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Results for “reproducible research”

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 163 records · Page 9

How life affects the geochemical cycle of carbon

Developing a quantitative understanding of the biogeochemical cycles of carbon as they have worked throughout Earth history on various time scales, how they have been affected by biological evolution, and how changes in the carbon content of ocean and atmosphere may have affected climate and the evolution of life are the goals of the research. Theoretical simulations were developed that can be tuned to reproduce such data as exist and, once tuned, can be used to predict properties that have not yet been observed. This is an ongoing process, in which models and results are refined as new data and interpretations become available and as understanding of the global system improves. Results of the research are described in several papers which were published or submitted for publication. These papers are summarized. Future research plans are presented.

Walker, James C. G.↗

Reproducibility in materials informatics: lessons from ‘A general-purpose machine learning framework for predicting properties of inorganic materials’

The integration of machine learning techniques in materials discovery has become prominent in materials science research and has been accompanied by an increasing trend towards open data and open-source tools to propel the field. Despite the increasing usefulness and capabilities of these tools, developers neglecting to follow reproducible practices presents a significant barrier for other researchers looking to use or build upon their work. In this study, we investigate the challenges encountered while attempting to reproduce a section of the results presented in “A general-purpose machine learning framework for predicting properties of inorganic materials.” Our analysis identifies four major categories of challenges: (1) reporting software dependencies, (2) recording and sharing version logs, (3) sequential code organization, and (4) clarifying code references within the manuscript. The result is a proposed set of tangible action items for those aiming to make material informatics tools accessible to, and useful for the community.

36 MATERIALS SCIENCE↗

Triboelectric Nanogenerator Repeatability and Reproducibility Study

The development of triboelectric nanogenerators (TENGs) has largely focused on optimizing output performance, often at the expense of other critical research considerations such as the development of reliable technical procedures. In particular, the reliability of reported results—specifically repeatability and reproducibility—remains underexplored and is frequently limited to brief discussion within available literature. Without rigorous validation through repeatability and reproducibility studies, the credibility and broader applicability of reported findings remain uncertain. This study addresses this gap by systematically evaluating the repeatability and reproducibility of TENG performance data. Five polymer materials—Kapton, polyethylene (PE), polyethylene terephthalate (PET), polytetrafluoroethylene (PTFE), and polyvinylidene fluoride (PVDF)—were investigated across all pairwise combinations of 25 total combinations for the reproducibility study and three selected pairs of the 25 samples were selected for the repeatability study. For each TENG pairing, we analyzed the methodology, experimental procedures, and resulting performance data to quantify consistency and reliability. The objective of this work is to assess the validity of the collected dataset and determine whether the observed performance trends are consistent for use in future TENG design and optimization studies. Establishing reliable and reproducible data is essential for advancing the development of high-output TENG systems and ensuring their dependable implementation in practical applications.

36 MATERIALS SCIENCE↗

Current status and future outlook for patient‐derived cancer models from a rare cancer research perspective

Abstract Rare cancers are a group of approximately 200 malignancies with extremely low incidences and with a wide variety of genotypes and phenotypes. Collectively, they are more common than any single malignancy. However, given the small numbers of individuals diagnosed with rare cancers, it is difficult to design clinical trials with sufficient patient numbers. Therefore, few effective anticancer drugs have been developed, and evidence‐based medicine is not always feasible for rare cancers. Consequently, their clinical outcomes are generally poorer. Cancer research requires adequate models that faithfully recapitulate molecular features and reproduce treatment responses of the original tumors. Such models allow us to focus on more efficacious drugs in the clinical studies. For rare cancers, patient‐derived cancer models are particularly important because the enrollment of sufficient patients is rarely attainable within a reasonable period of time. However, extremely few models are available for rare cancers. For example, cell lines and xenografts are available for only a limited number of histological subtypes of sarcomas; therefore, most sarcoma research is performed without such models, and a lack of adequate cancer models causes a lag in therapeutic development. The establishment of novel rare cancer models will dramatically facilitate rare cancer research and treatment development in the near future. This review focuses on the status of patient‐derived rare cancer models and discusses their pivotal problems and possibilities, using sarcomas as a representative rare cancer type. Multi‐institutional collaboration will help address the scarcity of patient‐derived rare cancer models.

