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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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NASA NTRS1989

Multinode reconfigurable pipeline computer

A multinode parallel-processing computer is made up of a plurality of innerconnected, large capacity nodes each including a reconfigurable pipeline of functional units such as Integer Arithmetic Logic Processors, Floating Point Arithmetic Processors, Special Purpose Processors, etc. The reconfigurable pipeline of each node is connected to a multiplane memory by a Memory-ALU switch NETwork (MASNET). The reconfigurable pipeline includes three (3) basic substructures formed from functional units which have been found to be sufficient to perform the bulk of all calculations. The MASNET controls the flow of signals from the memory planes to the reconfigurable pipeline and vice versa. the nodes are connectable together by an internode data router (hyperspace router) so as to form a hypercube configuration. The capability of the nodes to conditionally configure the pipeline at each tick of the clock, without requiring a pipeline flush, permits many powerful algorithms to be implemented directly.

Nosenchuck, Daniel M.↗
NASA NTRS2011

Time-Distance Helioseismology Data-Analysis Pipeline for Helioseismic and Magnetic Imager Onboard Solar Dynamics Observatory (SDO-HMI) and Its Initial Results

The Helioseismic and Magnetic Imager onboard the Solar Dynamics Observatory (SDO/HMI) provides continuous full-disk observations of solar oscillations. We develop a data-analysis pipeline based on the time-distance helioseismology method to measure acoustic travel times using HMI Doppler-shift observations, and infer solar interior properties by inverting these measurements. The pipeline is used for routine production of near-real-time full-disk maps of subsurface wave-speed perturbations and horizontal flow velocities for depths ranging from 0 to 20 Mm, every eight hours. In addition, Carrington synoptic maps for the subsurface properties are made from these full-disk maps. The pipeline can also be used for selected target areas and time periods. We explain details of the pipeline organization and procedures, including processing of the HMI Doppler observations, measurements of the travel times, inversions, and constructions of the full-disk and synoptic maps. Some initial results from the pipeline, including full-disk flow maps, sunspot subsurface flow fields, and the interior rotation and meridional flow speeds, are presented.

Sun: helioseismology↗
NASA NTRS1979

VLSI system for synthetic aperture radar /SAR/ processing

The paper discusses an SAR problem based on actual requirements set forth by NASA for a spaceborne application. The requirements for high resolution and high quality necessitate a data sampling rate of 7.5 MHz. For each data value 1,025 4-bit complex multiply + add operations are needed, which is equivalent to 7.7 GHz complex multiply + add operation rate. Since this rate is much too high for general purpose systems, a special-purpose device was sought. This paper discusses two architectures based on parallel operation of 1,025 identical cells, each of which is capable of performing arithmetic, storage, and several control operations. The operation rate in each device is only 7.5 MHz, which is quite manageable, especially with the help of a substantial degree of pipelining. A computational-mathematical analysis is used as a primary tool for evaluating the design and some of its tradeoffs. Two different approaches are discussed and compared; both are based on having 1,025 identical cells working in parallel, but differ in their dual approaches to the flow of data.

Cohen, D.↗
NASA NTRSDate not supplied

Transitioning a Flexible and Scalable Satellite Ground Station Observation Network (GSON) Framework to an Operational Environment

Obtaining accurate and timely satellite observations is of paramount importance in fields like disaster management, weather diagnoses/forecasting, and Earth Sciences remote sensing. Stored mission data (SMD), from low Earth orbiting (LEO) satellite sensors, provides important observations for these fields and applications, however data access to SMD can be delayed from one and half hours to three hours from the time the observations were made. This data latency poses a significant impact on data product optimal use. We developed a Ground Station Observation Network (GSON) that utilizes commercial ground station as a service (GSaaS) providers to acquire low latency direct broadcast (DB) data from AQUA, SNPP, and JPSS-1 satellites using antennas located in strategic locations around the world. We will discuss techniques to improve the deployment efficiency and code reliability and quality of the GSON framework. Topics include right-sizing and containerization of the code to facilitate integration and adaptation with continuous delivery (CD) pipeline, locating non-code assets in referenceable repositories separated from code, adaptation of pipelines as code and simplification of CD, intersecting with code quality tests and checks as part of the pipeline execution and deployment, and establishing distributed repositories, registries, and system identities in a way that mitigates compromise to the CD pipeline. These techniques enable deployment of processing systems that are both highly specific but also dynamically modifiable. This new class of system allows for a flexible and scalable deployment while avoiding the “black box” issues that can plague large system deployments.

