scientific standards for reuse (subject and assay metadata; processing pipelines; dataset formats and uniformed structures for machine-readability), and 2) collaborate to mine-reuse OSDR data conducting scientific analysis. OSDR has enabled 60 publications as of September 2023, many directly from AWG collaborations most notably the Cell Press package in 2020. Lastly, there are at least 15 articles which mine OSDR data part of a package of ~50 articles across Nature Portfolio with research stemming from I4, the Japan Aerospace Exploration Agency, NASA Space Biology, and the NASA Human Research Program.

open access↗

NASA NTRSDate not supplied

RadLab: A Comprehensive Database and Graphical and Programming Interfaces for Biologically Relevant Space Radiation Data

RadLab, a new component of the NASA Open Science Data Repository (OSDR), is a platform built upon a database of radiation data relevant to space biology. RadLab provides visual and programmatic interfaces for interrogation of its database, as well as a submission process for inclusion of data from investigators. The RadLab application programming interface (API) implements a request syntax enabling users to retrieve data filtered by various combinations of parameters (detector type, location, direction, timespan, etc), which are delivered in machine-readable text formats, ready to be ingested by downstream analysis pipelines; while the graphical user interface (GUI) provides easy means to iteratively modify query parameters and incorporates a number of standard analyses and visualizations (time series plots, geospatial visualizations, detector comparison). Investigators from many countries, including US, Russia, Japan, Canada, the Czech Republic, Germany, Hungary, and Italy, have committed to provide data from their instruments located on the ISS; RadLab will also include data from other spacecraft in LEO (e.g., the Space Shuttle, the Mir space station), BLEO (e. g. BioSentinel, Mars Orbiter, among others), and on other celestial bodies (e. g. Chang’e 4, Curiosity). The first release of RadLab has been made available to the public. Once fully operational, RadLab will provide a comprehensive and ever-growing compendium of space radiation data, facilitating straightforward access to multiple types of readings and enabling space biology researchers to perform intercomparisons of detectors and to determine the radiation environment of research missions, both via programmatic retrieval of these data and via the graphical analysis toolkit; as well as a user-friendly submission portal for ingesting data from space agencies and research institutions. Radiation scientists will be able to use RadLab to gain a deeper understanding of the space radiation environment for future human space exploration. The RadLab Working Group has been formed to foster close collaborations among data contributors and users, to identify data sources, to put in place standards for data normalization, to guide the development of features of the analysis toolkit, to establish the use of RadLab in space radiation biology research, and eventually to provide a forum for discussing relevant research issues that can take advantage of RadLab's capabilities.

