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Elevating the Quality of Space Omics Sequencing Data: Innovations and Methodologies from NASA GeneLab Sample Processing Laboratory

NASA’s GeneLab, part of the NASA Open Science Data Repository, is a space-related database that hosts a diverse range of transcriptomics, proteomics, epigenomics and genomics data. The NASA GeneLab Sample Processing Laboratory (SPL) generates omics data from biological experiments conducted aboard the International Space Station, Space Shuttle and space related ground experiments, this omics data then hosted on the GeneLab repository. Samples generated such experiments pose numerous technical challenges such as small experimental sample size, variance in dissection times, limited tissue preservation methods, prolonged storage time, and more. GeneLab SPL team had developed specialized expertise in nucleic acid extraction, library preparation and sequencing of such biological samples via extensive training and years of experience. In order to ensure data accuracy and consistency across experiments, SPL has developed standardized protocols for each species and tissue type. These protocols in conjunction with quality control metrics and data standards are crucial in generating of high-quality data. SPL protocols and standards have been developed in collaboration with the scientific community and had been made publicly available on the GeneLab portal, guaranteeing comparability of datasets across spaceflight experiments. To ensure reliability of data generation, SPL leverages cutting-edge innovations in laboratory automation for sample processing. By leveraging these state-of-the-art platforms, SPL achieves high levels of data reproducibility while significantly minimizing sources of bias and variability, especially across experiments with large numbers of samples. Over the past few years, the space biology investigator community has accessed SPL-generated data from the Open Science Data Repository for a myriad of data re-analysis and re-use studies. We observe a trend that in-house SPL-generated data consistently outperforms outsourced sequencing data in terms of technical standards, quality control metrics, timeliness of data delivery, and sequencing and reagent efficiency. Superior data generation has and will continue to enable discoveries in disease, diagnostic tools, and the biological effects of long duration spaceflight.

GeneLab↗

NASA NTRS2002

From Field to Laboratory: A New Database Approach for Linking Microbial Field Ecology with Laboratory Studies

The Ames Exobiology Culture Collection Database (AECC-DB) has been developed as a collaboration between microbial ecologists and information technology specialists. It allows for extensive web-based archiving of information regarding field samples to document microbial co-habitation of specific ecosystem micro-environments. Documentation and archiving continues as pure cultures are isolated, metabolic properties determined, and DNA extracted and sequenced. In this way metabolic properties and molecular sequences are clearly linked back to specific isolates and the location of those microbes in the ecosystem of origin. Use of this database system presents a significant advancement over traditional bookkeeping wherein there is generally little or no information regarding the environments from which microorganisms were isolated. Generally there is only a general ecosystem designation (i.e., hot-spring). However within each of these there are a myriad of microenvironments with very different properties and determining exactly where (which microenvironment) a given microbe comes from is critical in designing appropriate isolation media and interpreting physiological properties. We are currently using the database to aid in the isolation of a large number of cyanobacterial species and will present results by PI's and students demonstrating the utility of this new approach.

Bebout, Leslie↗

NASA NTRS1988

Electronic data generation and display system

The Electronic Data Generation and Display System (EDGADS) is a field tested paperless technical manual system. The authoring provides subject matter experts the option of developing procedureware from digital or hardcopy inputs of technical information from text, graphics, pictures, and recorded media (video, audio, etc.). The display system provides multi-window presentations of graphics, pictures, animations, and action sequences with text and audio overlays on high resolution color CRT and monochrome portable displays. The database management system allows direct access via hierarchical menus, keyword name, ID number, voice command or touch of a screen pictoral of the item (ICON). It contains operations and maintenance technical information at three levels of intelligence for a total system.

Wetekamm, Jules↗

NASA NTRS2012

Sub-Audible Speech Recognition Based upon Electromyographic Signals

Method and system for processing and identifying a sub-audible signal formed by a source of sub-audible sounds. Sequences of samples of sub-audible sound patterns ("SASPs") for known words/phrases in a selected database are received for overlapping time intervals, and Signal Processing Transforms ("SPTs") are formed for each sample, as part of a matrix of entry values. The matrix is decomposed into contiguous, non-overlapping two-dimensional cells of entries, and neural net analysis is applied to estimate reference sets of weight coefficients that provide sums with optimal matches to reference sets of values. The reference sets of weight coefficients are used to determine a correspondence between a new (unknown) word/phrase and a word/phrase in the database.