cluster↗
NASA NTRS2000

A Tool for Automatic Data Distribution for CFD Applications on Structured Grids

Development of HPF versions of NPB and ARC3D has shown that HPF provides an efficient, concise way to express parallelism and to organize data traffic. The use of HPF, as noted in the papers, requires an intimate knowledge of the applications and a detailed analysis of data affinity, data movement, and data granularity. To simplify and accelerate the task of developing HPF versions of existing CFD applications we have designed and implemented ADAPT (Automatic Data Alignment and Placement Tool). ADAPT analyzes a CFD application working on a single structured grid and generates HPF TEMPLATE, (RE)DISTRIBUTION, ALIGNMENT, and INDEPENDENT directives. The directives can be generated on the nest level, subroutine level, application level, or on the application interface level. ADAPT annotates an existing CFD FORTRAN application, performing computations on single or multiple grids. On each grid the application is considered as a sequence of operators, each applied to a set of variables defined in a particular grid domain. ADAPT automatically detects implicit operators (i.e., having data dependences) and explicit operators (without data dependences). For parallelization of an explicit operator ADAPT creates a template for the operator domain, aligns arrays used in the operator with the template, distributes the template, and declares the loops over the distributed dimensions as INDEPENDENT. For parallelization of an implicit operator, the distribution of the operator's domain should be consistent with the operator's dependences. Any dependence between sections distributed on different processors would preclude parallelization if the compiler does not have an ability to pipeline computations. If a data distribution is "orthogonal" to the dependences of an implicit operator, then the loop which implements the operator can be declared as INDEPENDENT. ADAPT starts with an analysis of array index expressions of the loop nests. For each pair of arrays referenced in an assignment statement, it generates an arc in the alignment graph and annotates it with an affinity relation. The template, alignment, and distribution directives for a particular loop nest are then derived from a transitive closure of the affinity relation. A compromise of data distributions in different nests and subroutines is achieved by merging annotated alignment graphs for adjacent nests/stibroutine calls in the nest/call graph of the application in the process called distribution lifting. ADAPT has been implemented as a C++ program running in conjunction with a parallelization tool called CAPTools. ADAPT uses the parse tree, interprocedural analysis and application database generated by CAPTools. It also uses the Directed Graph class, initially implemented in p2d2 (parallel debugger oi distributed programs), and some other classes supporting symbolic computations. ADAPT uses data distribution techniques described. ADAPT was tested with ARC3D and the FT benchmark and has demonstrated a code performance within a factor of 1.5 of handwritten versions.

Frumkin, Michael↗
NASA NTRS2004

MER SPICE Interface

MER SPICE Interface is a software module for use in conjunction with the Mars Exploration Rover (MER) mission and the SPICE software system of the Navigation and Ancillary Information Facility (NAIF) at NASA's Jet Propulsion Laboratory. (SPICE is used to acquire, record, and disseminate engineering, navigational, and other ancillary data describing circumstances under which data were acquired by spaceborne scientific instruments.) Given a Spacecraft Clock value, MER SPICE Interface extracts MER-specific data from SPICE kernels (essentially, raw data files) and calculates values for Planet Day Number, Local Solar Longitude, Local Solar Elevation, Local Solar Azimuth, and Local Solar Time (UTC). MER SPICE Interface was adapted from a subroutine, denoted m98SpiceIF written by Payam Zamani, that was intended to calculate SPICE values for the Mars Polar Lander. The main difference between MER SPICE Interface and m98SpiceIf is that MER SPICE Interface does not explicitly call CHRONOS, a time-conversion program that is part of a library of utility subprograms within SPICE. Instead, MER SPICE Interface mimics some portions of the CHRONOS code, the advantage being that it executes much faster and can efficiently be called from a pipeline of events in a parallel processing environment.