radiation↗

NASA NTRSDate not supplied

GeoAI advances in specific landform mapping

Landform mapping (also referred to as geomorphology or geomorphometry) can be divided into two domains: general and specific (Evans 2012). Whereas general landform mapping categorizes all elements of the study area into landform classes, such as ridges, valleys, peaks, and depressions, the mapping of specific landforms requires the delineation (even if fuzzy) of individual landforms. The former is mainly driven by physical properties such as elevation, slope, and curvature. The latter, however, must consider the cognitive (human) reasoning that discriminates individual landforms in addition to these physical properties (Arundel and Sinha 2018). Both mapping forms are important. General geomorphometry is needed to understand geological and ecological processes and as boundary layer input to climate and environmental models. Specific geomorphometry supports such activities as disaster management and recovery, emergency response, transportation, and navigation. In the United States, individual landforms of interest are named in the U.S. Geological Survey (USGS) Geographic Names Information System, a point dataset captured specifically to digitize geographic names from the USGS Historical Topographic Map Collection (HTMC). Named landform extent is represented only by the name placement in the HTMC. Recent work has investigated CNN-based deep learning methods to capture these extents in machine-readable form. These studies first relied on physical properties (Arundel et al. 2020) and then included the HTMC as a band in RGB images in limited testing (Arundel et al. 2023). Results from the HTMC dataset surpassed those using just physical properties and using the HTMC alone performed best due to the hillshading and elevation (contour) data incorporated into the topographic maps. However, results fell short of an operational capacity to map all named landforms in the United States. Thus, our current work expands upon past research by focusing on the HTMC and physical information as inputs and the named landform label extents. Specifically, we propose to leverage pre-trained foundation models for segmentation and optical character recognition (OCR) models to jointly map landforms in the United States. Our approach aims to bridge the disparities among the independent information sources to facilitate informed decision-making. The modeling pipeline performs (1) segmentation using the physical information and (2) information extraction using OCR, in parallel. Then a computer vision approach merges the two branches into a labeled segmentation. References: Arundel, Samantha T., Wenwen Li, and Sizhe Wang. 2020. “GeoNat v1.0: A Dataset for Natural Feature Mapping with Artificial Intelligence and Supervised Learning.” Transactions in GIS 24 (3): 556–72. https://doi.org/10.1111/tgis.12633. Arundel, Samantha T, and Gaurav Sinha. 2018. “Validating GEOBIA Based Terrain Segmentation and Classification for Automated Delineation of Cognitively Salient Landforms BT - Proceedings of Workshops and Posters at the 13th International Conference on Spatial Information Theory (COSIT 2017).” In Proceedings of Workshops and Posters at the 13th International Conference on Spatial Information Theory (COSIT 2017), Lecture Notes in Geoinformation and Cartography, edited by Paolo Fogliaroni, Andrea Ballatore, and Eliseo Clementini, 9–14. Cham: Springer International Publishing. Arundel, Samantha T., Gaurav Sinha, Wenwen Li, David P. Martin, Kevin G. McKeehan, and Philip T. Thiem. 2023. “Historical Maps Inform Landform Cognition in Machine Learning.” Abstracts of the ICA 6 (August): 1–2. https://doi.org/10.5194/ica-abs-6-10-2023. Evans, Ian S. 2012. “Geomorphometry and Landform Mapping: What Is a Landform?” Geomorphology 137 (1): 94–106. https://doi.org/10.1016/j.geomorph.2010.09.029.

machine learning↗

NASA NTRSDate not supplied

Requirement Discovery Using Embedded Knowledge Graph With ChatGPT

The field of Advanced Air Mobility (AAM) is witnessing a transformation with innovations such as electric aircraft and increasingly automated airspace operations. Within AAM, the Urban Air Mobility (UAM) con-cept focuses on providing air-taxi services in densely populated urban areas. This research introduces the utilization of Large Language Models (LLMs), such as OpenAI's GPT-4, to enhance the UAM Requirement discovery process. This study explores two distinct approaches to leverage LLMs in the context of UAM Requirement discovery. The first approach evaluates the LLM's ability to provide responses without relying on additional outside systems, such as a relational or graph database. Instead, a vector store provides relevant information to the LLM based on the user’s question, a process known as Retrieval Augmented Generation (RAG). The second approach integrates the LLM with a graph database. The LLM acts as an intermediary between the user and the graph database, translating user questions into cypher queries for the database and database responses into human-readable answers for the user. Our team implemented and tested both solutions to analyze require-ments within a UAM dataset. This paper will talk about our approaches, implementations, and findings related to both approaches.

systems engineering↗

NASA NTRSDate not supplied

Requirement Discovery Using Embedded Knowledge Graph with ChatGPT

The field of Advanced Air Mobility (AAM) is witnessing a transformation with innovations such as electric aircraft and increasingly automated airspace operations. Within AAM, the Urban Air Mobility (UAM) concept focuses on providing air-taxi services in densely populated urban areas. This research introduces the utilization of Large Language Models (LLMs), such as OpenAI's GPT-4, to enhance the UAM Requirement discovery process. This study explores two distinct approaches to leverage LLMs in the context of UAM Requirement discovery. The first approach evaluates the LLM's ability to provide responses without relying on additional outside systems, such as a relational or graph database. Instead, a vector store provides relevant information to the LLM based on the user’s question, a process known as Retrieval Augmented Generation (RAG). The second approach integrates the LLM with a graph database. The LLM acts as an intermediary between the user and the graph database, translating user questions into cypher queries for the database and database responses into human-readable answers for the user. Our team implemented and tested both solutions to analyze requirements within a UAM dataset. This paper will talk about our approaches, implementations, and findings related to both approaches.