Jorgensen, Charles C.↗

NASA NTRS1998

The Deontic Transaction Model in Multi-Agent Normative Systems

In the area of multi-agent systems, much research is devoted to the coordination of the agents. There exist several issues, two of which are summarized. The first is that, although agents are said to be autonomous, they always react in a predictable way to each message, and they cannot decide to violate the conventions that are hard-wired into the protocol. In fact, there might be circumstances in which the agent violates a convention in order to realize a private goal that it considers to be more important. Another issue is that, if the protocols that agents use to react to the environment are fixed, they have no way to respond to changes. However, an important characteristic of agents is that they eon react to a changing environment. Although transaction models ([BOH92], [GR93]) evolved from the database domain, they establish a general execution paradigm that ideally covers all the subsystems invoked in a sequence of transactions. So transaction models apply to multi-agent systems. Recently, some research has been devoted to overcoming the limitations of the traditional transaction models which are suitable for conventional systems and focus on system integrity, e,g., [SJ97]. Here we solve above issues by turning to a deontic concept: obligation. In multi-agent systems, agents interact with each other according to norms, We use deontic logic ([And58], [Aqv84], [B C96], [JS94], [MW93]) to model norms. Here the norms prescribe how the agents ought to behave, but-- and this is essential-- they do not exclude the possibility of "bad" behavior (i.e., the actual behavior may deviate from the ideal), and so they also prescribe what should be done in circumstances of norm violation. Thus, we propose a new approach --- a deontic transaction model for multi-agent normative systems. Our approach improves the protocol of "abort/commit" of traditional transaction models to a protocol of "abort/exception/commit". In multi-agent normative systems, we can see the violation of a norm as an exception and how the other agents react to the violation as exception handling. This paper concentrates on our formal model.

Huang, Yonghua↗

NASA NTRS2014

Monitoring with Data Automata

We present a form of automaton, referred to as data automata, suited for monitoring sequences of data-carrying events, for example emitted by an executing software system. This form of automata allows states to be parameterized with data, forming named records, which are stored in an efficiently indexed data structure, a form of database. This very explicit approach differs from other automaton-based monitoring approaches. Data automata are also characterized by allowing transition conditions to refer to other parameterized states, and by allowing transitions sequences. The presented automaton concept is inspired by rule-based systems, especially the Rete algorithm, which is one of the well-established algorithms for executing rule-based systems. We present an optimized external DSL for data automata, as well as a comparable unoptimized internal DSL (API) in the Scala programming language, in order to compare the two solutions. An evaluation compares these two solutions to several other monitoring systems.

log analysis↗

NASA NTRS2005

Designing and Implementing a Distributed System Architecture for the Mars Rover Mission Planning Software (Maestro)

Distributed systems allow scientists from around the world to plan missions concurrently, while being updated on the revisions of their colleagues in real time. However, permitting multiple clients to simultaneously modify a single data repository can quickly lead to data corruption or inconsistent states between users. Since our message broker, the Java Message Service, does not ensure that messages will be received in the order they were published, we must implement our own numbering scheme to guarantee that changes to mission plans are performed in the correct sequence. Furthermore, distributed architectures must ensure that as new users connect to the system, they synchronize with the database without missing any messages or falling into an inconsistent state. Robust systems must also guarantee that all clients will remain synchronized with the database even in the case of multiple client failure, which can occur at any time due to lost network connections or a user's own system instability. The final design for the distributed system behind the Mars rover mission planning software fulfills all of these requirements and upon completion will be deployed to MER at the end of 2005 as well as Phoenix (2007) and MSL (2009).

Goldgof, Gregory M.↗

NASA NTRS1994

The design and implementation of EPL: An event pattern language for active databases

The growing demand for intelligent information systems requires closer coupling of rule-based reasoning engines, such as CLIPS, with advanced data base management systems (DBMS). For instance, several commercial DBMS now support the notion of triggers that monitor events and transactions occurring in the database and fire induced actions, which perform a variety of critical functions, including safeguarding the integrity of data, monitoring access, and recording volatile information needed by administrators, analysts, and expert systems to perform assorted tasks; examples of these tasks include security enforcement, market studies, knowledge discovery, and link analysis. At UCLA, we designed and implemented the event pattern language (EPL) which is capable of detecting and acting upon complex patterns of events which are temporally related to each other. For instance, a plant manager should be notified when a certain pattern of overheating repeats itself over time in a chemical process; likewise, proper notification is required when a suspicious sequence of bank transactions is executed within a certain time limit. The EPL prototype is built in CLIPS to operate on top of Sybase, a commercial relational DBMS, where actions can be triggered by events such as simple database updates, insertions, and deletions. The rule-based syntax of EPL allows the sequences of goals in rules to be interpreted as sequences of temporal events; each goal can correspond to either (1) a simple event, or (2) a (possibly negated) event/condition predicate, or (3) a complex event defined as the disjunction and repetition of other events. Various extensions have been added to CLIPS in order to tailor the interface with Sybase and its open client/server architecture.