Sayfi, Elias↗
NASA NTRS2010

Rapid Corner Detection Using FPGAs

In order to perform precision landings for space missions, a control system must be accurate to within ten meters. Feature detection applied against images taken during descent and correlated against the provided base image is computationally expensive and requires tens of seconds of processing time to do just one image while the goal is to process multiple images per second. To solve this problem, this algorithm takes that processing load from the central processing unit (CPU) and gives it to a reconfigurable field programmable gate array (FPGA), which is able to compute data in parallel at very high clock speeds. The workload of the processor then becomes simpler; to read an image from a camera, it is transferred into the FPGA, and the results are read back from the FPGA. The Harris Corner Detector uses the determinant and trace to find a corner score, with each step of the computation occurring on independent clock cycles. Essentially, the image is converted into an x and y derivative map. Once three lines of pixel information have been queued up, valid pixel derivatives are clocked into the product and averaging phase of the pipeline. Each x and y derivative is squared against itself, as well as the product of the ix and iy derivative, and each value is stored in a WxN size buffer, where W represents the size of the integration window and N is the width of the image. In this particular case, a window size of 5 was chosen, and the image is 640 480. Over a WxN size window, an equidistance Gaussian is applied (to bring out the stronger corners), and then each value in the entire window is summed and stored. The required components of the equation are in place, and it is just a matter of taking the determinant and trace. It should be noted that the trace is being weighted by a constant k, a value that is found empirically to be within 0.04 to 0.15 (and in this implementation is 0.05). The constant k determines the number of corners available to be compared against a threshold sigma to mark a valid corner. After a fixed delay from when the first pixel is clocked in (to fill the pipeline), a score is achieved after each successive clock. This score corresponds with an (x,y) location within the image. If the score is higher than the predetermined threshold sigma, then a flag is set high and the location is recorded.

Morfopoulos, Arin C.↗
NASA NTRS2013

The Hopkins Ultraviolet Telescope: The Final Archive

The Hopkins Ultraviolet Telescope (HUT) was a 0.9 m telescope and moderate-resolution (Delta)lambda equals 3 A) far-ultraviolet (820-1850 Å) spectrograph that flew twice on the space shuttle, in 1990 December (Astro-1, STS-35) and 1995 March (Astro-2, STS-67). The resulting spectra were originally archived in a nonstandard format that lacked important descriptive metadata. To increase their utility, we have modified the original datareduction software to produce a new and more user-friendly data product, a time-tagged photon list similar in format to the Intermediate Data Files (IDFs) produced by the Far Ultraviolet Spectroscopic Explorer calibration pipeline. We have transferred all relevant pointing and instrument-status information from locally-archived science and engineering databases into new FITS header keywords for each data set. Using this new pipeline, we have reprocessed the entire HUT archive from both missions, producing a new set of calibrated spectral products in a modern FITS format that is fully compliant with Virtual Observatory requirements. For each exposure, we have generated quicklook plots of the fully-calibrated spectrum and associated pointing history information. Finally, we have retrieved from our archives HUT TV guider images, which provide information on aperture positioning relative to guide stars, and converted them into FITS-format image files. All of these new data products are available in the new HUT section of the Mikulski Archive for Space Telescopes (MAST), along with historical and reference documents from both missions. In this article, we document the improved data-processing steps applied to the data and show examples of the new data products.

