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NASA NTRSDate not supplied

Optimizing a Small RNAseq Analysis Pipeline for NASA GeneLab Using Open-Source Tools and Libraries

Small RNA sequencing (small RNAseq) is a powerful tool for studying the regulation of gene expression in various organisms. Small RNAseq has been leveraged in space biology research to study how expression of small RNAs, e.g. micro RNAs (miRNAs), small interfering RNAs (siRNAs), and piwi-interacting RNAs (piRNAs), change upon exposure to the space environment. NASA GeneLab currently hosts small RNAseq raw data derived from space-relevant experiments on the Open Science Data Repository (OSDR). To maximize the accessibility of these data to the scientific community, in addition to hosting raw data, which is only interpretable by bioinformaticians, GeneLab plans to process all small RNAseq datasets and make those processed data available to the scientific community via the OSDR. In this study, we present the development of the GeneLab standardized pipeline for processing small RNAseq datasets. Using human, plant, and synthetic small RNAseq datasets, we interrogate various open-source software and publicly available databases to evaluate their accuracy and reproducibility in each step of the pipeline. For quality control and adapter detection and trimming, we evaluated TrimGalore!, FASTX, SeqKit, and DNApi methods to optimize alignment to reference genomes. We compared BWA, Bowtie, and Bowtie2 to determine the optimal alignment tool. For each alignment tool we also assessed various reference databases, including Ensembl reference genomes and different types of small RNA reference databases, including genome, hairpin, and miRNA references from the miRbase and MirGeneDB databases. To quantify the aligned data, we compared SAMtools, HTSeq, and RSEM for counting alignment events from each alignment tool used. Finally, we evaluated various tools, including DESeq2 and EdgeR, for data normalization and subsequent differential expression analysis. We will present the results from our comparative analyses for each pipeline step and propose a consensus pipeline for processing small RNAseq data derived from various organisms exposed to the space environment.

SmallRNAseq, NASA GeneLab, quality control, adapte↗

DOE OSTI2026

Exploring Sustainability in Scientific Software through Code Quality & Test Coverage Metrics

Context: Scientific open-source software (SciOSS) plays a foundational role in research and engineering, yet its long-term sustainability has often been overlooked and remains a significant concern. Objective: This study investigates the long-term sustainability of SciOSS through code and test quality metrics. Method: We analyze CASS Software Portfolio projects, classifying them by sustainability and comparing their code structure, test coverage, and links between code quality and testing across the dataset. Results: Sustainable projects show higher, more consistent test coverage and clearer code-test correlations, while unsustainable ones show weaker patterns. Overall, test coverage is low in scientific software, and high complexity and coupling reduce testability. Conclusion: In this study, we present a practical, data-driven approach for assessing sustainability in scientific software, offering a foundation for evaluating long-term software health and supporting future efforts in quality assurance and sustainability monitoring.

Md mushfiqur rahman, Sheikh [University of Tenness↗

NASA NTRS2021

On-demand Command and Control of ASTERIA with Cloud-based Ground Station Services

ASTERIA (Arcsecond Space Telescope Enabling Research in Astrophysics) was a 6-unit CubeSat technology demonstration mission that deployed from the International Space Station on November 20th, 2017. After successfully completing its 90-day primary mission that demonstrated arcsecond-level line-of-sight pointing and focal plane thermal stability for exoplanet detection, it entered an extended mission performing onboard software demonstrations to mature technology both in space and on the ground. One of the technologies was a completely cloud-based ground system leveraging Amazon Web Services (AWS) Ground Station service.Announced in December 2018 and launched in May 2019, AWS Ground Station is a fully managed ground station service that aims to reduce the overhead associated with developing and maintaining ground system infrastructure throughout the mission lifecycle. AWS Ground Station makes available the suite of features required for any ground system in support of low-Earth orbit (LEO) and medium-Earth Orbit (MEO) satellite operations on-demand and without setting up or maintaining long-term contracts. Charges are incurred on a per-minute basis for antenna usage during scheduled tracks. Support is available for S-band uplink and downlink, along with X-band narrowband and wideband downlink. Missions that use the service may reserve tracks with any licensed AWS Ground Station antennas located across each service region and have direct access to any AWS services in support of mission operations.The cloud-based architecture built around the AWS Ground Station service greatly enhanced ASTERIA mission operations by enabling end-to-end pass automation, on-demand contact scheduling and contingency planning, along with more efficient data downlink through station availability and station-to-station handovers. It incorporated open-source software, particularly NASA's AMMOS Instrument Toolkit (AIT) and Open Mission Control Technologies (OpenMCT), along with the AWS application programming interfaces (API) to the Ground Station, Elastic Compute Cloud (EC2) and Simple Storage Service (S3) services. After showcasing operability in August 2019, the team continued using and improving this novel ground system architecture until the end of mission in December 2019. This paper describes the cloud-based ground system, how it was designed, tested, and evaluated with an in-orbit spacecraft, the operational capabilities that it enabled, along with lessons learned and recommendations for future missions.