Giuffrida, G.↗

NASA NTRS2002

Planetary and Stellar Data Products Expected From The Kepler Mission

The Kepler Mission is a Discovery-class mission scheduled to be launched in the 2006-2007 time frame. It is a wide field of view photometer with a 95 m aperture designed to attain a photometric precision of 2 parts in 10^5 for the 12th magnitude stars. It will continually observe 100,000 main-sequence stars from 9th to 14th magnitude for a period of four years with a cadence of 4/hour. This database should be unique in its photometric precision, cadence, and duration of observations. Several hundred terrestrial-size planets will be detected if they are common around solar-like stars. Based on the current results of Doppler-velocity searches, over a thousand giant planets will also be found. A guest investigator program is planned that would provide the opportunity to observe thousands of other objects in the 105 square degree FOV. Such objects could include stars with micro-variability, other intrinsic variables, cataclysmic variables, eclipsing binaries (including x-ray binaries), and possibly AGN. A ground-based program to classify all 225,000 stars in the FOV and to do a detailed examination of a subset of the stars that show planetary companions is planned. Doppler-velocity observations will be made to find the presence of giant planets not seen in transit. The data will be rapidly released to the community for follow up observations and for changes to the guest investigator program.

Borucki, W. J.↗

NASA NTRS2011

Common Bolted Joint Analysis Tool

Common Bolted Joint Analysis Tool (comBAT) is an Excel/VB-based bolted joint analysis/optimization program that lays out a systematic foundation for an inexperienced or seasoned analyst to determine fastener size, material, and assembly torque for a given design. Analysts are able to perform numerous what-if scenarios within minutes to arrive at an optimal solution. The program evaluates input design parameters, performs joint assembly checks, and steps through numerous calculations to arrive at several key margins of safety for each member in a joint. It also checks for joint gapping, provides fatigue calculations, and generates joint diagrams for a visual reference. Optimum fastener size and material, as well as correct torque, can then be provided. Analysis methodology, equations, and guidelines are provided throughout the solution sequence so that this program does not become a "black box:" for the analyst. There are built-in databases that reduce the legwork required by the analyst. Each step is clearly identified and results are provided in number format, as well as color-coded spelled-out words to draw user attention. The three key features of the software are robust technical content, innovative and user friendly I/O, and a large database. The program addresses every aspect of bolted joint analysis and proves to be an instructional tool at the same time. It saves analysis time, has intelligent messaging features, and catches operator errors in real time.

Imtiaz, Kauser↗

NASA NTRS1993

An on-line expert system for diagnosing environmentally induced spacecraft anomalies using CLIPS

A new rule-based, expert system for diagnosing spacecraft anomalies is under development. The knowledge base consists of over two-hundred rules and provide links to historical and environmental databases. Environmental causes considered are bulk charging, single event upsets (SEU), surface charging, and total radiation dose. The system's driver translates forward chaining rules into a backward chaining sequence, prompting the user for information pertinent to the causes considered. The use of heuristics frees the user from searching through large amounts of irrelevant information (varying degrees of confidence in an answer) or 'unknown' to any question. The expert system not only provides scientists with needed risk analysis and confidence estimates not available in standard numerical models or databases, but it is also an effective learning tool. In addition, the architecture of the expert system allows easy additions to the knowledge base and the database. For example, new frames concerning orbital debris and ionospheric scintillation are being considered. The system currently runs on a MicroVAX and uses the C Language Integrated Production System (CLIPS).

