KBase Narrative - natrialba
The genome sequence revealed PHB synthase gene in Natrialba swarupiae. The genome-scale metabolic model was built based on the ModelSEED pipeline using the Build Metabolic Model App in KBase.
59 BASIC BIOLOGICAL SCIENCES↗
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Results for “Science Pipeline”
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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STEM Professional Development Program for Nuclear Security Science and Technology Consortium
This oral presentation captures the technical and developmental aspect of the program in support of UNLV. The goal of this project is to develop a steady pipeline of STEM educated professionals in area of national and international nuclear security. The goal is to train university students at NNSS laboratories in studies motivated by global nuclear security topics ranging from nuclear emergency response and management to physics experiments for stockpile stewardship program.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
Primary Mission Threshold Crossing Events in the TESS SPOC Transit Search
We present an overview of the single- and multiple-sector results of the Science Processing Operations Center (SPOC) transit search in the primary Transiting Exoplanet Survey Satellite (TESS) mission. TESS was designed to survey bright stars in the greater Solar neighborhood in search of transiting exoplanets. Data were acquired at a 2-minute cadence for 16,000-20,000 pre-selected target stars in each 28-day observation sector and processed in the SPOC pipeline at NASA Ames Research Center. The photometry pipeline produced a systematic error corrected light curve for each target star. Light curves were searched for transiting planet signatures by sector for all target stars, and separately for target stars observed in multiple sectors. Potential transit signals for which the transiting planet detection threshold was exceeded and a series of transit consistency tests were passed are referred to as Threshold Crossing Events (TCEs). We highlight the full TCE population and the population of SPOC TCEs that were later identified as TESS Objects of Interest (TOIs). Characteristics of the TCE populations implied by limb-darkened transiting planet model fits are also presented. SPOC pipeline data products are delivered to the Mikulski Archive for Space Telescopes (MAST)(http://archive.stsci.edu/missions-and-data/tess) for access by the community. Funding for the TESS Mission has been provided by the NASA Science Mission Directorate.
TESS↗
Dynamic Black-Level Correction and Artifact Flagging in the Kepler Data Pipeline
Instrument-induced artifacts in the raw Kepler pixel data include time-varying crosstalk from the fine guidance sensor (FGS) clock signals, manifestations of drifting moiré pattern as locally correlated nonstationary noise and rolling bands in the images which find their way into the calibrated pixel time series and ultimately into the calibrated target flux time series. Using a combination of raw science pixel data, full frame images, reverse-clocked pixel data and ancillary temperature data the Keplerpipeline models and removes the FGS crosstalk artifacts by dynamically adjusting the black level correction. By examining the residuals to the model fits, the pipeline detects and flags spatial regions and time intervals of strong time-varying blacklevel (rolling bands ) on a per row per cadence basis. These flags are made available to downstream users of the data since the uncorrected rolling band artifacts could complicate processing or lead to misinterpretation of instrument behavior as stellar. This model fitting and artifact flagging is performed within the new stand-alone pipeline model called Dynablack. We discuss the implementation of Dynablack in the Kepler data pipeline and present results regarding the improvement in calibrated pixels and the expected improvement in cotrending performances as a result of including FGS corrections in the calibration. We also discuss the effectiveness of the rolling band flagging for downstream users and illustrate with some affected light curves.
