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At least 235 records · Page 13

Better together: Elements of successful scientific software development in a distributed collaborative community

Many scientific disciplines rely on computational methods for data analysis, model generation, and prediction. Implementing these methods is often accomplished by researchers with domain expertise but without formal training in software engineering or computer science. This arrangement has led to underappreciation of sustainability and maintainability of scientific software tools developed in academic environments. Some software tools have avoided this fate, including the scientific library Rosetta. We use this software and its community as a case study to show how modern software development can be accomplished successfully, irrespective of subject area. Rosetta is one of the largest software suites for macromolecular modeling, with 3.1 million lines of code and many state-of-the-art applications. Since the mid 1990s, the software has been developed collaboratively by the RosettaCommons, a community of academics from over 60 institutions worldwide with diverse backgrounds including chemistry, biology, physiology, physics, engineering, mathematics, and computer science. Developing this software suite has provided us with more than two decades of experience in how to effectively develop advanced scientific software in a global community with hundreds of contributors. Here we illustrate the functioning of this development community by addressing technical aspects (like version control, testing, and maintenance), community-building strategies, diversity efforts, software dissemination, and user support. We demonstrate how modern computational research can thrive in a distributed collaborative community. The practices described here are independent of subject area and can be readily adopted by other software development communities

97 MATHEMATICS AND COMPUTING↗

Introduction to Analysis Methods for Big Earth Data

Big Earth Data are too big to be tractable to simple data inspection and require models to make sense of all the data. Useful models for Big Earth Data may be physical, statistical, or machine learning based. In many cases, hybrid models combine attributes of two or more of these types.

parallel processing (computers)↗

The GLAS physical inversion method for analysis of HIRS2/MSU sounding data

Goddard Laboratory for Atmospheric Sciences has developed a method to derive atmospheric temperature profiles, sea or land surface temperatures, sea ice extent and snow cover, and cloud heights and fractional cloud, from HIRS2/MSU radiance data. Chapter 1 describes the physics used in the radiative transfer calculations and demonstrates the accuracy of the calculations. Chapter 2 describes the rapid transmittance algorithm used and demonstrates its accuracy. Chapter 3 describes the theory and application of the techniques used to analyze the satellite data. Chapter 4 shows results obtained for January 1979.

Susskind, J.↗

BEYONDPLANCK II. CMB mapmaking through Gibbs sampling

We present a Gibbs sampling solution to the mapmaking problem for cosmic microwave background (CMB) measurements that builds on existing destriping methodology. Gibbs sampling breaks the computationally heavy destriping problem into two separate steps: noise filtering and map binning. Considered as two separate steps, both are computationally much cheaper than solving the combined problem. This provides a huge performance benefit as compared to traditional methods and it allows us, for the first time, to bring the destriping baseline length to a single sample. Here, we applied the Gibbs procedure to simulated Planck 30 GHz data. We find that gaps in the time-ordered data are handled efficiently by filling them in with simulated noise as part of the Gibbs process. The Gibbs procedure yields a chain of map samples, from which we are able to compute the posterior mean as a best-estimate map. The variation in the chain provides information on the correlated residual noise, without the need to construct a full noise covariance matrix. However, if only a single maximum-likelihood frequency map estimate is required, we find that traditional conjugate gradient solvers converge much faster than a Gibbs sampler in terms of the total number of iterations. The conceptual advantages of the Gibbs sampling approach lies in statistically well-defined error propagation and systematic error correction. This methodology thus forms the conceptual basis for the mapmaking algorithm employed in the BEYONDPLANCK framework, which implements the first end-to-end Bayesian analysis pipeline for CMB observations.