Lauriente, Michael↗

NASA NTRS2005

Explore Full Range of QSO/AGN Properties

The goal of the proposal is to perform ISO spectroscopic studies, including data analysis and modeling, of star formation regions using an ensemble of archival space-based data from the Infrared Space Observatory s Long Wavelength Spectrometer and Short Wavelength Spectrometer, but including as well some other spectroscopic databases. Four kinds of regions are considered in the studies: (1) disks around more evolved objects; (2) young, low or high mass pre-main sequence stars in star formation regions; (3) star formation in external, bright IR galaxies; and (4) the galactic center. One prime focus of the program is the OH lines in the far infrared. The program had the following goals: 1) Refine the data analysis of IS0 observations to obtain deeper and better SNR results on selected sources. The IS0 data itself underwent "pipeline 10" reductions in early 2001, and additional "hands-on data reduction packages" were supplied by the IS0 teams in 2001. The Fabry-Perot database is particularly sensitive to noise and slight calibration errors. 2) Model the atomic and molecular line shapes, in particular the OH lines, using revised monte- carlo techniques developed by the SWAS team at the Center for Astrophysics; 3) Attend scientific meetings and workshops; 4) Do E&PO activities related to infrared astrophysics and/or spectroscopy.

Oliversen, Ronald↗

NASA NTRS2003

ISO Key Project: Exploring the Full Range of Quasar/Agn Properties

While most of the work on this program has been completed, as previously reported, the portion of the program dealing with the subtopic of ISO LWS data analysis and reduction for the LWS Extragalactic Science Team and its leader, Dr. Howard Smith, is still active. This program in fact continues to generate results, and newly available computer modeling has extended the value of the datasets. As a result the team requests a one-year no-cost extension to this program, through 31 December 2004. The essence of the proposal is to perform ISO spectroscopic studies, including data analysis and modeling, of star-formation regions using an ensemble of archival space-based data from the Infrared Space Observatory's Long Wavelength Spectrometer and Short Wavelength Spectrometer, but including as well some other spectroscopic databases. Four kinds of regions are considered in the studies: (1) disks around more evolved objects; (2) young, low or high mass pre-main sequence stars in star-formation regions; (3) star formation in external, bright IR galaxies; and (4) the galactic center. One prime focus of the program is the OH lines in the far infrared. The program has the following goals: 1) Refine the data analysis of ISO observations to obtain deeper and better SNR results on selected sources. The ISO data itself underwent 'pipeline 10' reductions in early 2001, and additional 'hands-on data reduction packages' were supplied by the ISO teams in 2001. The Fabry-Perot database is particularly sensitive to noise and slight calibration errors; 2) Model the atomic and molecular line shapes, in particular the OH lines, using revised Monte-Carlo techniques developed by the SWAS team at the Center for Astrophysics; 3) Attend scientific meetings and workshops; 4) Perform E&PO activities related to infrared astrophysics and/or spectroscopy.

Wilkes, Belinda↗

NASA NTRS2022

GRC MILab Software: Quick Start Guide

This document provides detailed installation and operating instructions for the GRC MILab Excel Add-In software developed at the NASA Glenn Research Center. The software described has been implemented to facilitate the process of importing into Microsoft Excel and analyzing materials test data from a wide range of materials tests. All resulting data is then ready for automated upload to the relevant table of the GRC Materials Intelligence (MI) database. This new software represents an update to the original MILab software developed by Granta Design Ltd.—a company specializing in materials software, data, and databases—for members of the Materials Data Management Consortium (MDMC), a collaboration between Granta, ASM International, NASA Glenn, and several other materials-oriented corporations and government agencies in the aerospace and defense industries. The updated software consists of the addition of two test type modules, the Generic and Generic Cyclic modules, with both representing a generalization of the original software. The Generic module supports the import and analysis of multiaxial data from any sequence of tensile, compression, relaxation, and/or creep test stages; and the Generic Cyclic module expands the functionality to include repeated sequences during cyclic testing. During processing, all imported data and analysis results are formatted by the software so as to be ready for immediate automated upload to the MI database, ensuring minimal overhead on the part of the user and access to persistent and reliable data for all relevant personnel.

Quick Start Guide↗

NASA NTRS2010

Systems Maintenance Automated Repair Tasks (SMART)

SMART is a uniform automated discrepancy analysis and repair-authoring platform that improves technical accuracy and timely delivery of repair procedures for a given discrepancy (see figure a). SMART will minimize data errors, create uniform repair processes, and enhance the existing knowledge base of engineering repair processes. This innovation is the first tool developed that links the hardware specification requirements with the actual repair methods, sequences, and required equipment. SMART is flexibly designed to be useable by multiple engineering groups requiring decision analysis, and by any work authorization and disposition platform (see figure b). The organizational logic creates the link between specification requirements of the hardware, and specific procedures required to repair discrepancies. The first segment in the SMART process uses a decision analysis tree to define all the permutations between component/ subcomponent/discrepancy/repair on the hardware. The second segment uses a repair matrix to define what the steps and sequences are for any repair defined in the decision tree. This segment also allows for the selection of specific steps from multivariable steps. SMART will also be able to interface with outside databases and to store information from them to be inserted into the repair-procedure document. Some of the steps will be identified as optional, and would only be used based on the location and the current configuration of the hardware. The output from this analysis would be sent to a work authoring system in the form of a predefined sequence of steps containing required actions, tools, parts, materials, certifications, and specific requirements controlling quality, functional requirements, and limitations.

