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All sourcesNASA NTRSDOE OSTI
NASA NTRS2008

Small-Body Extensions for the Satellite Orbit Analysis Program (SOAP)

An extension to the SOAP software allows users to work with tri-axial ellipsoid-based representations of planetary bodies, primarily for working with small, natural satellites, asteroids, and comets. SOAP is a widely used tool for the visualization and analysis of space missions. The small body extension provides the same visualization and analysis constructs for use with small bodies. These constructs allow the user to characterize satellite path and instrument cover information for small bodies in both 3D display and numerical output formats. Tri-axial ellipsoids are geometric shapes the diameters of which are different in each of three principal x, y, and z dimensions. This construct provides a better approximation than using spheres or oblate spheroids (ellipsoids comprising two common equatorial diameters as a distinct polar diameter). However, the tri-axial ellipsoid is considerably more difficult to work with from a modeling perspective. In addition, the SOAP small-body extensions allow the user to actually employ a plate model for highly irregular surfaces. Both tri-axial ellipsoids and plate models can be assigned to coordinate frames, thus allowing for the modeling of arbitrary changes to body orientation. A variety of features have been extended to support tri-axial ellipsoids, including the computation and display of the spacecraft sub-orbital point, ground trace, instrument footprints, and swathes. Displays of 3D instrument volumes can be shown interacting with the ellipsoids. Longitude/latitude grids, contour plots, and texture maps can be displayed on the ellipsoids using a variety of projections. The distance along an arbitrary line of sight can be computed between the spacecraft and the ellipsoid, and the coordinates of that intersection can be plotted as a function of time. The small-body extension supports the same visual and analytical constructs that are supported for spheres and oblate spheroids in SOAP making the implementation of the more complex algorithms largely transparent to the user.

Carnright, Robert↗
NASA NTRS2000

Atomistic Method Applied to Computational Modeling of Surface Alloys

The formation of surface alloys is a growing research field that, in terms of the surface structure of multicomponent systems, defines the frontier both for experimental and theoretical techniques. Because of the impact that the formation of surface alloys has on surface properties, researchers need reliable methods to predict new surface alloys and to help interpret unknown structures. The structure of surface alloys and when, and even if, they form are largely unpredictable from the known properties of the participating elements. No unified theory or model to date can infer surface alloy structures from the constituents properties or their bulk alloy characteristics. In spite of these severe limitations, a growing catalogue of such systems has been developed during the last decade, and only recently are global theories being advanced to fully understand the phenomenon. None of the methods used in other areas of surface science can properly model even the already known cases. Aware of these limitations, the Computational Materials Group at the NASA Glenn Research Center at Lewis Field has developed a useful, computationally economical, and physically sound methodology to enable the systematic study of surface alloy formation in metals. This tool has been tested successfully on several known systems for which hard experimental evidence exists and has been used to predict ternary surface alloy formation (results to be published: Garces, J.E.; Bozzolo, G.; and Mosca, H.: Atomistic Modeling of Pd/Cu(100) Surface Alloy Formation. Surf. Sci., 2000 (in press); Mosca, H.; Garces J.E.; and Bozzolo, G.: Surface Ternary Alloys of (Cu,Au)/Ni(110). (Accepted for publication in Surf. Sci., 2000.); and Garces, J.E.; Bozzolo, G.; Mosca, H.; and Abel, P.: A New Approach for Atomistic Modeling of Pd/Cu(110) Surface Alloy Formation. (Submitted to Appl. Surf. Sci.)). Ternary alloy formation is a field yet to be fully explored experimentally. The computational tool, which is based on the BFS (Bozzolo, Ferrante, and Smith) method for the calculation of the energetics, consists of a small number of simple PCbased computer codes that deal with the different aspects of surface alloy formation. Two analysis modes are available within this package. The first mode provides an atom-by-atom description of real and virtual stages 1. during the process of surface alloying, based on the construction of catalogues of configurations where each configuration describes one possible atomic distribution. BFS analysis of this catalogue provides information on accessible states, possible ordering patterns, and details of island formation or film growth. More importantly, it provides insight into the evolution of the system. Software developed by the Computational Materials Group allows for the study of an arbitrary number of elements forming surface alloys, including an arbitrary number of surface atomic layers. The second mode involves large-scale temperature-dependent computer 2. simulations that use the BFS method for the energetics and provide information on the dynamic processes during surface alloying. These simulations require the implementation of Monte-Carlo-based codes with high efficiency within current workstation environments. This methodology capitalizes on the advantages of the BFS method: there are no restrictions on the number or type of elements or on the type of crystallographic structure considered. This removes any restrictions in the definition of the configuration catalogues used in the analytical calculations, thus allowing for the study of arbitrary ordering patterns, ultimately leading to the actual surface alloy structure. Moreover, the Monte Carlo numerical technique used for the large-scale simulations allows for a detailed visualization of the simulated process, the main advantage of this type of analysis being the ability to understand the underlying features that drive these processes. Because of the simplicity of the BFS method for e energetics used in these calculations, a detailed atom-by-atom analysis can be performed at any point in the simulation, providing necessary insight on the details of the process. The main objective of this research program is to develop a tool to guide experimenters in understanding and interpreting often unexpected results in alloy formation experiments. By reducing the computational effort without losing physical accuracy, we expect that powerful simulation tools will be developed in the immediate future, which will allow material scientists to easily visualize and analyze processes at a level not achievable experimentally.