79 ASTRONOMY AND ASTROPHYSICS↗

Lunar and Planetary Science XXXV: Mars: Remote Sensing and Terrestrial Analogs

The session "Mars: Remote Sensing and Terrestrial Analogs" included the following:Physical Meaning of the Hapke Parameter for Macroscopic Roughness: Experimental Determination for Planetary Regolith Surface Analogs and Numerical Approach; Near-Infrared Spectra of Martian Pyroxene Separates: First Results from Mars Spectroscopy Consortium; Anomalous Spectra of High-Ca Pyroxenes: Correlation Between Ir and M ssbauer Patterns; THEMIS-IR Emissivity Spectrum of a Large Dark Streak near Olympus Mons; Geomorphologic/Thermophysical Mapping of the Athabasca Region, Mars, Using THEMIS Infrared Imaging; Mars Thermal Inertia from THEMIS Data; Multispectral Analysis Methods for Mapping Aqueous Mineral Depostis in Proposed Paleolake Basins on Mars Using THEMIS Data; Joint Analysis of Mars Odyssey THEMIS Visible and Infrared Images: A Magic Airbrush for Qualitative and Quantitative Morphology; Analysis of Mars Thermal Emission Spectrometer Data Using Large Mineral Reference Libraries ; Negative Abundance : A Problem in Compositional Modeling of Hyperspectral Images; Mars-LAB: First Remote Sensing Data of Mineralogy Exposed at Small Mars-Analog Craters, Nevada Test Site; A Tool for the 2003 Rover Mini-TES: Downwelling Radiance Compensation Using Integrated Line-Sight Sky Measurements; Learning About Mars Geology Using Thermal Infrared Spectral Imaging: Orbiter and Rover Perspectives; Classifying Terrestrial Volcanic Alteration Processes and Defining Alteration Processes they Represent on Mars; Cemented Volcanic Soils, Martian Spectra and Implications for the Martian Climate; Palagonitic Mars: A Basalt Centric View of Surface Composition and Aqueous Alteration; Combining a Non Linear Unmixing Model and the Tetracorder Algorithm: Application to the ISM Dataset; Spectral Reflectance Properties of Some Basaltic Weathering Products; Morphometric LIDAR Analysis of Amboy Crater, California: Application to MOLA Analysis of Analog Features on Mars; Airborne Radar Study of Soil Moisture at a Mars Analog Site: Tohachi Wash/Little Colorado River; and Antarctic Dry Valleys: Modification of Rocks and Soils and Implications for Mars The Arkaroola Mars Analogue Region, South Australia.

Source record↗

Anomaly detection in Hyper Suprime-Cam galaxy images with generative adversarial networks

ABSTRACT The problem of anomaly detection in astronomical surveys is becoming increasingly important as data sets grow in size. We present the results of an unsupervised anomaly detection method using a Wasserstein generative adversarial network (WGAN) on nearly one million optical galaxy images in the Hyper Suprime-Cam (HSC) survey. The WGAN learns to generate realistic HSC-like galaxies that follow the distribution of the data set; anomalous images are defined based on a poor reconstruction by the generator and outlying features learned by the discriminator. We find that the discriminator is more attuned to potentially interesting anomalies compared to the generator, and compared to a simpler autoencoder-based anomaly detection approach, so we use the discriminator-selected images to construct a high-anomaly sample of ∼13 000 objects. We propose a new approach to further characterize these anomalous images: we use a convolutional autoencoder to reduce the dimensionality of the residual differences between the real and WGAN-reconstructed images and perform UMAP clustering on these. We report detected anomalies of interest including galaxy mergers, tidal features, and extreme star-forming galaxies. A follow-up spectroscopic analysis of one of these anomalies is detailed in the Appendix; we find that it is an unusual system most likely to be a metal-poor dwarf galaxy with an extremely blue, higher-metallicity H ii region. We have released a catalogue with the WGAN anomaly scores; the code and catalogue are available at https://github.com/kstoreyf/anomalies-GAN-HSC; and our interactive visualization tool for exploring the clustered data is at https://weirdgalaxi.es.

79 ASTRONOMY AND ASTROPHYSICS↗

Research and operational efforts in support of Skylab experiment M093

The objectives of Skylab Experiment M093 were to measure electrocardiographic signals during spaceflight, to elucidate the electrophysiological basis for the changes observed, and to assess the effect of the change on the human cardiovascular system. Vectorcardiographic methods were used to quantitate changes, standardize data collection, and to facilitate reduction and statistical analysis of data. In this report the authors describe the M093 experiment design, the data transmission system, data reduction methods, and the analysis of data from the three Skylab missions. The report also includes clinical applications of the techniques developed for Skylab Experiment M093.

Smith, R. F.↗

Assessing Low-Temperature Geothermal Play Types: Relevant Data and Play Fairway Analysis Methods

