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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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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly

Abstract Background Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large sequencing and assembly initiatives for generation of de novo assemblies in non-model organisms. Though adapter contamination filtering is routine in traditional short-read analysis pipelines, it has not been widely adopted for HiFi workflows. Results Analysis of 55 publicly available HiFi datasets revealed that a read-sanitation step to remove sequence artifacts derived from PacBio library preparation from read pools is necessary as adapter sequences can be erroneously integrated into assemblies. Conclusions Here we describe the nature of adapter contaminated reads, their consequences in assembly, and present HiFiAdapterFilt, a simple and memory efficient solution for removing adapter contaminated reads prior to assembly.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2002

THz frequency receiver instrumentation for Herschel's Heterodyne Instrument for Far Infrared (HIFI)

The Heterodyne Instrument for Far Infrared (HIFI) on ESA's Herschel Space Observatory is comprised of five SIS receiver channels covering 480-1250 GHz and two HEB receiver channels covering 1410-1910 GHz. The NASA developed components represent a significant advancement in the available performance. The current state of the art for each of these devices is presented along with a programmatic view of the development effort.

heterodyne↗
NASA NTRS1990

The Hawaii Imaging Fabry-Perot Interferometer (HIFI)

At Mauna Kea Observatory, researchers conducted optical, imaging spectrophotometric studies of selected active galaxies using both the Canada-France-Hawaii 3.6m and University of Hawaii 2.2m telecopes (Tully, Bland and Cecil 1988). To maximize spatial resolution, researchers select galaxies independent of luminosity but known to possess interesting morphologies or high-velocity, extranuclear ionized gas (Walker 1968; Rubin and Ford 1968). They study both the large-scale patterns produced in IR-luminous, starburst systems (e.g., M82, NGC 253, NGC 6240) and those with compact, but spatially extended, circumnuclear, narrow line regions (e.g., M51, NGC 1068, NGC 4151). Current studies are restricted to the optical (SII), (NII) and (OIII) lines and the brightest Balmer recombination lines. These lines are, in principle, sufficient to constrain the dynamical structure and dominant excitation mechanism of the ionized component.

Bland, Jonathan↗
NASA NTRS1998

Development and Testing of Automatically Generated ACS Flight Software for the MAP Spacecraft

By integrating the attitude determination and control system (ACS) analysis and design, flight software development, and flight software testing processes, it is possible to improve the overall spacecraft development cycle, as well as allow for more thorough software testing. One of the ways to achieve this integration is to use code-generation tools to automatically generate components of the ACS flight software directly from a high-fidelity (HiFi) simulation. In the development of the Microwave Anisotropy Probe (MAP) spacecraft, currently underway at the NASA Goddard Space Flight Center, approximately 1/3 of the ACS flight software was automatically generated. In this paper, we will examine each phase of the ACS subsystem and flight software design life cycle: analysis, design, and testing. In the analysis phase, we scoped how much software we would automatically generate and created the initial interface. The design phase included parallel development of the HiFi simulation and the hand-coded flight software components. Everything came together in the test phase, in which the flight software was tested, using results from the HiFi simulation as one of the bases of comparison for testing. Because parts of the spacecraft HiFi simulation were converted into flight software, more care needed to be put into its development and configuration control to support both the HiFi simulation and flight software. The components of the HiFi simulation from which code was generated needed to be designed based on the fact that they would become flight software. This process involved such considerations as protecting against mathematical exceptions, using acceptable module and parameter naming conventions, and using an input/output interface compatible with the rest of the flight software. Maintaining good configuration control was an issue for the HiFi simulation and the flight software, and a way to track the two systems was devised. Finally, an integrated test approach was devised to support flight software testing at both the unit- and build-test levels using the HiFi simulation to generate data for performance verification. Another benefit of the simulation and code-generation application used on the MAP project is that it supported bringing flight software and test data into the HiFi simulation environment. It was possible to integrate parts of the hand-coded flight software into the HiFi simulation, and also possible to import flight software test data for comparison and performance verification. This capability was used to incorporate the flight software Kalman filter into the HiFi simulation. This enabled us to greatly increase the amount of testing that could be done on the filter, because we could exert a greater degree of control over the software-only simulation than over the flight software test environment. Also, since the simulation could be used to run the Kalman filter faster than real time, our testing efficiency was greatly increased. We will conclude our discussion with a summary of the lessons learned thus far using automatically- generated code for the MAP project, and the spacecraft status as we work towards our scheduled launch in the year 2000.

ODonnell, James R., Jr.↗
DOE OSTI2024

Evaluating the mutagenicity of N-nitrosodimethylamine in 2D and 3D HepaRG cell cultures using error-corrected next generation sequencing

Human liver-derived metabolically competent HepaRG cells have been successfully employed in both two-dimensional (2D) and 3D spheroid formats for performing the comet assay and micronucleus (MN) assay. In the present study, we have investigated expanding the genotoxicity endpoints evaluated in HepaRG cells by detecting mutagenesis using two error-corrected next generation sequencing (ecNGS) technologies, Duplex Sequencing (DS) and High-Fidelity (HiFi) Sequencing. Both HepaRG 2D cells and 3D spheroids were exposed for 72 h to N-nitrosodimethylamine (NDMA), followed by an additional incubation for the fixation of induced mutations. NDMA-induced DNA damage, chromosomal damage, and mutagenesis were determined using the comet assay, MN assay, and ecNGS, respectively. The 72-h treatment with NDMA resulted in concentration-dependent increases in cytotoxicity, DNA damage, MN formation, and mutation frequency in both 2D and 3D cultures, with greater responses observed in the 3D spheroids compared to 2D cells. The mutational spectrum analysis showed that NDMA induced predominantly A:T → G:C transitions, along with a lower frequency of G:C → A:T transitions, and exhibited a different trinucleotide signature relative to the negative control. These results demonstrate that the HepaRG 2D cells and 3D spheroid models can be used for mutagenesis assessment using both DS and HiFi Sequencing, with the caveat that severe cytotoxic concentrations should be avoided when conducting DS. With further validation, the HepaRG 2D/3D system may become a powerful human-based metabolically competent platform for genotoxicity testing.