Kondo, Tadashi↗

Measurement of Force Balance Repeatability and Reproducibility in the NTF

A recently published statistical approach for measuring and evaluating wind tunnel force balance repeatability and reproducibility is applied to three check standard tests in the National Transonic Facility at NASA Langley Research Center. Two different airframe models and force balances were used. The short-term repeatability and within-test reproducibility are separately estimated and correlations with tunnel parameters are carried out. Conjectures are presented for the development of scaling laws for predicting the repeatability and reproducibility of other force balance tests in the tunnel.

Hemsch, M. J.↗

A universal language for finding mass spectrometry data patterns

Despite being information rich, the vast majority of untargeted mass spectrometry data are underutilized; most analytes are not used for downstream interpretation or reanalysis after publication. The inability to dive into these rich raw mass spectrometry datasets is due to the limited flexibility and scalability of existing software tools. Here, in this study, we introduce a new language, the Mass Spectrometry Query Language (MassQL), and an accompanying software ecosystem that addresses these issues by enabling the community to directly query mass spectrometry data with an expressive set of user-defined mass spectrometry patterns. Illustrated by real-world examples, MassQL provides a data-driven definition of chemical diversity by enabling the reanalysis of all public untargeted metabolomics data, empowering scientists across many disciplines to make new discoveries. MassQL has been widely implemented in multiple open-source and commercial mass spectrometry analysis tools, which enhances the ability, interoperability and reproducibility of mining of mass spectrometry data for the research community.

Damiani, Tito [Czech Academy of Sciences (CAS), Pr↗

Power Hardware-In-the-Loop Hydropower and Ultracapacitor Hybrid Testbed

Widespread deployment of a proof-of-concept technological solution for power system performance improvement can be accelerated through onsite demonstration and pilot projects. Digital real-time simulation with power hardware-in-the-loop in controlled lab environment is the precursor to de-risk the timely and efficient execution of field demonstration and pilot projects. However, the detailed process of development, characterization, and calibration of such high fidelity simulation testbed needs to be documented in a reproducible and publicly accessible manner to leverage across broader research and development communities. This paper presents such a laboratory testbed to study black start capability of a run-of-river hydro + ultracapacitor hybrid system. Beside the high-fidelity model of the islanded grid with hydropower unit, the testbed includes the energy storage, grid following inverter, and grid emulator hardware. Several aspects such as storage characterization, control and various parameter settings necessary to capture frequency transients during load restoration are described in a comprehensive manner, which led to an effective and timely execution of black start field demonstration with an actual hydropower plant.

13 HYDRO ENERGY↗

Advances in Modeling Capabilities for Critical Mineral Separation Technologies: A PrOMMiS Overview

This is an oral presentation at the TechConnect conference on the work developed by PrOMMiS. PrOMMiS builds on and extends capabilities developed within the Department of Energy’s (DOE) Institute for the Design of Advanced Energy Systems (IDAES), Integrated Platform, and Water Treatment Technoeconomic Assessment Platform (WaterTAP), which have been successfully leveraged by other Department of Energy research areas. The open-source toolkit facilitates validation, reproducibility, and accountability, allowing for easy extension of the framework to other systems. This talk presents an overview of the PrOMMiS capabilities, including unit model library, advances in thermophysical properties models, and capital cost libraries for simulation and optimization of mineral processing technologies. The PrOMMiS applications include (1) conceptual design and superstructure optimization for screening different process configurations and identifying promising technologies; (2) dynamic modeling and optimization to enable the creation of digital twins; (3) surrogate modeling tools to leverage data when predictive thermodynamic models are not currently available; (4) technical risk reduction via uncertainty quantification and robust optimization to identify process designs that are robust to process variability and uncertainties; and (5) deployment of uncertainty quantification tools to maximize knowledge gained from experimental campaigns, while reducing the number of experiments required

critical minerals and materials↗

The case for free and open source software in research and scholarship

Free and open source software (FOSS) is any computer program released under a licence that grants users rights to run the program for any purpose, to study it, to modify it, and to redistribute it in original or modified form. Here, our aim is to explore the intersection between FOSS and computational reproducibility. We begin by situating FOSS in relation to other ‘open’ initiatives, and specifically open science, open research, and open scholarship. In this context, we argue that anyone who actively contributes to the research process today is a computational researcher, in that they use computers to manage and store information. We then provide a primer to FOSS suitable for anyone concerned with research quality and sustainability—including researchers in any field, as well as support staff, administrators, publishers, funders, and so on. Next, we illustrate how the notions introduced in the primer apply to resources for scientific computing, with reference to the GNU Scientific Library as a case study. We conclude by discussing why the common interpretation of ‘open source’ as ‘open code’ is misplaced, and we use this example to articulate the role of FOSS in research and scholarship today.

