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At least 145 records · Page 8

Using Docker Containers to Extend Reproducibility Architecture for the NASA Earth Exchange (NEX)

NASA Earth Exchange (NEX) is a data, supercomputing and knowledge collaboratory that houses NASA satellite, climate and ancillary data where a focused community can come together to address large-scale challenges in Earth sciences. As NEX has been growing into a petabyte-size platform for analysis, experiments and data production, it has been increasingly important to enable users to easily retrace their steps, identify what datasets were produced by which process chains, and give them ability to readily reproduce their results. This can be a tedious and difficult task even for a small project, but is almost impossible on large processing pipelines. We have developed an initial reproducibility and knowledge capture solution for the NEX, however, if users want to move the code to another system, whether it is their home institution cluster, laptop or the cloud, they have to find, build and install all the required dependencies that would run their code. This can be a very tedious and tricky process and is a big impediment to moving code to data and reproducibility outside the original system. The NEX team has tried to assist users who wanted to move their code into OpenNEX on Amazon cloud by creating custom virtual machines with all the software and dependencies installed, but this, while solving some of the issues, creates a new bottleneck that requires the NEX team to be involved with any new request, updates to virtual machines and general maintenance support. In this presentation, we will describe a solution that integrates NEX and Docker to bridge the gap in code-to-data migration. The core of the solution is saemi-automatic conversion of science codes, tools and services that are already tracked and described in the NEX provenance system, to Docker - an open-source Linux container software. Docker is available on most computer platforms, easy to install and capable of seamlessly creating and/or executing any application packaged in the appropriate format. We believe this is an important step towards seamless process deployment in heterogeneous environments that will enhance community access to NASA data and tools in a scalable way, promote software reuse, and improve reproducibility of scientific results.

earth exchange↗

Hector V3.2.0: Functionality and Performance of a Reduced-Complexity Climate Model

Hector is an open-source reduced complexity climate-carbon cycle model that models critical Earth system processes on a global and annual basis. Here we present an updated version of the model, Hector V3.2.0 (hereafter Hector V3) and document its new features, implementation of new science, and performance. Significant new features include permafrost thaw, a reworked energy balance submodel, and updated parameterizations throughout. Hector V3 results are in good general agreement with historical observations of atmospheric CO2 concentrations and global mean surface temperature, and its future temperature projections are consistent with more complex Earth System Model output data from the Sixth Coupled Model Intercomparison Project. We show that Hector V3 is a fully open source, flexible, performant, and robust simulator of global climate changes, note its limitations, and discuss future areas of improvement and research with respect to the model’s scientific, stakeholder, and educational priorities.

Kayln Dorheim↗

Computing with Beowulf

Parallel computers built out of mass-market parts are cost-effectively performing data processing and simulation tasks. The Supercomputing (now known as "SC") series of conferences celebrated its 10th anniversary last November. While vendors have come and gone, the dominant paradigm for tackling big problems still is a shared-resource, commercial supercomputer. Growing numbers of users needing a cheaper or dedicated-access alternative are building their own supercomputers out of mass-market parts. Such machines are generally called Beowulf-class systems after the 11th century epic. This modern-day Beowulf story began in 1994 at NASA's Goddard Space Flight Center. A laboratory for the Earth and space sciences, computing managers there threw down a gauntlet to develop a $50,000 gigaFLOPS workstation for processing satellite data sets. Soon, Thomas Sterling and Don Becker were working on the Beowulf concept at the University Space Research Association (USRA)-run Center of Excellence in Space Data and Information Sciences (CESDIS). Beowulf clusters mix three primary ingredients: commodity personal computers or workstations, low-cost Ethernet networks, and the open-source Linux operating system. One of the larger Beowulfs is Goddard's Highly-parallel Integrated Virtual Environment, or HIVE for short.

