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The PDS is exploring object-oriented data technology to support cross-discipline data access using a software component framework and a metadata driven implementation.
The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics dataand collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 220 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab sample processing lab. The GLDS contains rich metadata about each experiment and has recently integrated radiation dosimetery data from experiments flown on the Space Shuttle. GeneLab has also recently implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretationof the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 120 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. Discoveries made using GeneLabhave begunand will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.
The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data, and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 220 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab sample processing lab. The GLDS contains rich metadata about each experiment and has recently integrated radiation dosimetery data from experiments flown on the Space Shuttle. GeneLab has also recently implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 120 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.
The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 220 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab sample processing lab. The GLDS contains rich metadata about each experiment and has recently integrated radiation dosimetry data from experiments flown on the Space Shuttle. GeneLab has also recently implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 120 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.
The NASA GeneLab project capitalizes on multi-omic technologies to maximize the return on spaceflight experiments. To do this, GeneLab maintains a publicly accessible database (GLDS) that houses spaceflight and spaceflight relevant multi-omics data and collaborates with NASA principal investigators and projects to generate additional omics data. GeneLab houses more than 350 transcriptomic, proteomic, metabolomic and epigenomic datasets from plant, animal and microbial experiments, with a growing number of these having been produced by the GeneLab Sequencing Lab. The GLDS contains rich metadata about each experiment and has integrated radiation dosimetry data from experiments flown on the Space Shuttle, International Space Station, and Free Flying spacecrafts. With the increasing amount and complexity of omics data being generated, GeneLab utilizes community-defined, common models for metadata and terminology so that omics data and results are discoverable and reliably reproducible. GeneLab uses the ISA-Tab specification and semantic model for organizing and representing omics metadata. In addition to metadata standards, data files must be open-source file or common exchange formats to ensure accessibility and usability by all users. To ease data ingestion and transfer, the web-based submission tool allows PIs a user-friendly user interface to curate, organize, and publish their space relevant omics data. In the more recent years, data curation and submission portal has incorporated the FAIR principles making data findable, accessible, interoperable, and reusable. To increase reusability of data, GeneLab has implemented an effort to present processed data in the GLDS in addition to the raw omics data. The processed data will enable interpretation of the data by a larger group of students, scientists and the general public. Standard pipelines for the transformation of raw data into visualizations were developed by four GeneLab Analysis Working Groups (animals, plants, microbes, multi-omics) comprised of over 200 scientists from NASA, industry, and academia. To explore the data, the GLDS provides users various tools for data analysis, collaborative workspace for file storage and sharing, and a visualization portal. The analysis platform built using the Galaxy toolshed provides access to a broad variety of users including those with limited bioinformatics experience and students to learn how to analyze spaceflight omics data. The visualization portal takes GeneLab one step closer to data democratization by removing all bioinformatics requisites to interpret transcriptomics data hosted in the repository. To train the next generation of scientists, NASA offers training programs such as GeneLab 4 High School (GL4HS) and GeneLab 4 Universities. NLM Curation at a Scale Workshop 2022 | NASA GeneLab (GL4U) to teach students bioinformatics and computational biology methods to analyze omics data. Discoveries made using GeneLab have begun and will continue to deepen our understanding of biology, advance the field of genomics, and help to discover cures for diseases, create better diagnostic tools, and ultimately allow astronauts to better withstand the rigors of long-duration spaceflight.
We present a novel visual representation and interface named the matrix of isosurface similarity maps (MISM) for effective exploration of large time-varying multivariate volumetric data sets. MISM synthesizes three types of similarity maps (i.e., self, temporal, and variable similarity maps) to capture the essential relationships among isosurfaces of different variables and time steps. Additionally, it serves as the main visual mapping and navigation tool for examining the vast number of isosurfaces and exploring the underlying time-varying multivariate data set. We present temporal clustering, variable grouping, and interactive filtering to reduce the huge exploration space of MISM. In conjunction with the isovalue and isosurface views, MISM allows users to identify important isosurfaces or isosurface pairs and compare them over space, time, and value range. More importantly, we introduce path recommendation that suggests, animates, and compares traversal paths for effectively exploring MISM under varied criteria and at different levels-of-detail. A silhouette-based method is applied to render multiple surfaces of interest in a visually succinct manner. We demonstrate the effectiveness of our approach with case studies of several time-varying multivariate data sets and an ensemble data set, and evaluate our work with two domain experts.