The U.S. Department of Energy (DOE) Geothermal Technologies Office (GTO) is supporting the Geothermal Heating and Cooling Geospatial Datasets and Analysis project conducted by the National Renewable Energy Laboratory (NREL) as part of a broader effort to demonstrate the multi-faceted value of integrating geothermal power and geothermal heating and cooling (GHC) technologies into national decarbonization plans and community energy plans. Currently, there is a need to establish baseline low-temperature geothermal resource datasets and evaluate methods for deploying these technologies to provide the basis for supporting private sector investment. This project is focused on collecting baseline datasets, updating conceptual models, and creating Play Fairway Analysis (PFA) workflows for low-temperature (<150 degrees Celsius) geothermal resources of different geothermal play types (i.e., sedimentary basin, orogenic belts, and radiogenic geothermal play types) that could be used for geothermal heating and cooling (GHC), combined heat and power (CHP), and other geothermal direct uses (GDU) applications. Low-temperature geothermal resources are defined as reservoirs - natural or engineered - with temperatures <150 degrees Celsius. While the focus in the NREL effort is on GHC, resources at the upper end of this temperature range can also be used for small-scale power generation. This project does not include Ground Source Heat Pumps (GSHPs) technologies because they can be effectively developed almost anywhere. Low-temperature geothermal resources have not been studied as extensively as higher- to medium-temperature geothermal resources, but there is recent interest in improving understanding of these types of resources with an uptick of interest in geothermal technologies for decarbonizing heating and cooling systems. In addition, Enhanced Geothermal Systems (EGS) and other emerging technologies for exploiting petrothermal resources have opened the possibility of utilizing deep sedimentary basin systems, where porous media provide permeability and high temperatures can be reached at great depths. This project takes the approach of classifying low- temperature geothermal resources by geothermal play type (GPT). We defined and characterized three major classes of low-temperature GPT: sedimentary basins, orogenic systems, and radiogenic systems. We develop methodologies for evaluating and analyzing the potential for these resources building off the PFA approach to de-risking geothermal exploration and characterization. The proposed PFA approach for low-temperature geothermal resources includes: 1) identifying relevant data (e.g., datasets such bottom-hole temperatures from oil and gas wells, heat flow data, Quaternary faults and stress field data, geophysical data, etc.); 2) grouping and weighting of relevant datasets into PFA criteria (e.g., geological, risk, and economic criteria); 3) uncertainty quantification; 4) developing favorability or common risk maps for low-temperature geothermal resources to identify potential locations for more focused data collection; and 5) estimating electric power generation and heating potential at those locations using the GeoRePORT Resource Size Assessment Tool (RSAT). This project should facilitate future deployment of GHC, CHP, and GDU by providing data, tools, and a workflow applicable to low-temperature geothermal resources. Increased deployment of GHC and GDU will help achieve national and local decarbonization goals.

15 GEOTHERMAL ENERGY↗

Advances in geophysical forensic event monitoring

Forensic analysis of man-made, non-nuclear events (such as industrial accidents, explosion experiments and mine collapses) has become more frequent and detailed owing to advancements in geophysical monitoring. Here, in this Technical Review, we demonstrate how geophysical forensic monitoring using seismic, infrasound and hydroacoustic recordings provides insights on events in the solid earth, atmosphere and underwater. Advanced techniques, including machine-learning-based models, have been developed to detect, identify and investigate these events, providing information on location, subevents, sources and explosive yield. The increase in data availability, application of advanced methods and computation and the growth of multitechnology approaches have increased the accuracy of forensic event analysis and enabled more realistic characterization of uncertainties. For example, the 2020 Beirut explosion in Lebanon demonstrated that various seismic, acoustic and other methods could be used to estimate explosive yield (and yield uncertainties) of about 1 ktonne, providing confidence in the application of these methods to smaller events where data are available. However, forensic investigations remain largely limited to known events with identified sources. Increased access to data, sophisticated analysis methods and high-resolution earth models will improve forensic event analysis further, enabling civil and scientific applications, such as localization in the search for the lost ARA San Juan submarine.

geophysics↗

Analysis of flexible aircraft longitudinal dynamics and handling qualities. Volume 2: Data

Two analysis methods are applied to a family of flexible aircraft in order to investigate how and when structural (especially dynamic aeroelastic) effects affect the dynamic characteristics of aircraft. The first type of analysis is an open loop modal analysis technique. This method considers the effect of modal residue magnitudes on determining vehicle handling qualities. The second method is a pilot in the loop analysis procedure that considers several closed loop system characteristics. Both analyses indicated that dynamic aeroelastic effects caused a degradation in vehicle tracking performance, based on the evaluation of some simulation results. Volume 2 consists of the presentation of the state variable models of the flexible aircraft configurations used in the analysis applications mode shape plots for the structural modes, numerical results from the modal analysis frequency response plots from the pilot in the loop analysis and a listing of the modal analysis computer program.