systems engineering↗

NASA NTRSDate not supplied

GeoAI Advances in Specific Landform Mapping

Landform mapping (also referred to as geomorphology or geomorphometry) can be divided into two domains: general and specific (Evans 2012). Whereas general landform mapping categorizes all elements of the study area into landform classes, such as ridges, valleys, peaks, and depressions, the mapping of specific landforms requires the delineation (even if fuzzy) of individual landforms. The former is mainly driven by physical properties such as elevation, slope, and curvature. The latter, however, must consider the cognitive (human) reasoning that discriminates individual landforms in addition to these physical properties (Arundel and Sinha 2018). Both mapping forms are important. General geomorphometry is needed to understand geological and ecological processes and as boundary layer input to climate and environmental models. Specific geomorphometry supports such activities as disaster management and recovery, emergency response, transportation, and navigation. In the United States, individual landforms of interest are named in the U.S. Geological Survey (USGS) Geographic Names Information System, a point dataset captured specifically to digitize geographic names from the USGS Historical Topographic Map Collection (HTMC). Named landform extent is represented only by the name placement in the HTMC. Recent work has investigated CNN-based deep learning methods to capture these extents in machine-readable form. These studies first relied on physical properties (Arundel et al. 2020) and then included the HTMC as a band in RGB images in limited testing (Arundel et al. 2023). Results from the HTMC dataset surpassed those using just physical properties and using the HTMC alone performed best due to the hillshading and elevation (contour) data incorporated into the topographic maps. However, results fell short of an operational capacity to map all named landforms in the United States. Thus, our current work expands upon past research by focusing on the HTMC and physical information as inputs and the named landform label extents. Specifically, we propose to leverage pre-trained foundation models for segmentation and optical character recognition (OCR) models to jointly map landforms in the United States. Our approach aims to bridge the disparities among the independent information sources to facilitate informed decision-making. The modeling pipeline performs (1) segmentation using the physical information and (2) information extraction using OCR, in parallel. Then a computer vision approach merges the two branches into a labeled segmentation.

machine learning↗

NASA NTRSDate not supplied

Requirement Discovery Using Embedded Knowledge Graph With ChatGPT - Poster

The field of Advanced Air Mobility (AAM) is witnessing a transformation with innovations such as electric aircraft and increasingly automated airspace operations. Within AAM, the Urban Air Mobility (UAM) con-cept focuses on providing air-taxi services in densely populated urban areas. This research introduces the utilization of Large Language Models (LLMs), such as OpenAI's GPT-4, to enhance the UAM Requirement discovery process. This study explores two distinct approaches to leverage LLMs in the context of UAM Requirement discovery. The first approach evaluates the LLM's ability to provide responses without relying on additional outside systems, such as a relational or graph database. Instead, a vector store provides relevant information to the LLM based on the user’s question, a process known as Retrieval Augmented Generation (RAG). The second approach integrates the LLM with a graph database. The LLM acts as an intermediary between the user and the graph database, translating user questions into cypher queries for the database and database responses into human-readable answers for the user. Our team implemented and tested both solutions to analyze require-ments within a UAM dataset. This paper will talk about our approaches, implementations, and findings related to both approaches.

systems engineering↗

NASA NTRSDate not supplied

Inverse Text Normalization of Air Traffic Control System Command Center Planning Telecon Transcriptions

We present a hybrid neural network and rule-based Inverse Text Normalization (ITN) method for domains containing unique technical phraseology, specifically Air Traffic Control System Command Center (ATCSCC) planning telecon audio transcriptions. The ATCSCC hosts bi-hourly planning telephone conferences (or planning telecons) to ensure smooth operations within the National Airspace (NAS). Access to both live and post meeting transcripts of this speech audio would enable quick review of meetings. Provided speech transcripts, ITN is the process of converting unformatted raw Automated Speaker Recognition (ASR) model transcripts into a human (expert) readable written form. Our hybrid ITN framework utilizes a fine-tuned Bidirectional Encoder Representations from Transformers neural network to format conversational English, and rule-based methods to format domain-specific aviation text. With an overall Punctuation Error Rate (PER) of 25.56 and Word Error Rate with Punctuation and Capitalization (WER PC) of 5.47, we show that this method has vast potential in being applied to ATCSCC planning telecon audio and other audio/text based data available in ATM.