3D spheroids↗
NASA NTRS2001

Using Automation to Improve the Flight Software Testing Process

One of the critical phases in the development of a spacecraft attitude control system (ACS) is the testing of its flight software. The testing (and test verification) of ACS flight software requires a mix of skills involving software, attitude control, data manipulation, and analysis. The process of analyzing and verifying flight software test results often creates a bottleneck which dictates the speed at which flight software verification can be conducted. In the development of the Microwave Anisotropy Probe (MAP) spacecraft ACS subsystem, an integrated design environment was used that included a MAP high fidelity (HiFi) simulation, a central database of spacecraft parameters, a script language for numeric and string processing, and plotting capability. In this integrated environment, it was possible to automate many of the steps involved in flight software testing, making the entire process more efficient and thorough than on previous missions. In this paper, we will compare the testing process used on MAP to that used on previous missions. The software tools that were developed to automate testing and test verification will be discussed, including the ability to import and process test data, synchronize test data and automatically generate HiFi script files used for test verification, and an automated capability for generating comparison plots. A summary of the perceived benefits of applying these test methods on MAP will be given. Finally, the paper will conclude with a discussion of re-use of the tools and techniques presented, and the ongoing effort to apply them to flight software testing of the Triana spacecraft ACS subsystem.

ODonnell, James R., Jr.↗
NASA NTRS2001

Using Automation to Improve the Flight Software Testing Process

One of the critical phases in the development of a spacecraft attitude control system (ACS) is the testing of its flight software. The testing (and test verification) of ACS flight software requires a mix of skills involving software, knowledge of attitude control, and attitude control hardware, data manipulation, and analysis. The process of analyzing and verifying flight software test results often creates a bottleneck which dictates the speed at which flight software verification can be conducted. In the development of the Microwave Anisotropy Probe (MAP) spacecraft ACS subsystem, an integrated design environment was used that included a MAP high fidelity (HiFi) simulation, a central database of spacecraft parameters, a script language for numeric and string processing, and plotting capability. In this integrated environment, it was possible to automate many of the steps involved in flight software testing, making the entire process more efficient and thorough than on previous missions. In this paper, we will compare the testing process used on MAP to that used on other missions. The software tools that were developed to automate testing and test verification will be discussed, including the ability to import and process test data, synchronize test data and automatically generate HiFi script files used for test verification, and an automated capability for generating comparison plots. A summary of the benefits of applying these test methods on MAP will be given. Finally, the paper will conclude with a discussion of re-use of the tools and techniques presented, and the ongoing effort to apply them to flight software testing of the Triana spacecraft ACS subsystem.

ODonnell, James R., Jr.↗
NASA NTRS2002

The Maneuver Planning Process for the Microwave Anisotropy Probe (MAP) Mission

The Microwave Anisotropy Probe (MAP) was successfully launched from Kennedy Space Center's Eastern Range on June 30, 2001. MAP will measure the cosmic microwave background as a follow up to NASA's Cosmic Background Explorer (COBE) mission from the early 1990's. MAP will take advantage of its mission orbit about the Sun-Earth/Moon L2 Lagrangian point to produce results with higher resolution, sensitivity, and accuracy than COBE. A strategy comprising highly eccentric phasing loops with a lunar gravity assist was utilized to provide a zero-cost insertion into a lissajous orbit about L2. Maneuvers were executed at the phasing loop perigees to correct for launch vehicle errors and to target the lunar gravity assist so that a suitable orbit at L2 was achieved. This paper will discuss the maneuver planning process for designing, verifying, and executing MAP's maneuvers. A discussion of the tools and how they interacted will also be included. The maneuver planning process was iterative and crossed several disciplines, including trajectory design, attitude control, propulsion, power, thermal, communications, and ground planning. Several commercial, off-the-shelf (COTS) packages were used to design the maneuvers. STK/Astrogator was used as the trajectory design tool. All maneuvers were designed in Astrogator to ensure that the Moon was met at the correct time and orientation to provide the energy needed to achieve an orbit about L2. The Mathworks Matlab product was used to develop a tool for generating command quaternions. The command quaternion table (CQT) was used to drive the attitude during the perigee maneuvers. The MatrixX toolset, originally written by Integrated Systems, Inc., now distributed by Mathworks, was used to create HiFi, a high fidelity simulator of the MAP attitude control system. HiFi was used to test the CQT and to make sure that all attitude requirements were met during the maneuver. In addition, all ACS data plotting and output were generated in MatrixX. A final test used FlatSat, a real-time hardware-in-the-loop simulator, which used identical MAP flight code to simulate operations on the spacecraft. Simulations in FlatSat allowed the MAP team to verify maneuver commands, timing, and spacecraft configuration before the commands were sent up to the spacecraft for execution. The MAP maneuver team successfully pieced together all of these COTS tools for designing MAP's maneuvers and MAP is now collecting data at L2.

Mesarch, Michael A.↗