Bozzolo, Guillermo H.↗
DOE OSTI2016

SU-F-T-91: Development of Real Time Abdominal Compression Force (ACF) Monitoring System

Purpose: Hard-plate based abdominal compression is known to be effective, but no explicit method exists to quantify abdominal compression force (ACF) and maintain the proper ACF through the whole procedure. In addition, even with compression, it is necessary to do 4D CT to manage residual motion but, 4D CT is often not possible due to reduced surrogating sensitivity. In this study, we developed and evaluated a system that both monitors ACF in real time and provides surrogating signal even under compression. The system can also provide visual-biofeedback. Methods: The system developed consists of a compression plate, an ACF monitoring unit and a visual-biofeedback device. The ACF monitoring unit contains a thin air balloon in the size of compression plate and a gas pressure sensor. The unit is attached to the bottom of the plate thus, placed between the plate and the patient when compression is applied, and detects compression pressure. For reliability test, 3 volunteers were directed to take several different breathing patterns and the ACF variation was compared with the respiratory flow and external respiratory signal to assure that the system provides corresponding behavior. In addition, guiding waveform were generated based on free breathing, and then applied for evaluating the effectiveness of visual-biofeedback. Results: We could monitor ACF variation in real time and confirmed that the data was correlated with both respiratory flow data and external respiratory signal. Even under abdominal compression, in addition, it was possible to make the subjects successfully follow the guide patterns using the visual biofeedback system. Conclusion: The developed real time ACF monitoring system was found to be functional as intended and consistent. With the capability of both providing real time surrogating signal under compression and enabling visual-biofeedback, it is considered that the system would improve the quality of respiratory motion management in radiation therapy. This research was supported by the Mid-career Researcher Program through NRF funded by the Ministry of Science, ICT & Future Planning of Korea (NRF-2014R1A2A1A10050270) and by the Radiation Technology R&D program through the National Research Foundation of Korea funded by the Ministry of Science, ICT & Future Planning (No. 2013M2A2A7038291)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Stanford Thermal Earth Model for the Conterminous United States

Provided here are various forms of the Stanford Thermal Earth Model, as well as the data and methods used for its creation. The predictions produced by this model were visualized in two-dimensional spatial maps across the modeled depths (0-7 km) for the conterminous United States. The thermal earth model is made available as an application programming interface (API) and as feature layers on ArcGIS, which are both provided via links below. A data-driven spatial interpolation algorithm based on physics-informed graph neural networks was used to develop these national temperature-at-depth maps. The model satisfied the three-dimensional heat conduction law by predicting subsurface temperature, surface heat flow, and rock thermal conductivity. Many physical quantities, including bottomhole temperature, depth, geographic coordinates, elevation, sediment thickness, magnetic anomaly, gravity anomaly, gamma-ray flux of radioactive elements, seismicity, and electric conductivity were used as model inputs. Surface heat flow, temperature, and thermal conductivity predictions were constructed for depths of 0-7 km at an interval of 1 km with spatial resolution of 18 km2 per grid cell. The model showed superior temperature, surface heat flow and thermal conductivity mean absolute errors of 4.8C, 8.1 mW/m2 and 0.07 W/(C-m), respectively..