Hopkins↗
NASA NTRS1973

Study of a hybrid multispectral processor

A hybrid processor is described offering enough handling capacity and speed to process efficiently the large quantities of multispectral data that can be gathered by scanner systems such as MSDS, SKYLAB, ERTS, and ERIM M-7. Combinations of general-purpose and special-purpose hybrid computers were examined to include both analog and digital types as well as all-digital configurations. The current trend toward lower costs for medium-scale digital circuitry suggests that the all-digital approach may offer the better solution within the time frame of the next few years. The study recommends and defines such a hybrid digital computing system in which both special-purpose and general-purpose digital computers would be employed. The tasks of recognizing surface objects would be performed in a parallel, pipeline digital system while the tasks of control and monitoring would be handled by a medium-scale minicomputer system. A program to design and construct a small, prototype, all-digital system has been started.

Marshall, R. E.↗
NASA NTRSDate not supplied

Diversity and Inclusion in Spacecraft Science Teams: What Do We Know and What Can We Do About It?

Introduction: Not only does the planetary science community lack diversity [1-3], the subset of the community that participates on spacecraft science team is even less diverse than the community as a whole [1, 4]. Results of 2020 Workforce Survey: Previous studies of the diversity of members of spacecraft science teams made incorrect assumptions about the nature of the data before collecting the data. Those analyses assumed a binary gender and ignored the existence of planetary scientists who are neither men nor women [4-6]. We present here results where demographic data was collected without assumptions; each individual surveyed supplied their own answers to demographic questions. The April 2020 survey of Planetary Scientists, which was conducted by the Statistical Research Center of the American Institute of Physics (AIP) and funded by the American Astronomical Society (AAS)’s Division of Planetary Science (DPS) asked participants their gender with 4 possible responses: Woman, Man, Another identify (please specify if you wish), and Prefer not to answer. 32% of respondents chose Woman, 67% chose Man and 1% chose Another gender identity [1]. The survey also asked demographic questions on race, ethnicity, LGBTQ+ identity, and disability. For a full list of questions, see https://dps.aas.org/sites/dps.aas.org/files/reports/2020/survey2020_questionnaire.pdf. In addition to demographic questions, the 2020 Workforce survey asked how many times respondents had been involved in Mission proposals as a Principal Investigator (PI) and, separately, as a Co-Investigator (CoI) [1]. Answers to questions about mission involvement were correlated with answers to demographic questions and the results show that members of historically underrepresented groups (non-white scientists, women, members of the LGBTQ+ community, and disabled scientists) were less likely to be involved in spacecraft mission proposals than were members of historically overrepresented groups [1]. The figures below show the correlated responses for four different axes of underrepresentation [1]. Note that while the figure on gender shows only Women and Men (due to the small percentage of folks answering “Another gender”), non-binary respondents are included in the LGBTQ+ community figure. Conclusion: Being part of a spacecraft science team is a goal for many planetary scientists. With it comes brand new data, more stable funding, and a sense of awe and exploration. It can lead to a cascade of opportunities from conference and public presentations, to membership in subsequent mission teams, and prestige in the community [4]. As a result, participation in spacecraft teams can be used a measure of success within the field. From the survey results, we see that members of historically excluded groups, even after they have overcome barriers to participating in the field, are still experiencing barriers to success within the field itself. Why?: The diminishing percentage of members of underrepresented groups as a career progresses has been referred to as a “leaky pipeline”. However, this fails to adequately capture the experiences of the members of these underrepresented groups as it implies a passive process. In order to capture the active processes (bias, discrimination, harassment, and other exclusionary behaviors) that contribute to low retention in the workforce, the term “Hostile Obstacle Course” is more useful [7,8]. It is these processes that need to be addressed in order to retain valued members of our community. Moving Forward: In order to broaden participation in planetary science, particularly mission science teams, we need to address conditions that create hostile workplace climates. What can mission teams and other groups do to address these conditions? First, each group/team needs to evaluate their own members to determine what specific barriers exist in their own interactions. One tool to accomplish this would be an anonymous survey designed to understand how team members feel about working within the group. Working with professionals who know how to create and analyze such surveys (often called “climate surveys” when applied to University students, for example) would ensure that the survey meets its goals and does not make assumptions that counter the meaningfulness of the results. Such professionals in EDIA (Equity, Diversity, Inclusion, and Accessibility) and workplace culture can make suggestions for policy changes that would eliminate hostile workplace conditions. Policy changes that are often suggested include instituting professional EDIA training for the team and/or for team leadership, instituting and following a code of conduct [9], including more interactive group activities in group meetings, etc. Training and information on EDIA is available for all members of the planetary science community. The first place to look would be in your University or Institution’s EDIA or human resources offices. Bystander Intervention is often offered as part of other meetings [10]. A newer offering is a Workshop on EDIA for Leaders in Planetary Science led by Julie Rathbun (first author of this abstract) and JA Grier (https://edialps.psi.edu/). This 3-day workshop gives participants the tools they need to enact positive change in their personal and professional spheres. The first workshop was help in November 2022 and another workshop will take place in the late spring 2023 with exact dates to be announced soon.