Fesq, Lorraine↗

NASA NTRS2021

On-demand Command and Control of ASTERIA with Cloud-based Ground Station Services

ASTERIA (Arcsecond Space Telescope Enabling Research in Astrophysics) was a 6-unit CubeSat technology demonstration mission that deployed from the International Space Station on November 20th, 2017. After successfully completing its 90-day primary mission that demonstrated arcsecond-level line-of-sight pointing and focal plane thermal stability for exoplanet detection, it entered an extended mission performing onboard software demonstrations to mature technology both in space and on the ground. One of the technologies was a completely cloud-based ground system leveraging Amazon Web Services (AWS) Ground Station service. Announced in December 2018 and launched in May 2019, AWS Ground Station is a fully managed ground station service that aims to reduce the overhead associated with developing and maintaining ground system infrastructure throughout the mission lifecycle. AWS Ground Station makes available the suite of features required for any ground system in support of low-Earth orbit (LEO) and medium-Earth Orbit (MEO) satellite operations on-demand and without setting up or maintaining long-term contracts. Charges are incurred on a per-minute basis for antenna usage during scheduled tracks. Support is available for S-band uplink and downlink, along with X-band narrowband and wideband downlink. Missions that use the service may reserve tracks with any licensed AWS Ground Station antennas located across each service region and have direct access to any AWS services in support of mission operations. The cloud-based architecture built around the AWS Ground Station service greatly enhanced ASTERIA mission operations by enabling end-to-end pass automation, on-demand contact scheduling and contingency planning, along with more efficient data downlink through station availability and station-tostation handovers. It incorporated open-source software, particularly NASA's AMMOS Instrument Toolkit (AIT) and Open Mission Control Technologies (OpenMCT), along with the AWS application programming interfaces (API) to the Ground Station, Elastic Compute Cloud (EC2) and Simple Storage Service (S3) services. After showcasing operability in August 2019, the team continued using and improving this novel ground system architecture until the end of mission in December 2019. This paper describes the cloud-based ground system, how it was designed, tested, and evaluated with an inorbit spacecraft, the operational capabilities that it enabled, along with lessons learned and recommendations for future missions.

Fesq, Lorraine↗

NASA NTRS2020

DHMx (Digital Holographic Microscope Experience) Software Tool

The DHMx (Digital Holographic Microscope Experience) is an open-source software suite designed to perform reconstructions from off-axis holograms obtained from either a real-time stream or from disk with a graphical interface for commanding and display

Fregoso, S. Felipe↗

NASA NTRS2017

UAV Inspection of Electrical Transmission Infrastructure with Path Conformance Autonomy and Lidar-Based Geofences NASA Report on UTM Reference Mission Flights at Southern Company Flights November 2016