Clarke, B. D.↗
Corrosion of Zinc Cold Spray Coatings in a Wet Sweet and Sour Gas Environment
Internal corrosion is a problem for steel pipelines transporting natural gas or CO 2 containing water and partial pressures of H 2 S higher than 0.3 kPa (0.05 psi). This work aims to mitigate internal corrosion in steel pipelines transporting natural gas containing H 2 S using cold spray coatings. Two types of the cold spray binary metallic coatings (zinc chromium [ZnCr]. zinc niobium [ZnNb]) were studied using electrochemical techniques: potentiodynamic polarization, linear polarization resistance, and electrochemical impedance spectroscopy. The corrosion resistance of cold spray coatings (ZnCr, ZnNb) was evaluated in an environment containing 4 bar CO 2 pressure, simulating the partial pressures found in gas transmission lines over a solution of 3.5 wt% NaCl heated to 40°C. A concentration of 0.003 M Na 2 S 2 O 3 ·5H 2 O, corresponding to H 2 S partial pressures around 0.079 bar (1.146 psi), was used to simulate sour conditions. Postcorrosion surface characterization was performed using a scanning electron microscope (SEM) equipped with an energy-dispersive x-ray spectroscope (EDS) and x-ray diffraction analysis. The data showed that the presence of 0.003 M Na 2 S 2 O 3 ·5H 2 O shifted the corrosion potential to more anodic values and decreased the corrosion current density. Both coatings showed similar behavior after 1 h of exposure in the CO 2 /H 2 S environment, indicating that similar electrochemical reactions were occurring on ZnNb and ZnCr. SEM images and EDS surface analyses for specimens showed a significant change in the surface chemical composition of carbon steel coated with ZnNb and ZnCr after 24 h of immersion. In the presence of thiosulfate (under sour conditions), the formation of corrosion product layers (ZnCO 3 and ZnS) on top of ZnNb and ZnCr coatings increased their corrosion resistance, which helped to reduce their corrosion by a factor of 2. Under a sweet environment, the corrosion rates for steel coated with cold spray coatings after 14 d of exposure are lower than that for galvanized steel by a factor of 5 due to the ZnCO 3 layer formed on top of the coatings. The ZnCO 3 layer formed on the steel surface acts as a physical barrier against corrosion by blocking the diffusion of corrosive species to the surface. No localized attack was observed. ZnCr Cold spray coating with defect showed promising corrosion protection against CO 2 corrosion (sweet corrosion) after 14 d of exposure to a CO 2 environment. Here, the scratch on the coating simulated damage created in service, and it was deep enough to expose the substrate material (steel). The formation of zinc oxide (ZnO) and zinc carbonate (ZnCO 3 ) on the scratch confirmed the cathodic protection of the steel by ZnCr and ZnNb coatings.
36 MATERIALS SCIENCE↗
MetaboDirect: an analytical pipeline for the processing of FT-ICR MS-based metabolomic data
Background: Microbiomes are now recognized as the main drivers of ecosystem function ranging from the oceans and soils to humans and bioreactors. However, a grand challenge in microbiome science is to characterize and quantify the chemical currencies of organic matter (i.e., metabolites) that microbes respond to and alter. Critical to this has been the development of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), which has drastically increased molecular characterization of complex organic matter samples, but challenges users with hundreds of millions of data points where readily available, user-friendly, and customizable software tools are lacking. Results: Here, we build on years of analytical experience with diverse sample types to develop MetaboDirect, an open-source, command-line-based pipeline for the analysis (e.g., chemodiversity analysis, multivariate statistics), visualization (e.g., Van Krevelen diagrams, elemental and molecular class composition plots), and presentation of direct injection high-resolution FT-ICR MS data sets after molecular formula assignment has been performed. When compared to other available FT-ICR MS software, MetaboDirect is superior in that it requires a single line of code to launch a fully automated framework for the generation and visualization of a wide range of plots, with minimal coding experience required. Among the tools evaluated, MetaboDirect is also uniquely able to automatically generate biochemical transformation networks (ab initio) based on mass differences (mass difference network-based approach) that provide an experimental assessment of metabolite connections within a given sample or a complex metabolic system, thereby providing important information about the nature of the samples and the set of microbial reactions or pathways that gave rise to them. Finally, for more experienced users, MetaboDirect allows users to customize plots, outputs, and analyses. Conclusion: Application of MetaboDirect to FT-ICR MS-based metabolomic data sets from a marine phage-bacterial infection experiment and a Sphagnum leachate microbiome incubation experiment showcase the exploration capabilities of the pipeline that will enable the research community to evaluate and interpret their data in greater depth and in less time. It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User’s guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/), respectively.
54 ENVIRONMENTAL SCIENCES↗
GL4U: Using Space Biology Omics Data to Provide Bioinformatics Training for Students and Educators
NASA’s GeneLab project provides researchers open access to space-relevant multi-omics data via the Open Science Data Repository (OSDR) that can be mined to understand the effects of spaceflight on biological systems. To maximize the number of scientists who understand and utilize GeneLab data and data processing pipelines, GeneLab created GeneLab for Colleges and Universities (GL4U). GL4U provides space biology-relevant training in bioinformatics to the next generation of scientists through direct (training students) and indirect (training educators) approaches. The GL4U pilot programs were conducted in June 2021 (direct training) and 2022 (indirect training). During the pilots, students and educators at Historically Black Colleges and Universities (HBCUs) and Minority Serving Institutions (MSIs) participated in a week-long (direct training) or two-week-long (indirect training) bootcamp consisting of space biology-specific lectures and hands-on instruction using Jupyter Notebooks to analyze space biology RNA sequencing data from OSDR. During the educator pilot, participants received materials, training, and the necessary compute resources to enable them to run the bootcamp at their home institutions, thereby extending the reach of this initiative. In July 2023, GeneLab is partnering with JPL to expand GL4U to include amplicon sequencing (Amp-Seq) analysis training. During the GL4U Amp-Seq bootcamp, student and educator participants will receive training on how to analyze and interpret Amp-Seq data using the NASA GeneLab data processing pipeline. All bootcamp material, including instructions for requesting compute resources, will be made publicly available on GitHub for educators to teach the GL4U content in subsequent semesters. GL4U provides undergraduate students from underrepresented groups the opportunity to learn about NASA and Space Biology, and to enhance their career prospects by gaining hands-on experience analyzing omics data, a skillset that is highly applicable and marketable in the life sciences. We present results from pre- and post-training surveys completed by all participants of the Amp-Seq bootcamp.