ATM↗

NASA NTRS2021

SoMo: Fast and Accurate Simulations of Continuum Robots in Complex Environments

Engineers and scientists often rely on their intuition and experience when designing soft robotic systems. The development of performant controllers and motion plans for these systems commonly requires time-consuming iterations on hardware. We present the SoMo (Soft Motion) toolkit, a software framework that makes it easy to instantiate and control typical continuum manipulators in an accurate physics simulator. SoMo introduces a standardized and human-readable description format for continuum manipulators. It leverages this description format and the Bullet physics engine to enable fast and accurate simulations of soft and soft-rigid hybrid robots in environments with complex contact interactions. This allows users to vary design and control parameters across simulations with minimal effort. We compare the capabilities of SoMo to other physics simulators and highlight the benefits and accuracy of SoMo by demonstrating the agreement between simulation and real-world experiments on several examples; these include an in-hand manipulation task with continuum fingers, an automated exploration of how to design soft fingers for precision grasping, and a brief snake locomotion study. Overall, SoMo provides an accessible way for designers of soft robotic hardware and control systems to gain access to a simulation-accelerated workflow.

Moritz A. Graule↗

NASA NTRSDate not supplied

Inverse Text Normalization of Air Traffic Control System Command Center Planning Telecon Transcriptions

We present a hybrid neural network and rule-based Inverse Text Normalization (ITN) method for domains containing unique technical phraseology, specifically Air Traffic Control System Command Center (ATCSCC) planning telecon audio transcriptions. The ATCSCC hosts bi-hourly planning telephone conferences (or planning telecons) to ensure smooth operations within the National Airspace (NAS). Access to both live and post meeting transcripts of this speech audio would enable quick review of meetings. Provided speech transcripts, ITN is the process of converting unformatted raw Automated Speaker Recognition (ASR) model transcripts into a human (expert) readable written form. Our hybrid ITN framework utilizes a fine-tuned Bidirectional Encoder Representations from Transformers neural network to format conversational English, and rule-based methods to format domain-specific aviation text. With an overall Punctuation Error Rate (PER) of 25.56 and Word Error Rate with Punctuation and Capitalization (WER PC) of 5.47, we show that this method has vast potential in being applied to ATCSCC planning telecon audio and other audio/text based data available in ATM.