Flights at low altitudes in close proximity to electrical transmission infrastructure present serious navigational challenges: GPS and radio communication quality is variable and yet tight position control is needed to measure defects while avoiding collisions with ground structures. To advance unmanned aerial vehicle (UAV) navigation technology while accomplishing a task with economic and societal benefit, a high voltage electrical infrastructure inspection reference mission was designed. An integrated air-ground platform was developed for this mission and tested in two days of experimental flights to determine whether navigational augmentation was needed to successfully conduct a controlled inspection experiment. The airborne component of the platform was a multirotor UAV built from commercial off-the-shelf hardware and software, and the ground component was a commercial laptop running open source software. A compact ultraviolet sensor mounted on the UAV can locate 'hot spots' (potential failure points in the electric grid), so long as the UAV flight path adequately samples the airspace near the power grid structures. To improve navigation, the platform was supplemented with two navigation technologies: lidar-to-polyhedron preflight processing for obstacle demarcation and inspection distance planning, and trajectory management software to enforce inspection standoff distance. Both navigation technologies were essential to obtaining useful results from the hot spot sensor in this obstacle-rich, low-altitude airspace. Because the electrical grid extends into crowded airspaces, the UAV position was tracked with NASA unmanned aerial system traffic management (UTM) technology. The following results were obtained: (1) Inspection of high-voltage electrical transmission infrastructure to locate 'hot spots' of ultraviolet emission requires navigation methods that are not broadly available and are not needed at higher altitude flights above ground structures. (2) The sensing capability of a novel airborne UV detector was verified with a standard ground-based instrument. Flights with this sensor showed that UAV measurement operations and recording methods are viable. With improved sensor range, UAVs equipped with compact UV sensors could serve as the detection elements in a self-diagnosing power grid. (3) Simplification of rich lidar maps to polyhedral obstacle maps reduces data volume by orders of magnitude, so that computation with the resultant maps in real time is possible. This enables real-time obstacle avoidance autonomy. Stable navigation may be feasible in the GPS-deprived environment near transmission lines by a UAV that senses ground structures and compares them to these simplified maps. (4) A new, formally verified path conformance software system that runs onboard a UAV was demonstrated in flight for the first time. It successfully maneuvered the aircraft after a sudden lateral perturbation that models a gust of wind, and processed lidar-derived polyhedral obstacle maps in real time. (5) Tracking of the UAV in the national airspace using the NASA UTM technology was a key safety component of this reference mission, since the flights were conducted beneath the landing approach to a heavily used runway. Comparison to autopilot tracking showed that UTM tracking accurately records the UAV position throughout the flight path.

Moore, Andrew J.↗

NASA NTRSDate not supplied

NASA CARA Tools

The NASA Conjunction Assessment Risk Analysis (CARA) team has created and posted to GitHub a set of MATLAB software tools for collision assessment (CA) analysis. The software is provided to the public under a NASA Open-Source Software Agreement and is maintained/updated by the CARA Analysis team. Capabilities provided within the toolset include algorithms in assessing probability of collision (Pc), collision consequence, covariance realism, Orbit Determination (OD) quality assessment, and single covariance max Pc. Additionally, a set of utilities are provided for astrodynamics topics closely related to CA, such as: Conjunction Data Message (CDM) parsing, covariance transformations, coordinate system transformations, etc. The repository is regularly updated on a monthly basis and new functionality will be added as algorithms are approved for public release. This presentation will provide a brief introduction to the toolset, highlight some of the key components which can be used in operations, and will present information on algorithms that are in the release pipeline and can be expected soon. This software will enable operators to independently perform CA calculations using the same core algorithms that CARA uses in operations.

L. Baars↗

NASA NTRSDate not supplied

NASA CARA Tools

Luis Baars↗

NASA NTRS2011

The New Meteor Radar at Penn State: Design and First Observations

In an effort to provide new and improved meteor radar sensing capabilities, Penn State has been developing advanced instruments and technologies for future meteor radars, with primary objectives of making such instruments more capable and more cost effective in order to study the basic properties of the global meteor flux, such as average mass, velocity, and chemical composition. Using low-cost field programmable gate arrays (FPGAs), combined with open source software tools, we describe a design methodology enabling one to develop state-of-the art radar instrumentation, by developing a generalized instrumentation core that can be customized using specialized output stage hardware. Furthermore, using object-oriented programming (OOP) techniques and open-source tools, we illustrate a technique to provide a cost-effective, generalized software framework to uniquely define an instrument s functionality through a customizable interface, implemented by the designer. The new instrument is intended to provide instantaneous profiles of atmospheric parameters and climatology on a daily basis throughout the year. An overview of the instrument design concepts and some of the emerging technologies developed for this meteor radar are presented.

Urbina, J.↗

NASA NTRS2003

Developing an Open Source Option for NASA Software

We present arguments in favor of developing an Open Source option for NASA software; in particular we discuss how Open Source is compatible with NASA's mission. We compare and contrast several of the leading Open Source licenses, and propose one - the Mozilla license - for use by NASA. We also address some of the related issues for NASA with respect to Open Source. In particular, we discuss some of the elements in the External Release of NASA Software document (NPG 2210.1A) that will likely have to be changed in order to make Open Source a reality withm the agency.