15 GEOTHERMAL ENERGY↗
DOE OSTI2024

Complete Demonstration of a Prototype Version of FORCE User Interface and Conduct Analyst Survey Collecting Feedback on Interface Features and Usability

In 2024 the US Department of Energy (DOE) Office of Nuclear Energy (NE) Integrated Energy System (IES) program continued to develop the Framework for Optimization of Resources and Economics (FORCE) analysis ecosystem into a more traditional toolset with simplified software installation, automated workflows, and interactive results visualization. The DOE-NE Nuclear Energy Advanced Modeling and Simulation (NEAMS) Workbench continued to be leveraged for user input, application workflow and runtime environment, and interactive results visualization capabilities. This report documents the demonstration of a FORCE User Interface (UI) prototype and the results of a survey of analysts’ using the Holistic Energy Resource Optimization Network (HERON) tool in FORCE with the prototype UI.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1988

Research review for information management

The goal of RICIS research in information management is to apply currently available technology to existing problems in information management. Research projects include the following: the Space Business Research Center (SBRC), the Management Information and Decision Support Environment (MIDSE), and the investigation of visual interface technology. Several additional projects issued reports. New projects include the following: (1) the AdaNET project to develop a technology transfer network for software engineering and the Ada programming language; and (2) work on designing a communication system for the Space Station Project Office at JSC. The central aim of all projects is to use information technology to help people work more productively.

Bishop, Peter C.↗
NASA NTRS2011

Countermeasures to Enhance Sensorimotor Adaptability

During exploration-class missions, sensorimotor disturbances may lead to disruption in the ability to ambulate and perform functional tasks during the initial introduction to a novel gravitational environment following a landing on a planetary surface. The goal of our current project is to develop a sensorimotor adaptability (SA) training program to facilitate rapid adaptation to novel gravitational environments. We have developed a unique training system comprised of a treadmill placed on a motion-base facing a virtual visual scene that provides an unstable walking surface combined with incongruent visual flow designed to enhance sensorimotor adaptability. We have conducted a series of studies that have shown: Training using a combination of modified visual flow and support surface motion during treadmill walking enhances locomotor adaptability to a novel sensorimotor environment. Trained individuals become more proficient at performing multiple competing tasks while walking during adaptation to novel discordant sensorimotor conditions. Trained subjects can retain their increased level of adaptability over a six months period. SA training is effective in producing increased adaptability in a more complex over-ground ambulatory task on an obstacle course. This confirms that for a complex task like walking, treadmill training contains enough of the critical features of overground walking to be an effective training modality. The structure of individual training sessions can be optimized to promote fast/strategic motor learning. Training sessions that each contain short-duration exposures to multiple perturbation stimuli allows subjects to acquire a greater ability to rapidly reorganize appropriate response strategies when encountering a novel sensory environment. Individual sensory biases (i.e. increased visual dependency) can predict adaptive responses to novel sensory environments suggesting that customized training prescriptions can be developed to enhance adaptability. These results indicate that SA training techniques can be added to existing treadmill exercise equipment and procedures to produce a single integrated countermeasure system to improve performance of astro/cosmonauts during prolonged exploratory space missions.

Bloomberg, J. J.↗
NASA NTRS2014

Comprehension of Spacecraft Telemetry Using Hierarchical Specifications of Behavior

A key challenge in operating remote spacecraft is that ground operators must rely on the limited visibility available through spacecraft telemetry in order to assess spacecraft health and operational status. We describe a tool for processing spacecraft telemetry that allows ground operators to impose structure on received telemetry in order to achieve a better comprehension of system state. A key element of our approach is the design of a domain-specific language that allows operators to express models of expected system behavior using partial specifications. The language allows behavior specifications with data fields, similar to other recent runtime verification systems. What is notable about our approach is the ability to develop hierarchical specifications of behavior. The language is implemented as an internal DSL in the Scala programming language that synthesizes rules from patterns of specification behavior. The rules are automatically applied to received telemetry and the inferred behaviors are available to ground operators using a visualization interface that makes it easier to understand and track spacecraft state. We describe initial results from applying our tool to telemetry received from the Curiosity rover currently roving the surface of Mars, where the visualizations are being used to trend subsystem behaviors, in order to identify potential problems before they happen. However, the technology is completely general and can be applied to any system that generates telemetry such as event logs.