ATM↗

NASA NTRSDate not supplied

Volumetric Assessment of UPRITE Exercises From Marker-Based Motion Capture

BACKGROUND Lack of volumetric data on full-body movement of exercises presents a challenge to ensuring the fit of crew member’s full range of motion on the International Space Station (ISS). The Upright Proprioception Retention via In-flight Training and Evaluation (UPRITE) is a sensorimotor countermeasure device designed for maintaining crew members’ proprioception in a microgravity environment. A footplate—attached to a static base—rotates in two degrees of freedom (pitch and roll) up to a 20 deg angle. An initial volumetric assessment assuming an upright standing posture produced a cone-like shape with a narrow bottom and wide top. Such general volumetric assessments risk creating an overly conservative volume estimate, taking up more space than is necessary on the already limited interior space of the ISS, and neglecting necessary volume due to oversimplifying assumptions. Rather, higher-fidelity volumetric assessments offer more comprehensive insights in an environment where every area counts. The main objective of this work is to provide the spatial parameters of exercises on the UPRITE such that it is placed on the ISS according to its volumetric demands or that usage is adjusted to fit the available space. METHODS In 2023, a data collection was performed originally to inform loads and dynamics of system use and was recently leveraged for volumetric assessment. Three human subjects representing different body types (~63-76 inches in stature) performed a variety of board manipulations using UPRITE with body weight offload. The test collected the 3D positional data of a modified full-body Plug-in Gait marker set [1] via a 16-camera OptiTrack MoCap system. After processing – filling marker gaps and trimming data – in OptiTrack Motive, the recorded marker location data, which included device markers, was exported to a readable trajectory file. To accurately represent the full volume defining landmarks, additional markers were digitally added to an unscaled Modified Full Body Model [2]. The model was then scaled according to its subject parameters upon which an inverse kinematics analysis was performed. A custom plugin yielded model marker location data files. Volumetric analyses were performed on the recorded trajectory and model trajectory files using a custom Python-built tool that extracted the marker location data and plotted it in a 3D space. Concerned with only the maximum volume of the motion, a 3D convex hull analysis was applied to the plot, extracting the vertices or external points of the eventual 3D CAD output, dubbed aptly as a “volume shell”. This overall approach was based on guidance in a NASA-STD-3001 Technical Brief [3]. RESULTS AND DISCUSSION Batch volumetric assessment on the exercises for each subject was performed, producing high-fidelity volume shells in minimal time. Preliminary results highlighted the value in higher-fidelity volumes based on collected data when possible. For example, revolving a single posture in the cone assessment would not have sufficiently captured a single leg stance; rather, it would need to involve swinging the leg both forward and back. Additional observations and the maximal dimensions of the volumes, including those based on scaled data for ISS anthropometric requirements, will be presented at the Human Research Program Investigator’s Workshop. CONCLUSIONS While this work’s primary objective was for the UPRITE-to-ISS integration, the tool built to conduct this analysis has wide applications for future exercise systems as an informational tool for optimal device placement. The tool and its findings also have implications for exercise device design and spacecraft interior considerations on Gateway, the Lunar Pressurized Rover, and beyond. REFERENCES [1] Bell, C. A., et al. (2023) Recent Improvements and Verification of a Full Body Model in OpenSim. NASA Human Research Program Investigator’s Workshop. https://ntrs.nasa.gov/citations/20230001080 [2] Lostroscio, K., et al (2023) The Digital Astronaut Simulation. AHFE International Conference on Human Factors in Design, Engineering, and Computing for All. [3] Exercise Overview. (2023) NASA-STD-3001 Technical Brief. https://www.nasa.gov/wp-content/uploads/2023/12/ochmo-tb-031-exercise-overview.pdf?emrc=9d454c?emrc=9d454c

L D Quinto↗

NASA NTRSDate not supplied

Beyond Fair: Engagement, Data Usability, and Open Community Productivity through the NASA Open Science Data Repository