Moran, Patrick J.↗

NASA NTRSDate not supplied

Emulation of Core Flight System Applications for Flight Software Development and Validation

The Mars Sample Return (MSR) campaign is an unprecedented attempt in the return of Martian samples back to Earth. The ascent from the surface will be performed by the Mars Ascent Vehicle (MAV), a critical element in the mission that National Aeronautics and Space Administration (NASA) Marshall Space Flight Center (MSFC) is developing. To this end, innovations in flight software development, verification, and validation are occurring. The MAV flight computer will run Core Flight System (cFS), an open-source software environment developed by NASA Goddard Space Flight Center (GSFC). NASA Marshall’s MAV Mission and Fault Management (M&FM) Team has implemented an emulation of two applications of this architecture: Limit Checker and Stored Command. Using an emulation of the functionalities of these applications allows for rapid prototyping of table-based algorithms. Further, M&FM is leveraging an in-house, low-fidelity but high-throughput State Analysis Model (SAM), an integrated MATLAB Stateflow Plant and Software model. This model is run in parallel with the cFS emulation for full flyout testing of the M&FM algorithms, verification of intent of these algorithms, and for future auto-generation of application-ingestible M&FM tables. The tables can then be delivered to the MAV Flight Software (FSW) team in a seamless process, reducing the cost of traditional FSW development and the risk of starting M&FM FSW development at later points in the NASA program life cycle.

Cody Wheeler↗

NASA NTRSDate not supplied

Emulation of Core Flight System Applications for Flight Software Development and Validation

Cody Wheeler↗

NASA NTRS2007

NASA's Core Trajectory Sub-System Project: Using JBoss Enterprise Middleware for Building Software Systems Used to Support Spacecraft Trajectory Operations

NASA's Johnson Space Center (JSC) / Flight Design and Dynamics Division (DM) has prototyped the use of Open Source middleware technology for building its next generation spacecraft mission support system. This is part of a larger initiative to use open standards and open source software as building blocks for future mission and safety critical systems. JSC is hoping to leverage standardized enterprise architectures, such as Java EE, so that its internal software development efforts can be focused on the core aspects of their problem domain. This presentation will outline the design and implementation of the Trajectory system and the lessons learned during the exercise.

Stensrud, Kjell C.↗

NASA NTRS2011

DAQ: Software Architecture for Data Acquisition in Sounding Rockets

A multithreaded software application was developed by Jet Propulsion Lab (JPL) to collect a set of correlated imagery, Inertial Measurement Unit (IMU) and GPS data for a Wallops Flight Facility (WFF) sounding rocket flight. The data set will be used to advance Terrain Relative Navigation (TRN) technology algorithms being researched at JPL. This paper describes the software architecture and the tests used to meet the timing and data rate requirements for the software used to collect the dataset. Also discussed are the challenges of using commercial off the shelf (COTS) flight hardware and open source software. This includes multiple Camera Link (C-link) based cameras, a Pentium-M based computer, and Linux Fedora 11 operating system. Additionally, the paper talks about the history of the software architecture's usage in other JPL projects and its applicability for future missions, such as cubesats, UAVs, and research planes/balloons. Also talked about will be the human aspect of project especially JPL's Phaeton program and the results of the launch.

Ahmad, Mohammad↗

NASA NTRS2018

A GNSS Receiver for Small-Sats Enabling Precision POD, Radio Occultations and Reflections

A low cost, low power, and low mass GNSS receiver (called Cion) has been developed and is currently flying on the CICERO cubesats. The receiver was designed in less than a year by JPL for Tyvak and GeoOptics for use in the GeoOptics CICERO constellation and leverages 25 years of JPL GNSS reciever design experience. Cion uses a commercial off-the-shelf (COTS) computer along with existing space qualified RF down-converters, software, and firmware to produce atmospheric Radio Occultation (RO) data. By combining a FPGA with dual core ARM processor and an embedded system controller, the Xilinx Zynq processor is an enabling technology that provides a customizable digital signal processing platform integrated into the computer (System on a chip) and enables off-the-shelf hardware to become the main engine behind this software defined radio. Using Linux for the on-board computer allows for fast development times and liberal use of existing open source software libraries. The parts of the receiver that require realtime implementation are performed in the Field Programmable Gate Array (FPGA), which can also be reprogrammed in flight. While the Zynq is not rad hard, the silicon on insulator (SOI) technology is rad tolerant ‘by accident’, allowing for its use in many space-based applications. Early results show that the Cion is working as designed, has demonstrated the first known GLONASS occultations, and obtains high quality atmospheric profiles with excellent lower troposphere penetration (near Earth’s surface).