Amanda M Saravia-Butler↗
Subsurface Mapping
Target areas for sinking base holes, underground pipelines, etc., can be identified with the assistance of NASA Ames developed technology, by Airborne Pipeline Services, Inc. Subsurface features are computer processed; the system can cover 250 miles a day and was first developed by Applied Science, Inc.
Source record↗
On the Accuracy of the ALMA Flux Calibration in the Time Domain and across Spectral Windows
A diverse array of science goals requires accurate flux calibration of observations with the Atacama Large Millimeter/submillimeter array (ALMA); however, this goal remains challenging due to the stochastic time-variability of the “grid” quasars ALMA uses for calibration. In this work, we use 343.5 GHz (Band 7) ALMA Atacama Compact Array observations of four bright and stable young stellar objects over seven epochs to independently assess the accuracy of the ALMA flux calibration and to refine the relative calibration across epochs. The use of these four extra calibrators allows us to achieve an unprecedented relative ALMA calibration accuracy of ~3%. On the other hand, when the observatory calibrator catalog is not up to date, the Band 7 data calibrated by the ALMA pipeline may have a flux calibration poorer than the nominal 10%, which can be exacerbated by weather-related phase decorrelation when self-calibration of the science target is either not possible or not attempted. We also uncover a relative flux calibration uncertainty between spectral windows of 0.8%, implying that measuring spectral indices within a single ALMA band is likely highly uncertain. We thus recommend various methods for science goals requiring high flux accuracy and robust calibration, in particular, the observation of additional calibrators combined with a relative calibration strategy, and observation of solar system objects for high absolute accuracy.
79 ASTRONOMY AND ASTROPHYSICS↗
The Nasa SRA Process as It Relates to Open-Source Workflows Developed for GeneLab Data Processing
To release open, standards-compliant processed data sets in the Open Science Data Repository (OSDR), the GeneLab Data Processing team works with the scientific community through the OSDR Analysis Working Groups to design and build open-source data processing pipelines. Once baselined internally, these pipelines are wrapped into workflows and published on the NASA GeneLab Data Processing public GitHub repository along with detailed instructions for installation and use. Each workflow must be approved through NASA's Software Release Authorization (SRA) process prior to publishing. However, the SRA process lacks sufficient documentation and clarity regarding which forms are applicable for new open-source software that utilizes publicly available 3rd party tools, and the SRA process can take several months to complete, making sharing software outside of NASA cumbersome and in contradiction with the concept of Open Science. Furthermore, the SRA process was designed as a one-size fits all approach and thus many of the questions asked are not applicable to our open-source workflows. Here we describe the software provided on the NASA GeneLab Data Processing GitHub repository, summarize our experiences with the SRA process to release these software, and propose a more stream-lined approach for review of open-source projects.
Software Release Authorization↗
The NASA SRA Process as it Relates to Open-Source Workflows Developed for GeneLab Data Processing
To release open, standards-compliant processed data sets in the Open Science Data Repository (OSDR), the GeneLab Data Processing team works with the scientific community through the OSDR Analysis Working Groups to design and build open-source data processing pipelines. Once baselined internally, these pipelines are wrapped into workflows and published on the NASA GeneLab Data Processing public GitHub repository along with detailed instructions for installation and use. Each workflow must be approved through NASA's Software Release Authorization (SRA) process prior to publishing. However, the SRA process lacks sufficient documentation and clarity regarding which forms are applicable for new open-source software that utilizes publicly available 3rd party tools, and the SRA process can take several months to complete, making sharing software outside of NASA cumbersome and in contradiction with the concept of Open Science. Furthermore, the SRA process was designed as a one-size fits all approach and thus many of the questions asked are not applicable to our open-source workflows. Here we describe the software provided on the NASA GeneLab Data Processing GitHub repository, summarize our experiences with the SRA process to release these software, and propose a more stream-lined approach for review of open-source projects.