The FAIR principle (findable, accessible, interoperable, and reusable) governs the storage and sharing of NASA space biology and health data[1]. These guiding principles maximize reuse of data and the reproducibility of scientific findings. The NASA Open Science Data Repository (OSDR; an expansion of NASA GeneLab) was built on the FAIR principles and houses over 500 studies and close to 1000 datasets from decades of space life sciences experiments. OSDR embodies the FAIR principles through data governance that includes mediated, embargoed, and fully open access data. The FAIR data governance principles were recently proposed to be expanded to encompass a FAIREST framework for assessing research data repositories (FAIR + Engagement, Social connections, and Trust)[2]. FAIREST emphasizes the importance of data repositories engaging with the scientific community and gaining the trust of researchers regarding data quality. Trust also refers to the TRUST principles developed for assessment of digital repositories: Transparency, Responsibility, User Focus, Sustainability, Technology[3]. We present the “Open Science for Life in Space” Analysis Working Groups (AWGs) as evidence regarding the power of engagement, social connections, and trust which has enhanced OSDR’s capabilities and productivity. AWG members engage in two main activities. One, members provide feedback on OSDR scientific standards for data ingestion, curation, and reuse (study, subject and assay metadata; processing pipelines; dataset formats and uniformed structures for machine-readability). Two, AWG members collaborate to mine-reuse OSDR data to conduct scientific analysis. With nearly 800 active members, the AWGs have resulted in 32 publications re-using OSDR data and contributed many papers in two major special issues in Cell (2020) and Nature (2024). AWGs also serve as networking groups, facilitate social connections between researchers at all levels of experience, and also have a social online ‘Forum’ used to keep members informed on projects and opportunities. This community-centric, productive, and trustworthy data culture has resulted in a broader effect with international space agencies, academics, and the commercial space sector wanting to submit their data to OSDR. Ten studies of Inspiration 4 data were recently publicly released by OSDR, as were some JAXA human data. Coming up soon in OSDR are data submissions from the European Space Agency, Virgin Galactic PIs, and SpaceX Polaris Dawn. A major benefit of OSDR is the array of standardized and uniformly formatted data (which was developed through AWG member consensus), from which visualization tools, analysis tools, and machine learning models can be built or trained. This talk will cover the Multi-Study Visualization Tool, the Environmental Data Application, RadLab, and a UCSF-NSF funded knowledge graph biomedical health discovery tool ‘SPOKE’ currently being integrated with OSDR. OSDR also provides training programs in bioinformatics and machine learning to improve the scientific community’s awareness of data availability and to boost their ability to perform data analysis. The increasing engagement of the scientific community and the public with technologies powered by artificial intelligence (AI) heightens the need for data analysis to be transparent. The AI for Life in Space initiative leverages the data products provided in OSDR to train AI models, with an emphasis on explainable and trustworthy AI, which would not be possible without FAIR data and metadata. Overall, here we will demonstrate the importance for NASA life sciences data repositories to adhere to the FAIREST framework, by providing examples and success stories from different aspects of OSDR.

data↗

NASA NTRSDate not supplied

Enhancing accessibility and usability of Algorithm Theoretical Basis Documents through the Algorithm Publication Tool

Effective communication of scientific theories is crucial for transforming raw instrument data into valuable Earth observation products. The NASA Earth science data community disseminates this knowledge through Algorithm Theoretical Basis Documents (ATBDs). Historically, these documents lacked a standardized format, were designed for human readability rather than machine interpretation, and were challenging to locate due to the absence of a centralized repository. The Algorithm Publication Tool (APT) transforms how ATBD content is presented, simplifying the processes of creating, updating, and locating these documents. APT offers authors the option to use its user-friendly cloud-based interface or standardized templates for ATBD development. The primary advantage of the interface is its capability to manage the entire ATBD creation process within a single environment, ensuring comprehensive tracking of all activities and facilitating user tasks. Conversely, the use of standardized ATBD templates allows users to create documents using familiar tools like Google Docs, Microsoft Word, or Overleaf for LaTeX. APT also provides a centralized repository, enabling easy search and discovery of published ATBDs. This presentation showcases APT's functionalities, illustrates its contributions to advancing open science, and highlights potential benefits for broader community adoption.

Bradley Baker↗

DOE OSTI2016

FASTQ quality control dashboard

FQCDB builds up existing open source software, FastQC, implementing a modern web interface for across parsed output of FastQC. In addition, FQCDB is extensible as a web service to include additional plots of type line, boxplot, or heatmap, across data formatted according to guidelines. The interface is also configurable via more readable JSON format, enabling customization by non-web programmers.