J. A. Rathbun↗
NASA NTRS1994

A low-cost transportable ground station for capture and processing of direct broadcast EOS satellite data

The Earth Observing System (EOS), part of a cohesive national effort to study global change, will deploy a constellation of remote sensing spacecraft over a 15 year period. Science data from the EOS spacecraft will be processed and made available to a large community of earth scientists via NASA institutional facilities. A number of these spacecraft are also providing an additional interface to broadcast data directly to users. Direct broadcast of real-time science data from overhead spacecraft has valuable applications including validation of field measurements, planning science campaigns, and science and engineering education. The success and usefulness of EOS direct broadcast depends largely on the end-user cost of receiving the data. To extend this capability to the largest possible user base, the cost of receiving ground stations must be as low as possible. To achieve this goal, NASA Goddard Space Flight Center is developing a prototype low-cost transportable ground station for EOS direct broadcast data based on Very Large Scale Integration (VLSI) components and pipelined, multiprocessing architectures. The targeted reproduction cost of this system is less than $200K. This paper describes a prototype ground station and its constituent components.

Davis, Don↗
NASA NTRS2016

Laboratory Testing and Performance Verification of the CHARIS Integral Field Spectrograph

The Coronagraphic High Angular Resolution Imaging Spectrograph (CHARIS) is an integral field spectrograph (IFS) that has been built for the Subaru telescope. CHARIS has two imaging modes; the high-resolution mode is R82, R69, and R82 in J, H, and K bands respectively while the low-resolution discovery mode uses a second low-resolution prism with R19 spanning 1.15-2.37 microns (J+H+K bands). The discovery mode is meant to augment the low inner working angle of the Subaru Coronagraphic Extreme Adaptive Optics (SCExAO) adaptive optics system, which feeds CHARIS a coronagraphic image. The goal is to detect and characterize brown dwarfs and hot Jovian planets down to contrasts five orders of magnitude dimmer than their parent star at an inner working angle as low as 80 milliarcseconds. CHARIS constrains spectral crosstalk through several key aspects of the optical design. Additionally, the repeatability of alignment of certain optical components is critical to the calibrations required for the data pipeline. Specifically the relative alignment of the lens let array, prism, and detector must be highly stable and repeatable between imaging modes. We report on the measured repeatability and stability of these mechanisms, measurements of spectral crosstalk in the instrument, and the propagation of these errors through the data pipeline. Another key design feature of CHARIS is the prism, which pairs Barium Fluoride with Ohara L-BBH2 high index glass. The dispersion of the prism is significantly more uniform than other glass choices, and the CHARIS prisms represent the first NIR astronomical instrument that uses L-BBH2as the high index material. This material choice was key to the utility of the discovery mode, so significant efforts were put into cryogenic characterization of the material. The final performance of the prism assemblies in their operating environment is described in detail. The spectrograph is going through final alignment, cryogenic cycling, and is being delivered to the Subaru telescope in April 2016. This paper is a report on the laboratory performance of the spectrograph, and its current status in the commissioning process so that observers will better understand the instrument capabilities. We will also discuss the lessons learned during the testing process and their impact on future high-contrast imaging spectrographs for wavefront control.