Young, Larry↗

DOE OSTI2024

Development of Real-Time High-Density Pulsar Data Transmission and Processing for Grid Synchronization

Taking advantage of the extreme stability of the pulsar period, it can serve as the timing source for grid synchronization to compensate for the timing drift instigated by the loss of GPS signal. Nevertheless, the real-time transmission and processing of the pulsar data suffer from its high-frequency data rate, varying from megahertz to gigahertz, resulting in reduced computing speed and increased time delay. To mitigate this issue, the hardware and software frameworks are implemented for the high-density pulsar data transmission and processing for grid synchronization in this research. Initially, the high-density pulsar data is transferred using open-source software. The complementary duty cycle timing module is designed to coordinate the operation of the dual-channel high-speed interface and software. Subsequently, the multiple-threading is applied to the receiving, parsing, and splicing pulsar data. Next, the pulsar signal extraction method is implemented based on the polyphase filterbank and time of arrival estimation. Ultimately, real-time performance verification experiments are carried out for different components under two hardware platforms. Finally, the results demonstrate that only 0.482 s is required for processing 4 Gigabyte data through multiple-threading, which is 3.8 times faster than the single thread. The pulsar signal extraction can also be executed within 707 ms for 4.8 seconds of data, thereby indicating that real-time requirements can be met.

24 POWER TRANSMISSION AND DISTRIBUTION↗

NASA NTRS2014

Avionics Architectures for Exploration: Ongoing Efforts in Human Spaceflight

The field of Avionics is advancing far more rapidly in terrestrial applications than in spaceflight applications. Spaceflight Avionics are not keeping pace with expectations set by terrestrial experience, nor are they keeping pace with the need for increasingly complex automation and crew interfaces as we move beyond Low Earth Orbit. NASA must take advantage of the strides being made by both space-related and terrestrial industries to drive our development and sustaining costs down. This paper describes ongoing efforts by the Avionics Architectures for Exploration (AAE) project chartered by NASA's Advanced Exploration Systems (AES) Program to evaluate new avionic architectures and technologies, provide objective comparisons of them, and mature selected technologies for flight and for use by other AES projects. The AAE project team includes members from most NASA centers, and from industry. It is our intent to develop a common core avionic system that has standard capabilities and interfaces, and contains the basic elements and functionality needed for any spacecraft. This common core will be scalable and tailored to specific missions. It will incorporate hardware and software from multiple vendors, and be upgradeable in order to infuse incremental capabilities and new technologies. It will maximize the use of reconfigurable open source software (e.g., Goddard Space Flight Center's (GSFC's) Core Flight Software (CFS)). Our long-term focus is on improving functionality, reliability, and autonomy, while reducing size, weight, and power. Where possible, we will leverage terrestrial commercial capabilities to drive down development and sustaining costs. We will select promising technologies for evaluation, compare them in an objective manner, and mature them to be available for future programs. The remainder of this paper describes our approach, technical areas of emphasis, integrated test experience and results as of mid-2014, and future plans. As a part of the AES Program, we are encouraged to set aggressive goals and fall short if necessary, rather than to set our sights too low. We are also asked to emphasize providing our personnel with hands-on experience in development, integration, and testing. That we have embraced both of these philosophies will be evident in the descriptions below.

Goforth, Montgomery B.↗

NASA NTRSDate not supplied

Intercomparing Open Source Surface Water Extent Mapping Products & Software Packages

The open source revolution of Earth Observation (EO) science has resulted in increased openness of EO data, workflows to transform that data into end products (e.g. surface water extent maps), and the products themselves. However, this revolution has oversaturated decision-makers with products that can give conflicting results. Thus, it is increasingly crucial for scientists to communicate their methodologies and assumptions so scientific products can be used accurately. Recognizing this challenge, SERVIR – a joint initiative between NASA, USAID, and geospatial organizations in Asia, Africa, and Latin America – is conducting a regional intercomparison of open source surface water extent products and packages. SERVIR’s Hindu Kush Himalaya and Southeast Asia “hubs” have developed satellite-based surface water mapping services involving customizable code packages that are operationally run at each hub. These services are regionally and locally tailored to inform specific decisions and early actions. Conversely, the scientific community has released surface water products that are global or near-global, but are not customizable. These packages and products employ different methodologies and sensors, causing decision-makers to evaluate trade-offs related to physical sensor characteristics (e.g. spectral, temporal, and spatial resolution, and latency). We will discuss the tradeoffs, strengths, and weaknesses of the sensor characteristics and methodologies associated with each product/package, and provide preliminary results of a validation effort intercomparing products/packages for case studies in South and Southeast Asia. Understanding the strengths and weaknesses of these products is crucial in both the aftermath of a flood event and in preparing for future floods.

Micky Maganini↗