Source record↗

DOE OSTI2016

DIVA V2.0

The DIVA software interfaces a process in which researchers design their DNA with a web-based graphical user interface, submit their designs to a central queue, and a few weeks later receive their sequence-verified clonal constructs. Each researcher independently designs the DNA to be constructed with a web-based BioCAD tool, and presses a button to submit their designs to a central queue. Researchers have web-based access to their DNA design queues, and can track the progress of their submitted designs as they progress from "evaluation", to "waiting for reagents", to "in progress", to "complete". Researchers access their completed constructs through the central DNA repository. Along the way, all DNA construction success/failure rates are captured in a central database. Once a design has been submitted to the queue, a small number of dedicated staff evaluate the design for feasibility and provide feedback to the responsible researcher if the design is either unreasonable (e.g., encompasses a combinatorial library of a billion constructs) or small design changes could significantly facilitate the downstream implementation process. The dedicated staff then use DNA assembly design automation software to optimize the DNA construction process for the design, leveraging existing parts from the DNA repository where possible and ordering synthetic DNA where necessary. SynTrack software manages the physical locations and availability of the various requisite reagents and process inputs (e.g., DNA templates). Once all requisite process inputs are available, the design progresses from "waiting for reagents" to "in progress" in the design queue. Human-readable and machine-parseable DNA construction protocols output by the DNA assembly design automation software are then executed by the dedicated staff exploiting lab automation devices wherever possible. Since the all employed DNA construction methods are sequence-agnostic, standardized (utilize the same enzymatic master mixes and reaction conditions), completely independent DNA construction tasks can be aggregated into the same multi-well plates and pursued in parallel. The resulting sets of cloned constructs can then be screened by high-throughput next-gen sequencing platforms for sequence correctness. A combination of long read-length (e.g., PacBio) and paired-end read platforms (e.g., Illumina) would be exploited depending the particular task at hand (e.g., PacBio might be sufficient to screen a set of pooled constructs with significant gene divergence). Post sequence verification, designs for which at least one correct clone was identified will progress to a "complete" status, while designs for which no correct clones wereidentified will progress to a "failure" status. Depending on the failure mode (e.g., no transformants), and how many prior attempts/variations of assembly protocol have been already made for a given design, subsequent attempts may be made or the design can progress to a "permanent failure" state. All success and failure rate information will be captured during the process, including at which stage a given clonal construction procedure failed (e.g., no PCR product) and what the exact failure was (e.g. assembly piece 2 missing). This success/failure rate data can be leveraged to refine the DNA assembly design process.

CHEN, JOANNA↗

DOE OSTI2016

Smoke detection

Various apparatus and methods for smoke detection are disclosed. In one embodiment, a method of training a classifier for a smoke detector comprises inputting sensor data from a plurality of tests into a processor. The sensor data is processed to generate derived signal data corresponding to the test data for respective tests. The derived signal data is assigned into categories comprising at least one fire group and at least one non-fire group. Linear discriminant analysis (LDA) training is performed by the processor. The derived signal data and the assigned categories for the derived signal data are inputs to the LDA training. The output of the LDA training is stored in a computer readable medium, such as in a smoke detector that uses LDA to determine, based on the training, whether present conditions indicate the existence of a fire.

47 OTHER INSTRUMENTATION↗

DOE OSTI2016

Resonant Frequency Control For the PIP-II Injector Test RFQ: Control Framework and Initial Results

For the PIP-II Injector Test (PI-Test) at Fermilab, a four-vane radio frequency quadrupole (RFQ) is designed to accelerate a 30-keV, 1-mA to 10-mA, H- beam to 2.1 MeV under both pulsed and continuous wave (CW) RF operation. The available headroom of the RF amplifiers limits the maximum allowable detuning to 3 kHz, and the detuning is controlled entirely via thermal regulation. Fine control over the detuning, minimal manual intervention, and fast trip recovery is desired. In addition, having active control over both the walls and vanes provides a wider tuning range. For this, we intend to use model predictive control (MPC). To facilitate these objectives, we developed a dedicated control framework that handles higher-level system decisions as well as executes control calculations. It is written in Python in a modular fashion for easy adjustments, readability, and portability. Here we describe the framework and present the first control results for the PI-Test RFQ under pulsed and CW operation.

43 PARTICLE ACCELERATORS↗

DOE OSTI2016

Open Data and the Free Access to Law Movement in the United States

US President Barack Obama issued Executive Order 13642-Making Open and Machine Readable the New Default for Government - on May, 9 2013, mandating, wherever legally permissible and possible, that US Government information be made open to the public.[1] This edict accelerated the construction of and framework for data repositories, and data citation principles and practices, such as data.gov. As a corollary, researchers across the country's national laboratories found themselves creating data management plans, applying data set metadata standards, and ensuring the long-term access of data for federally funded scientific research.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