High-throughput sequencing based techniques, such as 16S rRNA gene profiling, have the potential to elucidate the complex inner workings of natural microbial communities - be they from the world's oceans or the human gut. A key step in exploring such data is the identification of dependencies between members of these communities, which is commonly achieved by correlation analysis. However, it has been known since the days of Karl Pearson that the analysis of the type of data generated by such techniques (referred to as compositional data) can produce unreliable results since the observed data take the form of relative fractions of genes or species, rather than their absolute abundances. Using simulated and real data from the Human Microbiome Project, we show that such compositional effects can be widespread and severe: in some real data sets many of the correlations among taxa can be artifactual, and true correlations may even appear with opposite sign. Additionally, we show that community diversity is the key factor that modulates the acuteness of such compositional effects, and develop a new approach, called SparCC (available at https://bitbucket.org/yonatanf/sparcc), which is capable of estimating correlation values from compositional data. To illustrate a potential application of SparCC, we infer a rich ecological network connecting hundreds of interacting species across 18 sites on the human body. Using the SparCC network as a reference, we estimated that the standard approach yields 3 spurious species-species interactions for each true interaction and misses 60% of the true interactions in the human microbiome data, and, as predicted, most of the erroneous links are found in the samples with the lowest diversity.
NASA Ames' Exploration Ground Data Systems (xGDS) supports rapid scientific decision making by synchronizing information in time and space, including video and still images, scientific instrument data, and science and operations notes in geographic and temporal context. We have deployed xGDS at multiple NASA field analog missions over the past decade.In the last two years, we have participated in SUBSEA, a multi-institution collaborative project. SUBSEA used the research ship E/V Nautilus along with its two remotely operated vehicles (ROVs), Hercules and Argus, to explore deep ocean volcanic vents as an analog for ocean worlds (e.g. Enceladus). This work allowed us to compare the existing oceanographic operations methods and technologies used for ocean exploration with corresponding tools and approaches developed and used at NASA. In the first year of SUBSEA we observed existing remote science operations from the Inner Space Center (ISC). In the second year, we deployed xGDS at ISC to complement existing capabilities with xGDS tools designed to support remote Nautilus science operations from the ISC. During operations, video, ROV position and instrument telemetry were streamed from the ship to the ISC. As the science team watched dive operations, they could annotate the data with observations that were relevant to their work domain. Later, the team members could review the data at their own pace to collaboratively develop a dive plan for the next day, which had to be delivered on a fixed daily schedule.The opportunity to compare operations under different conditions enabled us to make several key observations about conducting remote science and planning operations efficiently: (i) Reviewing data collaboratively and interactively with temporal and spatial context was critical for the remote science team's ability to plan dive operations on the Nautilus. (ii) Science team members were actively engaged with the remote dive operations because they could interact with the collected data and visualize it as they desired. (iii) Being able to replay past events at accelerated speeds, and jump to points in time and spaced based on search results, provided efficient access to critical points of interest in a massive volume of data, so the remote science team could deliver plans on time. SUBSEA (Systematic Underwater Biogeochemical Science and Exploration Analog) is a multi-institution collaboration supported by NASA, NOAA's Office of Exploration Research (OER), the Ocean Exploration Trust (OET) and the University of Rhode Island's Graduate School of Oceanography (GSO). ISC is GSO's telepresence operations facility.
The impact of electron scattering at surfaces and grain boundaries in nanometric polycrystalline tungsten (W) films was studied. A series of polycrystalline W films ranging in thickness from 10 to 310 nm and lateral grain size from 74 to 133 nm were prepared on thermally oxidized Si. The Fuchs-Sondheimer surface-scattering model and Mayadas-Shatzkes grain-boundary scattering model were employed for quantitative analyses. Predictions from the theoretical models were found to deviate systematically from the experimental data. Possible reasons for the failure of the theoretical models to describe the experimental data are explored. Finally, a discussion of the crucial features lacking from existing models is presented, along with possible avenues for improving the models to result in better agreement with experimental data.