Cohen, Jarrett↗

Hail Storm Risk Assessment Using Space-Borne Remote Sensing Observations and Reanalyses

Much of the world is impacted by severe thunderstorms, but whether they become disasters depends upon resilience--our capacity to prepare, mitigate, respond, and recover. Hail is the costliest severe weather hazard for the insurance industry, generating ~70% of severe convective storm losses due to damage to assets such as homes, businesses, agriculture, and infrastructure. Most insurance companies do not reserve enough capital to cover catastrophes, so they acquire reinsurance. The reinsurance industry uses catastrophe models (CatModels) to statistically estimate risk to an insurer’s portfolio. Hail CatModels are developed with climatologies that define hailstorm frequency and severity. Hail-prone areas can be defined using hail reports from trained spotters, the media, and the general public. Extremely severe hail (2+ inch diameter) occurs nearly every day across the world. Weather radars can detect hail because hailstones strongly reflect microwave signals that they emit. However, hail climatologies are difficult to derive because hail covers small areas and there are neither hail reporting mechanisms (e.g. website or mobile app) nor radar networks in most places outside the US and Europe. This lack of ground truth on severe hail puts society and economies at risk. Hail is generated within storms by strong updrafts. These updrafts exhibit unique signatures in NASA and other agency satellite observations, offering new opportunities for hailstorm analysis. Geostationary (GEO) visible and infrared imagery has been collected for ~15-25 years across the world (region dependent) and methods have been developed at NASA Langley Research Center (LaRC) to detect hailstorm updrafts using GEO imagery. Climatological GEO updraft data has been used by Willis Towers Watson (WTW), a leader in catastrophe risk assessment for the insurance industry, and Karlsruhe Institute of Technology to develop CatModels over Europe and Australia. Hail can also be inferred with passive microwave imagery collected by low-Earth-orbiting sensors such as the GPM GMI, TRMM TMI, AMSR-E, AMSR-2, SSM/I, and SSMIS over the last 20+ years using methods developed at the Marshall Space Flight Center (MSFC). Hailstorms generate enhanced lightning flash rates that can be tracked using new GOES-R series GEO Lightning Mapping (GLM) imagery. Atmospheric reanalyses can be used to define favorable hailstorm environments for combination with the satellite-based storm detections. This presentation will describe a framework for developing continental to global hail climatologies and CatModels based on NASA satellite data and capabilities. This is a collaboration between LaRC and MSFC, WTW, and partners in Brazil, Argentina, and South Africa. This project seeks to mitigate hail disasters by aiding development of new satellite-based severe storm nowcasting tools by regional partners and developing climatologies to improve societal understanding of hail frequency. GEOO visible and infrared metrics of storm intensity, environmental conditions based on reanalyses, spotter hail reports and radar MESH observations are intercompared to quantify the detectability of hailstorms, and our ability to discriminate hailstorms from other severe storms. We are also maturing methods using land surface imaging satellite data (e.g. MODIS, Landsat, Sentinel 1 and 2) to identify hail damage to agriculture. Work with WTW will improve socioeconomic resilience through development of new CatModels. Southern Brazil, Uruguay, Paraguay, and Argentina feature some of the most intense thunderstorms on Earth. South America and South Africa are developing insurance markets of interest to WTW clients, and is similar to other regions routinely impacted by hail that do not have comprehensive hail reporting or radars to assess hailstorm frequency. Project datasets will be made available via online GIS-enabled tools developed at the LaRC Atmospheric Science Data Center (ASDC) which will visualize data and provide it in multiple formats for use in a wide range of open source and commercial tools.

Kristopher Michael Bedka↗

Frameworks Coordinate Scientific Data Management

Jet Propulsion Laboratory computer scientists developed a unique software framework to help NASA manage its massive amounts of science data. Through a partnership with the Apache Software Foundation of Forest Hill, Maryland, the technology is now available as an open-source solution and is in use by cancer researchers and pediatric hospitals.

Source record↗

PolarMERRA: A Polar-Focused Global Reanalysis Project for Scientific and Stakeholder Needs

The adequate modeling of physical processes in the Arctic and Antarctic is vital for developing prediction capabilities and for obtaining an understanding of rapidly evolving polar conditions, including their potential global impacts. These processes are often poorly represented in global models and reanalyses, owing to a legacy modeling focus on midlatitude processes, as well as a scarcity of observations needed for model development in polar regions. The polarMERRA initiative, a joint effort between NASA’s Cryospheric Sciences and Modeling and Prediction programs, seeks to improve the representation of cryospheric and polar atmospheric processes and to develop an open-source framework for a quantitively evaluation of polar-relevant variables against current and future satellite and in-situ observations, models, and reanalyses. Here, we evaluate the impacts of spatial resolution and modifications to sea ice, ice sheet, and atmospheric parameterizations on the representation of high latitude conditions by using a quantitative scorecard approach that leverages NASA’s extensive satellite record. Investigations are conducted using the NASA Goddard Earth Observing System model (GEOS) and its data assimilation system (GEOS DAS). Through a quantitative identification of process deficiencies, bias reductions in key surface variables, including temperature and precipitation over cryospheric surfaces, may be achieved. The polarMERRA project additionally seeks to identify additional data sources for use in the GEOS DAS, and to incorporate data and parameterization improvements into future model and reanalysis products for scientific and stakeholder use.