Runtime monitoring↗
NASA NTRS2017

Fluid Shifts

Introduction. NASA's Human Research Program is focused on addressing health risks associated with long-duration missions on the International Space Station (ISS) and future exploration-class missions beyond low Earth orbit. Visual acuity changes observed after short-duration missions were largely transient, but now more than 50 percent of ISS astronauts have experienced more profound, chronic changes with objective structural findings such as optic disc edema, globe flattening and choroidal folds. These structural and functional changes are referred to as the visual impairment and intracranial pressure (VIIP) syndrome. Development of VIIP symptoms may be related to elevated intracranial pressure (ICP) secondary to spaceflight-induced cephalad fluid shifts, but this hypothesis has not been tested. The purpose of this study is to characterize fluid distribution and compartmentalization associated with long-duration spaceflight and to determine if a relation exists with vision changes and other elements of the VIIP syndrome. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as any VIIP-related effects of those shifts, are predicted by the crewmember's pre-flight status and responses to acute hemodynamic manipulations, specifically posture changes and lower body negative pressure. Methods. We will examine a variety of physiologic variables in 10 long-duration ISS crewmembers using the test conditions and timeline presented in the figure below. Measures include: (1) fluid compartmentalization (total body water by D2O, extracellular fluid by NaBr, intracellular fluid by calculation, plasma volume by CO rebreathe, interstitial fluid by calculation); (2) forehead/eyelids, tibia, and calcaneus tissue thickness (by ultrasound); (3) vascular dimensions by ultrasound (jugular veins, cerebral and carotid arteries, vertebral arteries and veins, portal vein); (4) vascular dynamics by MRI (head/neck blood flow, cerebrospinal fluid pulsatility); (5) ocular measures (optical coherence tomography; intraocular pressure; 2-dimensional ultrasound including optic nerve sheath diameter, globe flattening, and retina-choroid thickness; Doppler ultrasound of ophthalmic and retinal arteries and veins); (6) cardiac variables by ultrasound (inferior vena cava, tricuspid flow and tissue Doppler, pulmonic valve, stroke volume, right heart dimensions and function, four-chamber views); and (7) ICP measures (tympanic membrane displacement, otoacoustic emissions). Pre- and post-flight, acute head-down tilt will induce cephalad fluid shifts, whereas lower body negative pressure will oppose these shifts. Controlled Mueller maneuvers will manipulate cardiovascular variables. Through interventions applied before, during, and after flight, we intend to fully evaluate the relationship between fluid shifts and the VIIP syndrome. Discussion. Ten subjects have consented to participate in this experiment, including the recent One-Year Mission crewmembers, who have recently completed R plus180 testing; all other subjects have completed pre-flight testing. Preliminary results from the One-Year Mission crewmembers will be presented, including measures of ocular structure and function, vascular dimensions, fluid distribution, and non-invasive estimates of intracranial pressure.

Stenger, M. B.↗
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 NTRS2017

Access NASA Satellite Global Precipitation Data Visualization on YouTube

Since the satellite era began, NASA has collected a large volume of Earth science observations for research and applications around the world. The collected and archived satellite data at 12 NASA data centers can also be used for STEM education and activities such as disaster events, climate change, etc. However, accessing satellite data can be a daunting task for non-professional users such as teachers and students because of unfamiliarity of terminology, disciplines, data formats, data structures, computing resources, processing software, programming languages, etc. Over the years, many efforts including tools, training classes, and tutorials have been developed to improve satellite data access for users, but barriers still exist for non-professionals. In this presentation, we will present our latest activity that uses a very popular online video sharing Web site, YouTube (https://www.youtube.com/), for accessing visualizations of our global precipitation datasets at the NASA Goddard Earth Sciences (GES) Data and Information Services Center (DISC). With YouTube, users can access and visualize a large volume of satellite data without the necessity to learn new software or download data. The dataset in this activity is a one-month animation for the GPM (Global Precipitation Measurement) Integrated Multi-satellite Retrievals for GPM (IMERG). IMERG provides precipitation on a near-global (60 deg. N-S) coverage at half-hourly time interval, providing more details on precipitation processes and development compared to the 3-hourly TRMM (Tropical Rainfall Measuring Mission) Multisatellite Precipitation Analysis (TMPA, 3B42) product. When the retro-processing of IMERG during the TRMM era is finished in 2018, the entire video will contain more than 330,000 files and will last ~3.6 hours. Future plans include development of flyover videos for orbital data for an entire satellite mission or project. All videos, including the one-month animation, will be uploaded and available at the GES DISC site on YouTube (https://www.youtube.com/user/NASAGESDISC).

precipitation↗
NASA NTRS1990

Preliminary interpretation of the Mg II variability of L2 Puppis

L2 Pup is perhaps the brightest SRb/Mira variable in the sky, with extreme variability from 2.6 to 6.2 magnitudes visually and a normal variation between 3.5 to 5.5. More than 60 percent of its cycles show large amplitude (2 magnitude) variation that is Mira like; however at intervals of 40 to 50 cycles it goes into a phase of smaller amplitude variability. One of the small amplitude episodes began in 1986 while L2 Pup was being observed with IUE (International Ultraviolet Explorer) as part of the monitoring program. During the first three observed cycles, Mg II emission in L2 Pup behaved in a manner similar to that in other normal Miras, and L2 Pup's light curve was also Mira like. However, during the fourth cycle there was an abrupt change in the Mg II emission, although the visual light curve remained normal through that cycle. In the next cycle the light curve also decreased in amplitude, and the Mg II emission remained anomalously low.