97 MATHEMATICS AND COMPUTING↗

Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures

Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecology and biogeochemical studies. A blinded multi-laboratory intercomparison was conducted to assess comparability and reproducibility of taxonomic and functional results and their sensitivity to methodological variables. Euphotic zone samples from the Bermuda Atlantic Time-series Study (BATS) in the North Atlantic Ocean collected by in situ pumps and the autonomous underwater vehicle (AUV) Clio were distributed with a paired metagenome, and one-dimensional (1D) liquid chromatographic data-dependent acquisition mass spectrometry analysis was stipulated. Analysis of mass spectra from seven laboratories through a common bioinformatic pipeline identified a shared set of 1056 proteins from 1395 shared peptide constituents. Quantitative analyses showed good reproducibility: pairwise regressions of spectral counts between laboratories yielded R 2 values averaged 0.62±0.11, and a Sørensen similarity analysis of the top 1000 proteins revealed 70 %–80 % similarity between laboratory groups. Taxonomic and functional assignments showed good coherence between technical replicates and different laboratories. A bioinformatic intercomparison study, involving 10 laboratories using eight software packages, successfully identified thousands of peptides within the complex metaproteomic datasets, demonstrating the utility of these software tools for ocean metaproteomic research. Lessons learned and potential improvements in methods were described. Future efforts could examine reproducibility in deeper metaproteomes, examine accuracy in targeted absolute quantitation analyses, and develop standards for data output formats to improve data interoperability. Together, these results demonstrate the reproducibility of metaproteomic analyses and their suitability for microbial oceanography research, including integration into global-scale ocean surveys and ocean biogeochemical models.

59 BASIC BIOLOGICAL SCIENCES↗

Standardizing Interfaces for External Access to Data and Processing for the NASA Ozone Product Evaluation and Test Element (PEATE)

NASA's traditional science data processing systems have focused on specific missions, and providing data access, processing and services to the funded science teams of those specific missions. Recently NASA has been modifying this stance, changing the focus from Missions to Measurements. Where a specific Mission has a discrete beginning and end, the Measurement considers long term data continuity across multiple missions. Total Column Ozone, a critical measurement of atmospheric composition, has been monitored for'decades on a series of Total Ozone Mapping Spectrometer (TOMS) instruments. Some important European missions also monitor ozone, including the Global Ozone Monitoring Experiment (GOME) and SCIAMACHY. With the U.S.IEuropean cooperative launch of the Dutch Ozone Monitoring Instrument (OMI) on NASA Aura satellite, and the GOME-2 instrumental on MetOp, the ozone monitoring record has been further extended. In conjunction with the U.S. Department of Defense (DoD) and the National Oceanic and Atmospheric Administration (NOAA), NASA is now preparing to evaluate data and algorithms for the next generation Ozone Mapping and Profiler Suite (OMPS) which will launch on the National Polar-orbiting Operational Environmental Satellite System (NPOESS) Preparatory Project (NPP) in 2010. NASA is constructing the Science Data Segment (SDS) which is comprised of several elements to evaluate the various NPP data products and algorithms. The NPP SDS Ozone Product Evaluation and Test Element (PEATE) will build on the heritage of the TOMS and OM1 mission based processing systems. The overall measurement based system that will encompass these efforts is the Atmospheric Composition Processing System (ACPS). We have extended the system to include access to publically available data sets from other instruments where feasible, including non-NASA missions as appropriate. The heritage system was largely monolithic providing a very controlled processing flow from data.ingest of satellite data to the ultimate archive of specific operational data products. The ACPS allows more open access with standard protocols including HTTP, SOAPIXML, RSS and various REST incarnations. External entities can be granted access to various modules within the system, including an extended data archive, metadata searching, production planning and processing. Data access is provided with very fine grained access control. It is possible to easily designate certain datasets as being available to the public, or restricted to groups of researchers, or limited strictly to the originator. This can be used, for example, to release one's best validated data to the public, but restrict the "new version" of data processed with a new, unproven algorithm until it is ready. Similarly, the system can provide access to algorithms, both as modifiable source code (where possible) and fully integrated executable Algorithm Plugin Packages (APPs). This enables researchers to download publically released versions of the processing algorithms and easily reproduce the processing remotely, while interacting with the ACPS. The algorithms can be modified allowing better experimentation and rapid improvement. The modified algorithms can be easily integrated back into the production system for large scale bulk processing to evaluate improvements. The system includes complete provenance tracking of algorithms, data and the entire processing environment. The origin of any data or algorithms is recorded and the entire history of the processing chains are stored such that a researcher can understand the entire data flow. Provenance is captured in a form suitable for the system to guarantee scientific reproducability of any data product it distributes even in cases where the physical data products themselves have been deleted due to space constraints. We are currently working on Semantic Web ontologies for representing the various provenance information. A new web site focusing on consolidating informaon about the measurement, processing system, and data access has been established to encourage interaction with the overall scientific community. We will describe the system, its data processing capabilities, and the methods the community can use to interact with the standard interfaces of the system.