Lauren C Andrews↗

Analysis of Observed Contamination Through SAGE III's First Year on Orbit

SAGE III is a payload on the International Space Station that conducts measurements of ozone and other atmospheric constituents through the use of a moderate resolution spectrometer with an operating wavelength range of 290 nm to 1550 nm. Because of the optically sensitive nature of the payload, a suite of eight Thermoelectric Quartz Crystal Microbalances (TQCMs) were included to monitor the operating environment. During the rst year of operation, the SAGE III TQCMs were instrumental in detecting several periods of higher contamination and localizing their sources. A clear window made from quartz crystal covers the instrument assembly's aperture. Under nominal operating conditions, this window is only open during science gathering activities. However, if the rates of contamination accumulation are detected to be above the background rate, the window will be kept closed during science gathering to protect the optically sensitive instrument mirror. An analysis of the signal transmissions through the window for the wavelengths of 290 nm to 1550 nm has been conducted to determine any possible degradation of the window and potential in uence on science data collected to date, and established a baseline for future analysis.

Thompson, Michael P.↗

PandExo: A Community Tool for Transiting Exoplanet Science with JWST and HST

As we approach the James Webb Space Telescope (JWST) era, several studies have emerged that aim to (1) characterize how the instruments will perform and (2) determine what atmospheric spectral features could theoretically be detected using transmission and emission spectroscopy. To some degree, all these studies have relied on modeling of JWST's theoretical instrument noise. With under two years left until launch, it is imperative that the exoplanet community begins to digest and integrate these studies into their observing plans, as well as think about how to leverage the Hubble Space Telescope (HST) to optimize JWST observations. To encourage this and to allow all members of the community access to JWST & HST noise simulations, we present here an open-source Python package and online interface for creating observation simulations of all observatory-supported timeseries spectroscopy modes. This noise simulator, called PandExo, relies on some aspects of Space Telescope Science Institute's Exposure Time Calculator, Pandeia. We describe PandExo and the formalism for computing noise sources for JWST. Then we benchmark PandExoʼs performance against each instrument team's independently written noise simulator for JWST, and previous observations for HST. We find that PandExo is within 10% agreement for HST/WFC3 and for all JWST instruments.

Batalha, Natasha E.↗

Data Access Services that Make Remote Sensing Data Easier to Use

This slide presentation reviews some of the processes that NASA uses to make the remote sensing data easy to use over the World Wide Web. This work involves much research into data formats, geolocation structures and quality indicators, often to be followed by coding a preprocessing program. Only then are the data usable within the analysis tool of choice. The Goddard Earth Sciences Data and Information Services Center is deploying a variety of data access services that are designed to dramatically shorten the time consumed in the data preparation step. On-the-fly conversion to the standard network Common Data Form (netCDF) format with Climate-Forecast (CF) conventions imposes a standard coordinate system framework that makes data instantly readable through several tools, such as the Integrated Data Viewer, Gridded Analysis and Display System, Panoply and Ferret. A similar benefit is achieved by serving data through the Open Source Project for a Network Data Access Protocol (OPeNDAP), which also provides subsetting. The Data Quality Screening Service goes a step further in filtering out data points based on quality control flags, based on science team recommendations or user-specified criteria. Further still is the Giovanni online analysis system which goes beyond handling formatting and quality to provide visualization and basic statistics of the data. This general approach of automating the preparation steps has the important added benefit of enabling use of the data by non-human users (i.e., computer programs), which often make sub-optimal use of the available data due to the need to hard-code data preparation on the client side.