Brugel, Edward W.↗
NASA NTRS2016

Usable Translational Hand Controllers for NASA's Habitability Design Center

This summer I was given the opportunity to work at the Habitability Design Center (HDC). NASA Johnson Space Center's HDC is currently developing Cislunar and Mars spacecraft mockups. I contributed to this effort by designing from scratch low cost, functional translational hand controllers (THCs) that will be used in spacecraft mission simulation in low to medium fidelity exploration spacecraft mockups. This project fell under the category of mechatronics, a combination of mechanical, electrical, and computer engineering. Being an aerospace engineering student, I was out of my comfort zone. And that was a wonderful thing. The autonomy that my mentor, Dr. Robert Howard, allowed me gave me the opportunity to learn by trying, failing, and trying again. This project was not only a professional success for me, but a significant learning experience. I appreciated the freedom that I had to take the time to learn new things for myself rather than blindly follow instructions. I was the sole person working on this project, and was required to work independently to solve the many hardware and software challenges that the project entailed. I researched THCs that have been used on the ISS, the Space Shuttle, and the Orion MPVC and based my design off of these. I worked through many redesigns before finding an optimal configuration of the necessary mechanisms and electrical components for the THC. Once I had a functional hardware design, I dove into the challenge of getting an Arduino Uno, an extremely low cost and easily programmable microcontroller, to behave as a human interface device. The THCs I built needed to be able to integrate to a mission simulation designed by NASA's Graphics and Visualization Lab. This proved to be the most challenging aspect of the project. To accomplish this I learned how to change the firmware of the USB serial converter microcontroller. The process was very complicated as it involved multiple software programs and manual flashing of pins on the Arduino itself. When I successfully achieved the goal I wrote an instructions manual for the process so that the HDC will be able to do this easily in the future for any human interface device they may want to create. I also created a detailed CAD model of my THC design with construction instructions. My THC utilizes three ultrasonic sensors, one for each axis of motion. I wrote a code that stimulates these sensors continuously and feeds back values from each axis ranging from -%100 to %100 of the min/max position in relation to the neutral position of each axis. This was the data that the Graphics and Visualization Lab required to interface with their simulation. I truly enjoyed working in the HDC surrounded by passionate, proactive, and brilliantly creative people. I felt valued and respected as a part of their team. I was given the time and support of my mentor whenever I asked for it. Beyond my positive project experience, I was fortunate enough to be able to take advantage of many of the extra activities that JSC has to offer. I took Russian Phase One during my lunch break every day and can now read Russian and accomplish basic verbal communication. I was heavily involved with the co-tern music video, which led to numerous incredible experiences and friendships. I saw every facility, attended every lecture, and met everyone that I could. I had coffee with Lauri Hansen. I played on an intern volleyball team at the Gilruth. I traveled to Michoud, Stennis, NOLA, and Big Bend National Park. I had the time of my life and I fell in love with JSC. In the next month I will return to Maryland and start my senior year of my undergraduate degree. As I work through it I will remember that all of the studying I do, all of the concentration I give, and all of the sacrifices that I make for school are so that I can work at a place like JSC where I am proud and excited to go into work every day. This internship was an invaluable experience for me, both professionally and personally.

Westbrook, Kimberly↗
DOE OSTI2023

Bioimaging Science Program Principal Investigator Meetings Proceedings (2021)

As part of the 2021 Biological Systems Science Division (BSSD) Principal Investigator (PI) Meeting, the Bioimaging Science program (BSP), within BSSD's Biomolecular Characterization and Imaging Science portfolio, held its annual PI meeting virtually February 22–23. BSP's mission is to understand the translation of genomic information into the mechanisms that power living cells, communities of cells, and whole organisms. The goal of BSP is to develop new imaging and measurement technologies to visualize the spatial and temporal relationships of key metabolic processes governing phenotypic expression in plants and microbes. BSP convenes annual PI meetings to bring together its contributing investigators to review progress and current state-of-the-art bioimaging research. Holding the BSP meeting as part of the broader BSSD PI meeting allowed researchers to interact with the extended Genomic Science program community. This convergence provided a platform for networking and exchange of ideas, helping to forge new multidisciplinary collaborations among investigators from the two sister programs. An important highlight of the BSP meeting was the keynote presentation “Enhancing Fluorescence Microscopy with Computation” by Dr. Hari Shroff of the NIH National Institute of Biomedical Imaging and Bioengineering. All the BSP PIs made presentations describing their research focus and progress, and these were followed by roundtable discussions of each project. The meeting’s proceedings provide an outline of the program’s current state and potential future directions and opportunities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