Waszak, M. R.↗

Introduction to Analysis Methods for Big Earth Data

Big Earth Data are too big to be tractable to simple data inspection. Thus, they typically require models to make sense of all the data. Useful models for Big Earth Data may be physical, statistical, or machine learning based. While physical models are ideal for understanding the data, they are not always feasible, particularly when our ability to observe at finer scales exceeds our ability to incorporate the physics. Statistical models are more generalized, but computationally intensive for many Earth Observation datasets. Machine Learning models generally scale well but are sometimes limited in the physical understanding they can offer. Hybrid models combine attributes—and advantages—of two or more of these types.

Christopher Lynnes↗

Communication and Organization in Software Development: An Empirical Study

The empirical study described in this paper addresses the issue of communication among members of a software development organization. The independent variables are various attributes of organizational structure. The dependent variable is the effort spent on sharing information which is required by the software development process in use. The research questions upon which the study is based ask whether or not these attributes of organizational structure have an effect on the amount of communication effort expended. In addition, there are a number of blocking variables which have been identified. These are used to account for factors other than organizational structure which may have an effect on communication effort. The study uses both quantitative and qualitative methods for data collection and analysis. These methods include participant observation, structured interviews, and graphical data presentation. The results of this study indicate that several attributes of organizational structure do affect communication effort, but not in a simple, straightforward way. In particular, the distances between communicators in the reporting structure of the organization, as well as in the physical layout of offices, affects how quickly they can share needed information, especially during meetings. These results provide a better understanding of how organizational structure helps or hinders communication in software development.

Seaman, Carolyn B.↗

The statistical analysis of circadian phase and amplitude in constant-routine core-temperature data

Accurate estimation of the phases and amplitude of the endogenous circadian pacemaker from constant-routine core-temperature series is crucial for making inferences about the properties of the human biological clock from data collected under this protocol. This paper presents a set of statistical methods based on a harmonic-regression-plus-correlated-noise model for estimating the phases and the amplitude of the endogenous circadian pacemaker from constant-routine core-temperature data. The methods include a Bayesian Monte Carlo procedure for computing the uncertainty in these circadian functions. We illustrate the techniques with a detailed study of a single subject's core-temperature series and describe their relationship to other statistical methods for circadian data analysis. In our laboratory, these methods have been successfully used to analyze more than 300 constant routines and provide a highly reliable means of extracting phase and amplitude information from core-temperature data.

NASA Discipline Regulatory Physiology↗

Data handling and analysis for the 1971 corn blight watch experiment.

Review of the data handling and analysis methods used in the near-operational test of remote sensing systems provided by the 1971 corn blight watch experiment. The general data analysis techniques and, particularly, the statistical multispectral pattern recognition methods for automatic computer analysis of aircraft scanner data are described. Some of the results obtained are examined, and the implications of the experiment for future data communication requirements of earth resource survey systems are discussed.

Anuta, P. E.↗

Summary of NDC Capacity Building Workshop and Regional Seismic Travel Time (RSTT) in combination with Data Sharing and Integration Training

The NNSA Seismic Cooperation Program (SCP) sponsored Stephen Myers (LLNL), Michael Begnaud (LANL), Brian Young (SNL) and Istvan Bondar (Research Center for Astronomy and Earth Sciences, Hungary) to serve as a presenters/trainers at the “NDC Capacity Building Workshop and Regional Seismic Travel Time (RSTT) in combination with Data Sharing and Integration Training” September 4-8 2022 in Muscat, Oman (See Appendix A for the agenda). The workshop and training (workshop from here forward) was organized by the Comprehensive Nuclear-Test-Ban Treaty Organization (CTBTO) Provisional Technical Secretariat (PTS). The first half of the week was devoted to NDC workshop activities, and the second half was devoted to RSTT training. Fifty-five participants from 27 countries and the CTBTO-PTS attended the 5-day workshop (See Appendix B for list of participants and countries of origin). Presentations from the PTS described the International Monitoring System (IMS), International Data Centre (IDC) products, and metrics of regional data utilization. Contributed presentations from each country’s scientists included descriptions of regional and national networks, methods of data analysis, and needs for material and technical assistance. Training included an overview of the RSTT method and instruction on how to locate seismic events with the iLoc program, which utilizes RSTT travel times to reduce bias in event location estimates. Methods of seismic tomography and the need for a high-quality tomographic set, including seismological “ground truth”, were emphasized. Seismological “ground truth” or “GT” is a term that has come to mean both events with known location and events with well-characterized locations that are estimated using seismological data, typically with epicenter accuracy of 5 km or better. Notably, the instructional platform has migrated from UNIX shell scripts to Jupyter Notebooks. Jupyter Notebooks have the advantage being more visually intuitive, including display of graphics within the notebook. Each notebook includes every processing step that participants need to reproduce the entire exercise.

58 GEOSCIENCES↗