Coronagraphic High Angular Resolution Imaging Spec↗
NASA NTRS2008

NASA Tech Briefs, March 2008

Topics covered include: WRATS Integrated Data Acquisition System; Breadboard Signal Processor for Arraying DSN Antennas; Digital Receiver Phase Meter; Split-Block Waveguide Polarization Twist for 220 to 325 GHz; Nano-Multiplication-Region Avalanche Photodiodes and Arrays; Tailored Asymmetry for Enhanced Coupling to WGM Resonators; Disabling CNT Electronic Devices by Use of Electron Beams; Conical Bearingless Motor/Generators; Integrated Force Method for Indeterminate Structures; Carbon-Nanotube-Based Electrodes for Biomedical Applications; Compact Directional Microwave Antenna for Localized Heating; Using Hyperspectral Imagery to Identify Turfgrass Stresses; Shaping Diffraction-Grating Grooves to Optimize Efficiency; Low-Light-Shift Cesium Fountain without Mechanical Shutters; Magnetic Compensation for Second-Order Doppler Shift in LITS; Nanostructures Exploit Hybrid-Polariton Resonances; Microfluidics, Chromatography, and Atomic-Force Microscopy; Model of Image Artifacts from Dust Particles; Pattern-Recognition System for Approaching a Known Target; Orchestrator Telemetry Processing Pipeline; Scheme for Quantum Computing Immune to Decoherence; Spin-Stabilized Microsatellites with Solar Concentrators; Phase Calibration of Antenna Arrays Aimed at Spacecraft; Ring Bus Architecture for a Solid-State Recorder; and Image Compression Algorithm Altered to Improve Stereo Ranging.

Source record↗
NASA NTRS2016

Reaching the Diffraction Limit - Differential Speckle and Wide-Field Imaging for the WIYN Telescope

Speckle imaging allows telescopes to achieve diffraction limited imaging performance. The technique requires cameras capable of reading out frames at a very fast rate, effectively 'freezing out' atmospheric seeing. The resulting speckles can be correlated and images reconstructed that are at the diffraction limit of the telescope. These new instruments are based on the successful performance and design of the Differential Speckle Survey Instrument (DSSI).The instruments are being built for the Gemini-N and WIYN telescopes and will be made available to the community via the peer review proposal process. We envision their primary use to be validation and characterization of exoplanet targets from the NASA, K2 and TESS missions and RV discovered exoplanets. Such targets will provide excellent follow-up candidates for both the WIYN and Gemini telescopes. We expect similar data quality in speckle imaging mode with the new instruments. Additionally, both cameras will have a wide-field mode and standard SDSS filters. They will be highly versatile instruments and it is that likely many other science programs will request time on the cameras. The limiting magnitude for speckle observations will remain around 13-14th at WIYN and 16-17th at Gemini, while wide-field, normal CCD imaging operation should be able to go to much fainter, providing usual CCD imaging and photometric capabilities. The instruments will also have high utility as scoring cameras for telescope engineering purposes, or other applications where high time resolution is needed. Instrument support will be provided, including a software pipeline that takes raw speckle data to fully reconstructed images.

detector↗
NASA NTRS2016

Reaching the Diffraction Limit - Differential Speckle and Wide-Field Imaging for the Gemini-N Telescope