Tilmes, Curt A.↗

Dynamic Rupture Simulations of the Mw7.2 1992 Landers,California, Earthquake

An important part of the simulation technique implemented in the Recipe is the earthquake rupture characterization based on established empirical scaling relationships between source parameters and seismic moment. The scaling relationships used in the rupture characterization are derived from recorded data and are tested against dynamic and kinematic rupture models of crustal earthquakes. Currently, a revised three-stage source scaling relationship between the source rupture area and seismic moment of inland crustal earthquakes, initially proposed by Irikura and Miyake, is being used. Recent analysis of results obtained with the Recipe for the 2016 M7.1 Kumamoto earthquake performed by several researchers, including the PI, Arben Pitarka, indicate that in order to reproduce the near-fault long-period ground motions and the permanent displacements, observed during surface-rupturing earthquakes, the recipe needs modifications to the kinematic rupture parametrization in the shallow crustal weak zone. In particular, improvements are required in characterizing the slip rate function at shallow depths, above the sesimogenic zone. The main objective of this research project was the development of a dynamic rupture model for the Mw7.2 1992 Landers, California earthquake. The dynamic rupture model was used to derive kinematic rupture parameters, such as slip, slip-rate, rupture time distributions, and slip rate functions in the weak (0-4km) and seismogenic crustal zones. In addition to the knowledge gained from the dynamic rupture modeling of Chi-chi, Ridgecrest, Kumamoto and other crustal earthquakes, studied by the PI, the rupture characterization of the Landers earthquake can be helpful in updating the conventional recipe for broadband ground motion simulations of crustal earthquakes with shallow rupture. The project emphasizes the need for performing physics-based earthquake rupture modeling which ultimately will inform further improvements of rupture characterization. In particular, the modeling of rupture dynamics for recorded earthquakes, and numerical simulations for different rupture scenarios, provides physical constrains on slip evolution in time and space, used in adjustments of empirical source scaling relationships for large crustal earthquakes.

58 GEOSCIENCES↗

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↗

The DIARieS Ecosystem – A Software Ecosystem to Simplify Discovery, Implementation, Analysis, Reproducibility, and Sharing of Scientific Results and Environments in Heliophysics

The infrastructure of the Heliophysics discipline has promising components but with several missing gaps, drastically reducing research and development efficiency. Developing an online discovery and analysis software ecosystem will close several of these gaps. The five main focuses on this ecosystem should be Discovery, Implementation, Analysis, Reproducibility, and Sharing of results (DIARieS). In this paper, we give a detailed description of how the proposed software ecosystem should operate, and point out the large range of possible applications to benefit many disparate groups, such as researchers, operational staff, decision-makers, and educators. The infrastructure components and technological capabilities necessary for its completion are either currently available or in development, making such an ecosystem possible for the first time. One main focus of current infrastructure investments must be to adapt and connect these pieces together into a cohesive whole to increase our research and development efficiency.