Lynnes, Christopher↗

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↗

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↗

ncompare: A Python Package for Comparing netCDF Structures

Earth science researchers and data engineers have a common problem: they often need to compare data files to see what is different between them. A lot of time is spent developing code to test differences. When it comes to comparing multidimensional data file formats like netCDFs (Network Common Data Form), this is particularly challenging and time-consuming, since there is frequently a need to evaluate the differences between dimension sizes, variable structures, and variable attributes, especially for regression testing. Since netCDFs are widely used in Earth science — with climate models, oceanographic or atmospheric reanalyses, and observational data — improved means of evaluating netCDF files can help enable a wide range of applications. We have developed a reusable open source approach through `ncompare`, which is a Python package for comparing netCDF structures [[https://github.com/nasa/ncompare]]. The `ncompare` tool compares the structure of two Network Common Data Form (NetCDF) files at the command line. It facilitates rapid comparisons by generating a formatted display of the matching and non-matching groups, variables, and associated metadata between two NetCDF datasets. The user has the option to colorize the terminal output for ease of viewing, and `ncompare` can optionally save comparison reports in text, comma-separated value (CSV), and/or Microsoft Excel formats. Despite the availability of tools (such as ncmpidiff or nccmp) that compare the values of variables, there was not previously a readily available, Python-based tool for rapid visual comparisons of group and variable structures, attributes, and chunking. `ncompare` was developed at NASA’s Atmospheric Science Data Center (ASDC) and is a collaboration with NASA Openscapes [[https://nasa-openscapes.github.io]] mentors across 11 of NASA’s data centers. Openscapes’ overarching vision is to support scientific researchers using NASA Earthdata as they migrate their workflows to the cloud. Relevant links: - https://github.com/nasa/ncompare - https://github.com/pyOpenSci/software-submission/issues/146 - https://nasa-openscapes.github.io

Daniel Kaufman↗

A Computer Learning Center for Environmental Sciences

In the fall of 1998, MacMillan Hall opened at Brown University to students. In MacMillan Hall was the new Computer Learning Center, since named the EarthLab which was outfitted with high-end workstations and peripherals primarily focused on the use of remotely sensed and other spatial data in the environmental sciences. The NASA grant we received as part of the "Centers of Excellence in Applications of Remote Sensing to Regional and Global Integrated Environmental Assessments" was the primary source of funds to outfit this learning and research center. Since opening, we have expanded the range of learning and research opportunities and integrated a cross-campus network of disciplines who have come together to learn and use spatial data of all kinds. The EarthLab also forms a core of undergraduate, graduate, and faculty research on environmental problems that draw upon the unique perspective of remotely sensed data. Over the last two years, the Earthlab has been a center for research on the environmental impact of water resource use in and regions, impact of the green revolution on forest cover in India, the design of forest preserves in Vietnam, and detailed assessments of the utility of thermal and hyperspectral data for water quality analysis. It has also been used extensively for local environmental activities, in particular studies on the impact of lead on the health of urban children in Rhode Island. Finally, the EarthLab has also served as a key educational and analysis center for activities related to the Brown University Affiliated Research Center that is devoted to transferring university research to the private sector.

Mustard, John F.↗

Comparative Modeling Studies of Boreal Water and Carbon Balance

The coordination of the modeling and field efforts for an Intensive Field Campaign (IFC) may resemble the chicken and egg dilemma. This session's theme advocates that early and proactive involvement by modeling teams can produce a scientific and operational benefit for the IFC and Experiment. This talk will provide some examples and suggestions originating from the NASA funded IFC's of the FIFE First ISLSCP (International Satellite Land Surface Climatology Project) Field Experiment, Oregon Transect Ecosystem Research (OTTER) and predominately Boreal Ecosystem-Atmosphere Study (BOREAS) Experiments. In February 1994 and prior to the final selection of the BOREAS study sites, a group of funded BOREAS investigators agreed to run their models with data for five community types representing the proposed tower flux sites. All participating models were given identical initial values and boundary conditions and driven with identical climate data. The objectives of the intercomparison exercise were: 1) compare simulation results of participating terrestrial, hydrological, and atmospheric models over selected time frames; 2) learn about model behavior and sensitivity to estimated boreal site and vegetation definitions; 3) prioritize BOREAS field data collection efforts supporting modeling studies; 4) identify individual model deficiencies as early as possible. Out of these objectives evolved some important coordination and science issues for the BOREAS Experiment that can be generalized to IFCs and long term archiving of the data. Some problems are acceptable because they are endemic to maintaining fair and open competition prior to the peer review process. Others are logistical and addressable through application of planning, management, and information sciences. This investigator has identified one source of measurement and model incompatibility that is manifest in the IFC scaling approach. Although intuitively obvious, scaling problems are already more formally defined in the Geography literature. An example of the scaling problem will be demonstrated with Vegetation/Ecosystem Mapping and Analysis Project (VEMAP) and OTTER data.