Software Release Authorization↗
Framework for Integrating Science Data Processing Algorithms Into Process Control Systems
A software framework called PCS Task Wrapper is responsible for standardizing the setup, process initiation, execution, and file management tasks surrounding the execution of science data algorithms, which are referred to by NASA as Product Generation Executives (PGEs). PGEs codify a scientific algorithm, some step in the overall scientific process involved in a mission science workflow. The PCS Task Wrapper provides a stable operating environment to the underlying PGE during its execution lifecycle. If the PGE requires a file, or metadata regarding the file, the PCS Task Wrapper is responsible for delivering that information to the PGE in a manner that meets its requirements. If the PGE requires knowledge of upstream or downstream PGEs in a sequence of executions, that information is also made available. Finally, if information regarding disk space, or node information such as CPU availability, etc., is required, the PCS Task Wrapper provides this information to the underlying PGE. After this information is collected, the PGE is executed, and its output Product file and Metadata generation is managed via the PCS Task Wrapper framework. The innovation is responsible for marshalling output Products and Metadata back to a PCS File Management component for use in downstream data processing and pedigree. In support of this, the PCS Task Wrapper leverages the PCS Crawler Framework to ingest (during pipeline processing) the output Product files and Metadata produced by the PGE. The architectural components of the PCS Task Wrapper framework include PGE Task Instance, PGE Config File Builder, Config File Property Adder, Science PGE Config File Writer, and PCS Met file Writer. This innovative framework is really the unifying bridge between the execution of a step in the overall processing pipeline, and the available PCS component services as well as the information that they collectively manage.
Mattmann, Chris A.↗
A goldilocks computational protocol for inhibitor discovery targeting DNA damage responses including replication-repair functions
While many researchers can design knockdown and knockout methodologies to remove a gene product, this is mainly untrue for new chemical inhibitor designs that empower multifunctional DNA Damage Response (DDR) networks. Here, we present a robust Goldilocks (GL) computational discovery protocol to efficiently innovate inhibitor tools and preclinical drug candidates for cellular and structural biologists without requiring extensive virtual screen (VS) and chemical synthesis expertise. By computationally targeting DDR replication and repair proteins, we exemplify the identification of DDR target sites and compounds to probe cancer biology. Our GL pipeline integrates experimental and predicted structures to efficiently discover leads, allowing early-structure and early-testing (ESET) experiments by many laboratories. By employing an efficient VS protocol to examine protein-protein interfaces (PPIs) and allosteric interactions, we identify ligand binding sites beyond active sites, leveraging in silico advances for molecular docking and modeling to screen PPIs and multiple targets. A diverse 3,174 compound ESET library combines Diamond Light Source DSI-poised, Protein Data Bank fragments, and FDA-approved drugs to span relevant chemotypes and facilitate downstream hit evaluation efficiency for academic laboratories. Two VS per library and multiple ranked ligand binding poses enable target testing for several DDR targets. This GL library and protocol can thus strategically probe multiple DDR network targets and identify readily available compounds for early structural and activity testing to overcome bottlenecks that can limit timely breakthrough drug discoveries. By testing accessible compounds to dissect multi-functional DDRs and suggesting inhibitor mechanisms from initial docking, the GL approach may enable more groups to help accelerate discovery, suggest new sites and compounds for challenging targets including emerging biothreats and advance cancer biology for future precision medicine clinical trials.
59 BASIC BIOLOGICAL SCIENCES↗
Trust Not Verify? The Critical Need for Data Curation Standards in Materials Informatics
The importance of data curation has been recognized in multiple areas of research; however, the discussion of this important issue is only beginning to emerge in materials science. In this Perspective, we highlight the benefits of using the standardized data curation protocols in materials science and discuss current gaps in accurate and reproducible data reporting using case studies drawn from high-impact materials science papers and well-known databases such as the Crystallography Open Database (COD) and the Cambridge Structural Database (CSD). We argue that both experimental and computational materials scientists need to embrace a culture of rigorous data curation as part of modern research data management. We propose a sample data curation pipeline for materials chemistry and illustrate its use by creating two new materials chemistry databases. Here, we hope that this perspective will serve to catalyze further discussion and promote the continuous development of rigorous data curation practices within the materials science research community. We posit that adherence to best practices of data curation will promote and enhance the reliability, reproducibility, and integrity of materials research and enable the development of reliable AI and machine learning models that critically depend on the use of quality data.