ABSTRACT We introduce the Hawai‘i Supernova Flows project and present summary statistics of the first 1217 astronomical transients observed, 668 of which are spectroscopically classified Type Ia Supernovae (SNe Ia). Our project is designed to obtain systematics-limited distances to SNe Ia while consuming minimal dedicated observational resources. To date, we have performed almost 5000 near-infrared (NIR) observations of astronomical transients and have obtained spectra for over 200 host galaxies lacking published spectroscopic redshifts. In this survey paper, we describe the methodology used to select targets, collect/reduce data, calculate distances, and perform quality cuts. We compare our methods to those used in similar studies, finding general agreement or mild improvement. Our summary statistics include various parametrizations of dispersion in the Hubble diagrams produced using fits to several commonly used SN Ia models. We find the lowest dispersions using the SNooPy package’s EBV_model2, with a root mean square deviation of 0.165 mag and a normalized median absolute deviation of 0.123 mag. The full utility of the Hawai‘i Supernova Flows data set far exceeds the analyses presented in this paper. Our photometry will provide a valuable test bed for models of SN Ia incorporating NIR data. Differential cosmological studies comparing optical samples and combined optical and NIR samples will have increased leverage for constraining chromatic effects like dust extinction. We invite the community to explore our data by making the light curves, fits, and host galaxy redshifts publicly accessible.
The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. Genome Portal in the past 2 years was significantly updated, with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI. A critical aspect of handling big data in genomics is the development of visualization and analysis tools that allow scientists to derive meaning from what are otherwise terrabases of inert sequence. An interactive visualization tool developed in the group allows us to explore contigs resulting from a single metagenome assembly. Implemented with modern web technologies that take advantage of the power of the computer's graphical processing unit (gpu), the tool allows the user to easily navigate over a 100,000 data points in multiple dimensions, among many biologically meaningful parameters of a dataset such as relative abundance, contig length, and G+C content.
This layer contains the weakened basement rocks. Isostatic gravity was utilized to identify structural basin areas, characterized by gravity low values reflecting weakened basement rocks. Together interpreted regional fault zones and basin outlines define geothermal "exploration fairways", where the potential exists for deep, superheated fluid flow in the absence of Pliocene or younger volcanic units.
Borehole logging data from legacy wells directly constrain the contemporary distribution of subsea permafrost in the sedimentary section at discrete locations on the U.S. Beaufort Margin and complement recent regional analyses of exploration seismic data to delineate the permafrost's offshore extent. Most usable borehole data were acquired on a ~500 km stretch of the margin and within 30 km of the contemporary coastline from north of Lake Teshekpuk to nearly the U.S.-Canada border. Relying primarily on deep resistivity logs that should be largely unaffected by drilling fluids and hole conditions, the analysis reveals the persistence of several hundred vertical meters of ice-bonded permafrost in nearshore wells near Prudhoe Bay and Foggy Island Bay, with less permafrost detected to the east and west. Permafrost is inferred beneath many barrier islands and in some nearshore and lagoonal (back-barrier) wells. The analysis of borehole logs confirms the offshore pattern of ice-bearing subsea permafrost distribution determined based on regional seismic analyses and reveals that ice content generally diminishes with distance from the coastline. Lacking better well distribution, it is not possible to determine the absolute seaward extent of ice-bearing permafrost, nor the distribution of permafrost beneath the present-day continental shelf at the end of the Pleistocene. However, the recovery of gas hydrate from an outer shelf well (Belcher) and previous delineation of a log signature possibly indicating gas hydrate in an inner shelf well (Hammerhead 2) imply that permafrost may once have extended across much of the shelf offshore Camden Bay.