Speckle imaging allows telescopes to achieve di raction limited imaging performance. The technique requires cameras capable of reading out frames at a very fast rate, e ectively `freezing out' atmospheric seeing. The resulting speckles can be correlated and images reconstructed that are at the di raction limit of the telescope. These new instruments are based on the successful performance and design of the Di erential Speckle Survey Instrument (DSSI) [2, 1]. The instruments are being built for the Gemini-N and WIYN telescopes and will be made available to the community via the peer review proposal process. We envision their primary use to be validation and characterization of exoplanet targets from the NASA K2 and TESS missions and RV discovered exoplanets. Such targets will provide excellent follow-up candidates for both the WIYN and Gemini telescopes [3]. Examples of DSSI data are shown in the gures below. We expect similar data quality in speckle imaging mode with the new instruments. Additionally, both cameras will have a wide- eld mode and standard SDSS lters. They will be highly versatile instruments and it is that likely many other science programs will request time on the cameras. The limiting magnitude for speckle observations, will remain around 13-14th at WIYN and 16-17th at Gemini, while wide- eld, normal CCD imaging operation should be able to go to much fainter, providing usual CCD imaging and photometric capabilities. The instruments will also have high utility as scoring cameras for telescope engineering purposes, or other applications where high time resolution is needed. Instrument support will be provided, including a software pipeline that takes raw speckle data to fully reconstructed images.

Gemini-N↗
NASA NTRSDate not supplied

Benchmarking Computational Tools for Calling SNPs and Indels in Complex Microbial Populations

The NASA BioNutrients missions seek to understand the suitability of microorganisms for bioproduction during space flight. One topic of interest is the stability of microbial genomes during long-term ambient storage and subsequent rehydration and growth. To address these questions, samples from 8 species were flown to ISS for 5 years of desiccated storage at ambient temperature (Stasis Packs) and 2 species were packaged along with powdered media inside a bioreactor system to allow hydration and growth in microgravity (Production Packs). For both systems, Whole Genome Sequencing (WGS) of the DNA extracted from the returned samples and paired ground controls will be conducted to identify changes in genome stability due to time, storage conditions and growth in space. Across the technical replicates, ground controls, 10 timepoints, and multiple experimental conditions, ~300 samples have been selected for initial analysis with WGS sequencing to 100x coverage. A flexible and resource efficient mutation calling pipeline is needed to process this large dataset and allow for comparisons between species. Many bioinformatics tools for calling Indels and Single Nucleotide Variants (SNVs) are designed for use with pure isolates, where true variations from the reference genome are expected to dominate the reads aligning to the location of mutation. In contrast, DNA from the Stasis Pack (SP) samples was collected directly after recovery from desiccated storage and the Production Pack (PP) samples were collected after fermentation. In this context, reads with mutations are expected to be less frequent than reads that align with the reference genome, as each sample will include multiple lines of cells. Thus, BioNutrients samples are expected to be similar to samples from cancer cell or “pooled” sequencing approaches. In preparation for the analysis of the BioNutrients samples, we have tested three mutation calling tools (GATK for Microbes, BreSeq and DiscoSNP) designed for complex samples. A challenge of validating mutation identification pipelines is a lack of “Ground Truth” datasets, especially for complex samples. To compare these three tools, we sought to identify mutations in pre-existing WGS data collected from populations of Chlamydomonas reinhardtii that were exposed to UV mutagenesis and growth in LEO as part of the Space Algae-1 mission. Here we present a summary of these tools against the analysis originally conducted using the CRISP tool. Critical metrics are compared such as runtime, the number of SNPs, the number and size of Indels, and patterns of transversion and transitions identified by each tool are reported. By sharing these benchmarking results collected in support of the BioNutrients mission, we aim to guide others seeking to identify SNVs in similarly complex microbial samples.