Schuh, Joseph↗

NASA NTRS2005

Conservative Patch Algorithm and Mesh Sequencing for PAB3D

A mesh-sequencing algorithm and a conservative patched-grid-interface algorithm (hereafter Patch Algorithm ) have been incorporated into the PAB3D code, which is a computer program that solves the Navier-Stokes equations for the simulation of subsonic, transonic, or supersonic flows surrounding an aircraft or other complex aerodynamic shapes. These algorithms are efficient, flexible, and have added tremendously to the capabilities of PAB3D. The mesh-sequencing algorithm makes it possible to perform preliminary computations using only a fraction of the grid cells (provided the original cell count is divisible by an integer) along any grid coordinate axis, independently of the other axes. The patch algorithm addresses another critical need in multi-block grid situation where the cell faces of adjacent grid blocks may not coincide, leading to errors in calculating fluxes of conserved physical quantities across interfaces between the blocks. The patch algorithm, based on the Stokes integral formulation of the applicable conservation laws, effectively matches each of the interfacial cells on one side of the block interface to the corresponding fractional cell area pieces on the other side. This approach is comprehensive and unified such that all interface topology is automatically processed without user intervention. This algorithm is implemented in a preprocessing code that creates a cell-by-cell database that will maintain flux conservation at any level of full or reduced grid density as the user may choose by way of the mesh-sequencing algorithm. These two algorithms have enhanced the numerical accuracy of the code, reduced the time and effort for grid preprocessing, and provided users with the flexibility of performing computations at any desired full or reduced grid resolution to suit their specific computational requirements.

Pao, S. P.↗

NASA NTRS2018

Monitoring Astronaut Health with DNA Sequencing

In recent years microbe a plethora of microbe populations have been identified onboard the ISS (International Space Station). Approaches for real-time tracking of microbes for routine housekeeping and food/water safety monitoring will be critical for mission safety and crew health on future longer duration missions to the Moon or Mars. This work is a proof-of-concept study demonstrating an end-to-end phylogenetic identification and full genome sequencing effort of multiple microbial populations. Our methodology utilized the ISS flight-certified WetLab-2 molecular toolbox and the Biomolecule Sequencer projects for real-time end-to-end on-orbit microbial biological samples processing and molecular analysis with real time results generated utilizing only field "offline" analytic software. For this experiment we colony-cultured several ISS isolated microorganisms before generation of the pre-sequencing library via the automated VolTRAX device which enabled high library turnover with little wet-bench activity or potential future costly astronaut time. The pre-sequencing library is diluted in loading buffer and injected into the MinION sample port, drawn into the nanopore window by capillary action, and sequenced using the MinKnown. 16S and full genome alignment, nucleotide matching, gene identification, and phylogenetic sorting was accomplished utilizing the Epi2me software and the offline NCBI Blast viral, microbiome, and human somatic databases. In short, the methodologies developed herein replace the myriad of specific, often highly targeted microbiological tests used in the clinical laboratory, which would be difficult if not impossible to currently implement aboard the ISS or in deep space, with a single metagenomics test.

genomics↗

NASA NTRS2002

Infrared Spectroscopy of Star Formation in Galactic and Extragalactic Regions

This report details work done in a project involving spectroscopic studies, including data analysis and modeling, of star-formation regions using an ensemble of archival space-based data including some from the Infrared Space Observatory's Long Wavelength Spectrometer and Short Wavelength Spectrometer, and other spectroscopic databases. We will include four kinds of regions: (1) disks around more evolved objects; (2) young, low or high mass pre-main sequence stars in star-formation regions; (3) star formation in external, bright IR (infrared) galaxies; and (4) the galactic center. During this period, work proceeded fully on track and on time. Details on workshops and conferences attended and research results are presented. A preprint article entitled 'The Far Infrared Lines of OH as Molecular Cloud Diagnostics' is included as an appendix.

Smith, Howard A.↗