Large-scale bars and minor mergers are important drivers for the secular evolution of galaxies. Based on ground-based optical images and spectra as well as ultraviolet data from the Galaxy Evolution Explorer and infrared data from the Spitzer Space Telescope, we present a multi-wavelength study of star formation properties in the barred galaxy NGC 7479, which also has obvious features of a minor merger. Using various tracers of star formation, we find that under the effects of both a stellar bar and a minor merger, star formation activity mainly takes place along the galactic bar and arms, while the star formation rate changes from the bar to the disk. With the help of spectral synthesis, we find that strong star formation took place in the bar region about 100 Myr ago, and the stellar bar might have been {approx}10 Gyr old. By comparing our results with the secular evolutionary scenario from Jogee et al., we suggest that NGC 7479 is possibly in a transitional stage of secular evolution at present, and it may eventually become an earlier type galaxy or a luminous infrared galaxy. We also note that the probable minor merger event happened recently in NGC 7479, and we find two candidates for minor merger remnants.
Determination of lunar electrical conductivity profile from joint power spectral density analysis of data from Apollo 12 and Explorer 35 magnetometer data
The sixth annual Space and Earth Science Data Compression Workshop and the third annual Data Compression Industry Workshop were held as a single combined workshop. The workshop was held April 4, 1996 in Snowbird, Utah in conjunction with the 1996 IEEE Data Compression Conference, which was held at the same location March 31 - April 3, 1996. The Space and Earth Science Data Compression sessions seek to explore opportunities for data compression to enhance the collection, analysis, and retrieval of space and earth science data. Of particular interest is data compression research that is integrated into, or has the potential to be integrated into, a particular space or earth science data information system. Preference is given to data compression research that takes into account the scien- tist's data requirements, and the constraints imposed by the data collection, transmission, distribution and archival systems.
ElVis is a prototype system with allows for the interactive visualization of unsteady fluid flow. The increasing computational power applied to fluid dynamics simulations presents the enormous challenge to the visualization system designer to apply a wide range of technologies to the analysis process with ever increasing demands on performance. Visualization of the results of unsteady fluid flow simulations presents the challenge of exploring very large and complex data sets. Since exploration is a trial and error process, it is of utmost importance that the time required to execute a trial (i.e., create a visualization) be at a minimum in order to provide real time interaction.
The ongoing revolution of the natural sciences by the advent of machine learning and artificial intelligence sparked significant interest in the material science community in recent years. The intrinsically high dimensionality of the space of realizable materials makes traditional approaches ineffective for large-scale explorations. Modern data science and machine learning tools developed for increasingly complicated problems are an attractive alternative. An imminent climate catastrophe calls for a clean energy transformation by overhauling current technologies within only several years of possible action available. Tackling this crisis requires the development of new materials at an unprecedented pace and scale. For example, organic photovoltaics have the potential to replace existing silicon-based materials to a large extent and open up new fields of application. In recent years, organic light-emitting diodes have emerged as state-of-the-art technology for digital screens and portable devices and are enabling new applications with flexible displays. Reticular frameworks allow the atom-precise synthesis of nanomaterials and promise to revolutionize the field by the potential to realize multifunctional nanoparticles with applications from gas storage, gas separation, and electrochemical energy storage to nanomedicine. In the recent decade, significant advances in all these fields have been facilitated by the comprehensive application of simulation and machine learning for property prediction, property optimization, and chemical space exploration enabled by considerable advances in computing power and algorithmic efficiency. In this Account, we review the most recent contributions of our group in this thriving field of machine learning for material science. We start with a summary of the most important material classes our group has been involved in, focusing on small molecules as organic electronic materials and crystalline materials. Specifically, we highlight the data-driven approaches we employed to speed up discovery and derive material design strategies. Subsequently, our focus lies on the data-driven methodologies our group has developed and employed, elaborating on high-throughput virtual screening, inverse molecular design, Bayesian optimization, and supervised learning. We discuss the general ideas, their working principles, and their use cases with examples of successful implementations in data-driven material discovery and design efforts. Furthermore, we elaborate on potential pitfalls and remaining challenges of these methods. Finally, we provide a brief outlook for the field as we foresee increasing adaptation and implementation of large scale data-driven approaches in material discovery and design campaigns.