Biology↗
NASA NTRSDate not supplied

Bionutrients-1: Utilizing Genomics and Transcriptomics to Assess the Reliability of Microorganisms for In Situ Nutrient Production on Long Duration Missions

The resupply of current long-duration crewed missions to the ISS relies on ground-launched supplies. As NASA looks toward Mars, ground-based resupply will no longer be an option. Critical nutrients, including vitamin C, vitamin K, folate, and thiamin, degrade during long-term storage, and regular consumption of these nutrients is essential for astronaut health. Another challenge of current food systems is the difficulty of consuming sufficient calories when subsisting on the limited flavors of freeze-dried food, which can lead to weight loss. The inclusion of microorganism-based food systems could alleviate both concerns. For example, the fermentation of rehydrated milk into yogurt with microorganisms genetically incorporating genes to produce critical vitamins would allow for both in situ production of nutrients and a fresh food product with additional flavor profiles. In comparison to plant food production, microorganisms require less flight infrastructure. The BioNutrients-1 mission is demonstrating viability of microbial fermentation food production in microgravity and testing the reliability of this approach for long-duration missions lacking resupply. While the BioNutrients-1 mission includes the collection of multiple phenotypic measurements, this status update will focus on the processing of samples for genomics and transcriptomics analyses as well as the planned analysis pipelines. First, the BioNutrients-1 mission seeks to identify microorganisms capable of surviving long-duration storage at ambient temperatures while maintaining genetic fidelity. To achieve this, nine commonly employed microbial species were stored at ambient temperatures in Stasis Packs on the ISS for five years. The viability and mutation rates will be measured at multiple time points for both flown and ground control samples. From an omics perspective, the changes in the bulk rates of point mutations and genetic rearrangements across the Stasis Pack species during the five years of storage will be determined, providing valuable insights into the potential of these microorganisms for long-duration space missions. Second, the BioNutrients-1 mission is characterizing the impact of microgravity on fermentation. Two strains of the yeast Saccharomyces cerevisiae, each encoding antioxidants (β-carotene or zeaxanthin) were flown to ISS for storage and fermentation within simplified bioreactors (Production Packs). The impact of microgravity on the expression of the antioxidant production genes and general metabolic genes will be determined using RNA sequencing. Ultimately, the transcriptome data will be compared to phenotypic measurements, such as the antioxidant yield, end-state biomass, and the production of EtOH, to determine the impacts of microgravity and long-term storage on microbial fermentation. The findings from this research will be instrumental in understanding the challenges and opportunities of microorganism-based food systems in space missions.

BioNutrients↗
NASA NTRS2002

An End-to-End Architecture for Science Goal Driven Observing

New observatories will have greater on-board storage capacity and on-board processing capabilities. The new bottleneck will be download capacity. The cost of downlink time and limitations of bandwidth will end the era where all exposure data is downloaded and all data processing is performed on the ground. In addition, observing campaigns involving inherently variable targets will need scheduling flexibility to focus observing time and data download on exposures that are scientifically interesting. The ability to quickly recognize and react to such events by re-prioritizing the observing schedule will be an essential characteristic for maximizing scientific returns. It will also be a step towards increasing spacecraft autonomy, a major goal of NASA's strategic plan. The science goal monitoring (SGM) system is a proof-of-concept effort to address these challenges. We are developing an interactive distributed system that will use on-board processing and storage combined with event-driven interfaces with ground-based processing and operations, to enable fast re-prioritization of observing schedules, and to minimize time spent on non-optimized observations. SGM is initially aimed towards time-tagged observing modes used frequently in spectroscopic studies of varying targets. In particular, the SGM is collaborating with the proposed MIDEX-class mission Kronos team. The variable targets that Kronos seeks to study make an adaptive system such as SGM particularly valuable for achieving mission goals. However, the architecture and interfaces will also be designed for easy adaptability to other observing platforms, including ground-based systems and to work with different scheduling and pipeline processing systems. This talk will focus on our strategy for developing SGM and the technical challenges that we have encountered. We will discuss the SGM architecture as it applies to the Kronos mission and explain how it is scalable to other missions.

Jones, Jeremy↗