THE NASA AMES PAH IR SPECTROSCOPIC DATABASE VERSION 2.00: UPDATED CONTENT, WEB SITE, AND ON(OFF)LINE TOOLS

A significantly updated version of the NASA Ames PAH IR Spectroscopic Database, the first major revision since its release in 2010, is presented. The current version, version 2.00, contains 700 computational and 75 experimental spectra compared, respectively, with 583 and 60 in the initial release. The spectra span the 2.5-4000 μm (4000-2.5 cm{sup -1}) range. New tools are available on the site that allow one to analyze spectra in the database and compare them with imported astronomical spectra as well as a suite of IDL object classes (a collection of programs utilizing IDL's object-oriented programming capabilities) that permit offline analysis called the AmesPAHdbIDLSuite. Most noteworthy among the additions are the extension of the computational spectroscopic database to include a number of significantly larger polycyclic aromatic hydrocarbons (PAHs), the ability to visualize the molecular atomic motions corresponding to each vibrational mode, and a new tool that allows one to perform a non-negative least-squares fit of an imported astronomical spectrum with PAH spectra in the computational database. Finally, a methodology is described in the Appendix, and implemented using the AmesPAHdbIDLSuite, that allows the user to enforce charge balance during the fitting procedure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1995

Coronagraphic imaging of pre-main-sequence stars: Remnant evvelopes of star formation seen in reflection

We have obtained R- and I-band coronagraphic images of the vicinities of 11 pre-main sequence (PMS) stars to search for faint, small-scale reflection nebulae. The inner radius of the search and the field of view are 1.9 arcsec and 1x1 arcmin, respectively. Reflection nebulae were imaged around RY Tau, T Tau,DG Tau, SU Aur, AB Aur, FU Ori, and Z CMa. No nebulae were detected around HBC 347, GG Tau, V773 Tau, and V830 Tau. Categorically speaking, most of the classical T Tauri program stars and all the FU Orionis-type program stars are associated with the reflection nebulae, while none of the weak-line T Tauri program stars are associated with nebulae. The detected nebulae range in size from 250 to 37 000 AU. From the brightness ratios of the stars and nebulae, we obtain a lower limit to the visual extinction of PMS star light through the nebulae of (A(sub V))(sub neb) = 0.1. The lower limits of masses and volume densities of the nebulae associated with the classical T Tauri stars are 10(exp-6) Solar mass and N(sub H) = 10(exp 5)/cu cm, respectively. Lower limits for the nebulae around FU Orionis stars are 10(exp -5) Solar mass and n(sub H) = 10 (exp 5)/cu cm, respectively. Some reflection nebulae may trace the illuminated surfaces of the optically thick dust nebulae, so these mass estimates are not stringent. All the PMS stars with associated nebulae are strong far-infrared emitters. Both the far-infrared emission and the reflection nebulae appear to originate from the remnant envelopes of star formation. The 100 micrometers emitting regions of SU Aur and FU Ori are likely to be cospatial with the reflection nebulae. A spatial discontinuity between FU Ori and its reflection nebula may explain the dip in the far-infrared spectral energy distribution at 60 micrometers. The warped, disk-like nebulae around T Tau and Z CMa are aligned with and embrace the inner star/circumstellar disk systems. The arc-shaped nebula around DG Tau may be in contact with the coaligned inner star/disk system. These three-reflection nebulae may trace the surfaces of pseudodisks from which matter accretes onto the stars or the inner circumstellar disks. 19 stellar objects brighter than I = 19 were detected around 9 program stars. Using a color-magnitude diagram, we have identified three new PMS candidates aroun Z CMa and one previously known PMS candidate, GG Tau/c.

Nakajima, Tadashi↗
DOE OSTI2025

rcsb-api : Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.

FAIR principles↗
DOE OSTI2024

Updates to the Alliance of Genome Resources central infrastructure

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific “landing pages” and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).

59 BASIC BIOLOGICAL SCIENCES↗