infrastructure↗

Analyzers Measure Greenhouse Gases, Airborne Pollutants

In complete darkness, a NASA observatory waits. When an eruption of boiling water billows from a nearby crack in the ground, the observatory s sensors seek particles in the fluid, measure shifts in carbon isotopes, and analyze samples for biological signatures. NASA has landed the observatory in this remote location, far removed from air and sunlight, to find life unlike any that scientists have ever seen. It might sound like a scene from a distant planet, but this NASA mission is actually exploring an ocean floor right here on Earth. NASA established a formal exobiology program in 1960, which expanded into the present-day Astrobiology Program. The program, which celebrated its 50th anniversary in 2010, not only explores the possibility of life elsewhere in the universe, but also examines how life begins and evolves, and what the future may hold for life on Earth and other planets. Answers to these questions may be found not only by launching rockets skyward, but by sending probes in the opposite direction. Research here on Earth can revise prevailing concepts of life and biochemistry and point to the possibilities for life on other planets, as was demonstrated in December 2010, when NASA researchers discovered microbes in Mono Lake in California that subsist and reproduce using arsenic, a toxic chemical. The Mono Lake discovery may be the first of many that could reveal possible models for extraterrestrial life. One primary area of interest for NASA astrobiologists lies with the hydrothermal vents on the ocean floor. These vents expel jets of water heated and enriched with chemicals from off-gassing magma below the Earth s crust. Also potentially within the vents: microbes that, like the Mono Lake microorganisms, defy the common characteristics of life on Earth. Basically all organisms on our planet generate energy through the Krebs Cycle, explains Mike Flynn, research scientist at NASA s Ames Research Center. This metabolic process breaks down sugars for energy to fuel cellular functions. "We think this chemical process did not exist when life first formed on Earth," he says, "because it is based on oxygen being available, and there was little oxygen available on the early Earth." It is possible that there are anaerobic regions beneath the sea floor in which life forms like those early non-Krebs Cycle microbes may yet exist. To detect and potentially collect samples of life emerging from hydrothermal vents, Flynn and his colleagues created Medusa, a multi-sensor instrument designed for long-term observation of diked vents on the ocean floor. When the vents erupt, Medusa assesses indicators of life within the expelled water. If the results are positive, the observatory collects samples and detaches from the ocean floor, making the long journey to the surface for retrieval by scientists. One of the indicators Medusa measures is the ratio of carbon isotopes in the water, namely carbon-12 and carbon-13. Living organisms preferentially take up carbon-12, Flynn says, so examining the ratio of these isotopes can help to determine the source of carbon in an environment as either biological or non-biological. "On Mars, there is evidence of localized methane in the atmosphere, and that methane could come from biological sources or from geochemical ones," Flynn says. "Determining the background planetary carbon isotope ratios and then evaluating the specific carbon ratios in this methane would help to determine how it was formed." A long-duration observatory similar to Medusa could one day provide essential evidence for or against the presence of life on the Red Planet or beneath the ice-crusted oceans of Europa.

Source record↗

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO 2 emissions generated by each Galaxy job.

97 MATHEMATICS AND COMPUTING↗

Quantitative spatiotemporal mapping of thermal runaway propagation rates in lithium-ion cells using cross-correlated Gabor filtering

Abuse testing of lithium-ion batteries is widely performed in order to develop new safety standards and strategies. However, testing methodologies are not standardised across the research community, especially with failure mechanisms being inherently difficult to reproduce. High-speed X-ray radiography is proven to be a valuable tool to capture events occurring during cell failure, but the observations made remain largely qualitative. We have therefore developed a robust image processing toolbox that can quantify, for the first time, the rate of propagation of battery failure mechanisms revealed by high-speed X-ray radiography. Using Gabor filter, the toolbox selectively tracks the electrode structure at the onset of failure. This facilitated the estimation of the displacement of electrodes undergoing abuse via nail penetration, and also the tracking of objects, such as the nail, as it propagates through a cell. Further, by cross-correlating the Gabor signals, we have produced practical, illustrative spatiotemporal maps of the failure events. From these, we can quantify the propagation rates of electrode displacement prior to the onset of thermal runaway. The highest recorded acceleration (≈514 mm s -2 ) was when a nail penetrated a cell radially (perpendicular to the electrodes) as opposed to axially (parallel to the electrodes). The initiation of thermal runaway was also resolved in combination with electrode displacement, which occurred at a lower acceleration (≈108 mm s -2 ). Our assistive toolbox can also be used to study other types of failure mechanisms, extracting otherwise unattainable kinetic data. Ultimately, this tool can be used to not only validate existing theoretical mechanical models, but also standardise battery failure testing procedures.

25 ENERGY STORAGE↗

From Reproducible Edge–Cloud Experimentation to Real-World Practice: The E2Clab Experience

Reproducibility is already difficult in distributed systems; on the computing continuum, it becomes substantially harder. Applications that span sensing devices, edge and fog resources, and cloud platforms must be evaluated across heterogeneous hardware, variable network conditions, cross-layer orchestration decisions, and long-running workflow lifecycles. We use E2Clab as a case study to examine these challenges and their implications for experimental methodology. We explain why reproducible experimentation is harder on the continuum, then revisit E2Clab as an initial response based on explicit modeling of infrastructure, workflow lifecycle, and artifacts. Lastly, we discuss how its evolution toward more realistic application settings can be understood through the lens of Translational Computer Science. We argue that reproducible continuum experimentation requires methods that are rigorous enough for research while remaining adaptable to real-world practice.

42 ENGINEERING↗