Chemical structure↗
Feature Engineering and Ensemble Methods for Imbalanced ICS Intrusion Detection: Pipeline Audit and Constrained Evaluation
Industries are becoming increasingly connected and are more vulnerable to cyberattacks due to the widened attack surface. Industrial Control Systems (ICS) are among the most critical sectors that malicious actors can target, as such attacks can cause significant operational disruption and physical damage. It is imperative to detect such attacks as early as possible. This paper evaluates constraint-conditioned optimistic performance estimates for traditional ML models in ICS intrusion detection (i.e., estimates obtained under contiguous, non-shuffled temporal evaluation without test-set alteration, but with pre-split feature engineering that may introduce temporal leakage, due to dataset constraints). Our findings are threefold. First, we quantify how iterative feature engineering affects tree-based ensemble performance and examine how pipeline decisions (split strategy, sampling scope, and cleaning policy) can inflate or reduce reported IDS results under constraint-bound evaluation. Second, we compare intrinsic class-imbalance handling across ensemble models. Third, under our current pipeline constraints (including pre-split feature engineering), CatBoost achieves the best performance on Water Storage Tank (accuracy: 0.9831, class-1 F1: 0.9682), while Light- GBM achieves the best performance on Gas Pipeline (accuracy: 0.9618, class-1 F1: 0.9086).
97 MATHEMATICS AND COMPUTING↗
VA-Environmental Determinants of Health’s Software Pipeline Framework
In order to characterize US communities in terms of social and environmental determinants of health (EDH) that affect veterans, the Social and Environmental Determinants of Health (SEDH) project, a collaboration between the Veterans Affairs (VA) Social Department and the Oak Ridge National Laboratory (ORNL), aims to identify, extract, and prepare datasets that include community variables known to be associated with health outcomes in veterans. The EDH project's responsibilities include investigating SEDH data, providing technical documentation for SEDH datasets, and automating the download, extraction, and preparation of the data through the creation of a software pipeline framework.
54 ENVIRONMENTAL SCIENCES↗
Advances in S. cerevisiae Engineering for Xylose Fermentation and Biofuel Production: Balancing Growth, Metabolism, and Defense
Genetically engineering microorganisms to produce chemicals has changed the industrialized world. The budding yeast Saccharomyces cerevisiae is frequently used in industry due to its genetic tractability and unique metabolic capabilities. S. cerevisiae has been engineered to produce novel compounds from diverse sugars found in lignocellulosic biomass, including pentose sugars, like xylose, not recognized by the organism. Engineering high flux toward novel compounds has proved to be more challenging than anticipated since simply introducing pathway components is often not enough. Several studies show that the rewiring of upstream signaling is required to direct products toward pathways of interest, but doing so can diminish stress tolerance, which is important in industrial conditions. As an example of these challenges, we reviewed S. cerevisiae engineering efforts, enabling anaerobic xylose fermentation as a model system and showcasing the regulatory interplay’s controlling growth, metabolism, and stress defense. Enabling xylose fermentation in S. cerevisiae requires the introduction of several key metabolic enzymes but also regulatory rewiring of three signaling pathways at the intersection of the growth and stress defense responses: the RAS/PKA, Snf1, and high osmolarity glycerol (HOG) pathways. The current studies reviewed here suggest the modulation of global signaling pathways should be adopted into biorefinery microbial engineering pipelines to increase efficient product yields.
59 BASIC BIOLOGICAL SCIENCES↗
Workflows Community Summit 2022: A Roadmap Revolution
Scientific workflows have become integral tools in broad scientific computing use cases. Science discovery is increasingly dependent on workflows to orchestrate large and complex scientific experiments that range from the execution of a cloud-based data preprocessing pipeline to multi-facility instrument-to-edge-to-HPC computational workflows. Given the changing landscape of scientific computing (often referred to as a computing continuum) and the evolving needs of emerging scientific applications, it is paramount that the development of novel scientific workflows and system functionalities seek to increase the efficiency, resilience, and pervasiveness of existing systems and applications. Specifically, the proliferation of machine learning/artificial intelligence (ML/AI) workflows, need for processing large-scale datasets produced by instruments at the edge, intensification of near real-time data processing, support for long-term experiment campaigns, and emergence of quantum computing as an adjunct to HPC, have significantly changed the functional and operational requirements of workflow systems. Workflow systems now need to, for example, support data streams from the edge-to-cloud-to-HPC, enable the management of many small-sized files, allow data reduction while ensuring high accuracy, orchestrate distributed services (workflows, instruments, data movement, provenance, publication, etc.) across computing and user facilities, among others. Further, to accelerate science, it is also necessary that these systems implement specifications/standards and APIs for seamless (horizontal and vertical) integration between systems and applications, as well as enable the publication of workflows and their associated products according to the FAIR principles.
97 MATHEMATICS AND COMPUTING↗