Coughlan, J.↗

The interactions of atmospheric cosmogenic radionuclides with spacecraft surfaces

The discovery of the cosmogenic radionuclide Be-7 on the front surface (and the front surface only) of the Long Duration Exposure Facility (LDEF) spacecraft has opened opportunities to investigate new phenomena in several disciplines of space science. The experiments performed for this work show that the Be-7 results only if the source of the isotope is the atmosphere through which the spacecraft passed. We should expect that the uptake of beryllium in such circumstances will depend on the chemical form of the Be and the chemical nature of the substrate. It was found that the observed concentration of Be-7 does, in fact, differ between metal surfaces and organic surfaces such as PTFE (teflon). It is noted, however, that: (1) organic surfaces, even PTFE, are etched by the atomic oxygen found under these orbital conditions, and (2) the relative velocity of the species is 8 km(exp -1)s relative to the surface and the interaction chemistry and physics may differ from the norm. The Be-7 is formed by spallation of O and N nuclei under cosmic ray proton bombardment. The principal source region is at altitudes of 12-15 km. While very small quantities are produced above 300 km, the amount measured on the LDEF was 3 to 4 orders of magnitude higher than expected from production at orbital attitude. The most reasonable explanation is that Be-7 is rapidly transported from low altitudes by some unknown mechanism. The process must take place on a time scale similar to the half-life of the isotope (53 days). Many other isotopes are produced by cosmic ray reactions, and some of these are suited to measurement by the extremely sensitive methods of accelerator mass spectrometry. A program was initiated to search for these isotopes and it is hoped that such studies will provide new methods for studying mixing in the upper atmosphere.

Gregory, John C.↗

The interactions of atmospheric cosmogenic radionuclides with spacecraft surfaces

The discovery of the cosmogenic radionuclide Be-7 on the front surface of the Long Duration Exposure Facility (LDEF) spacecraft has opened opportunities to investigate new phenomena in several disciplines of space science. The experiments performed for this work show that the Be-7 results only if the source of the isotope is the atmosphere through which the spacecraft passed. We should expect that the uptake of beryllium in such circumstances will depend on the chemical form of the Be and the chemical nature of the substrate. It was found that the observed concentration of Be-7 does, in fact, differ between metal surfaces and organic surfaces such as PTFE (teflon). It is noted, however, that: (1) organic surfaces, even PTFE, are etched by the atomic oxygen found under these orbital conditions, and (2) the relative velocity of the species is 8 km(exp -1)s relative to the surface and the interaction chemistry and physics may differ from the norm. The Be-7 is formed by spallation of O and N nuclei under cosmic ray proton bombardment. The principal source region is at altitudes of 12-15 km. While very small quantities are produced above 300 km, the amount measured on the LDEF was 3 to 4 orders of magnitude higher than expected from production at orbital altitude. The most reasonable explanation is that Be-7 is rapidly transported from low altitudes by some unknown mechanism. The process must take place on a time scale similar to the half-life of the isotope (53 days). Many other isotopes are produced by cosmic ray reactions, and some of these are suited to measurement by the extremely sensitive methods of accelerator mass spectrometry. A program was initiated to search for these isotopes and it is hoped that such studies will provide new methods for studying mixing in the upper atmosphere.

Gregory, J. C.↗

Science Activity Planner for the MER Mission

The Maestro Science Activity Planner is a computer program that assists human users in planning operations of the Mars Explorer Rover (MER) mission and visualizing scientific data returned from the MER rovers. Relative to its predecessors, this program is more powerful and easier to use. This program is built on the Java Eclipse open-source platform around a Web-browser-based user-interface paradigm to provide an intuitive user interface to Mars rovers and landers. This program affords a combination of advanced display and simulation capabilities. For example, a map view of terrain can be generated from images acquired by the High Resolution Imaging Science Explorer instrument aboard the Mars Reconnaissance Orbiter spacecraft and overlaid with images from a navigation camera (more precisely, a stereoscopic pair of cameras) aboard a rover, and an interactive, annotated rover traverse path can be incorporated into the overlay. It is also possible to construct an overhead perspective mosaic image of terrain from navigation-camera images. This program can be adapted to similar use on other outer-space missions and is potentially adaptable to numerous terrestrial applications involving analysis of data, operations of robots, and planning of such operations for acquisition of scientific data.

Norris, Jeffrey S.↗