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NASA NTRS2018

The CEOS Data Cube Portal: A User-Friendly, Open Source Software Solution for the Distribution, Exploration, Analysis, and Visualization of Analysis Ready Data

There is an urgent need to increase the capacity of developing countries to take part in the study and monitoring of their environments through remote sensing and space-based Earth observation technologies. The Open Data Cube (ODC) provides a mechanism for efficient storage and a powerful framework for processing and analyzing satellite data. While this is ideal for scientific research, the expansive feature space can also be daunting for end-users and decision-makers who simply require a solution which provides easy exploration, analysis, and visualization of Analysis Ready Data (ARD). Utilizing innovative web-design and a modular architecture, the Committee on Earth Observation Satellites (CEOS) has created a web-based user interface (UI) which harnesses the power of the ODC yet provides a simple and familiar user experience: the CEOS Data Cube (CDC). This paper presents an overview of the CDC architecture and the salient features of the UI. In order to provide adaptability, flexibility, scalability, and robustness, we leverage widely-adopted and well-supported technologies such as the Django web framework and the AWS Cloud platform. The fully-customizable source code of the UI is available at our public repository. Interested parties can download the source and build their own UIs. The UI empowers users by providing features that assist with streamlining data preparation, data processing, data visualization, and sub-setting ARD products in order to achieve a wide variety of Earth imaging objectives through an easy to use web interface.

User Interface↗

NASA NTRSDate not supplied

NASA GeneLab: The NASA Systems Biology Platform for Spaceomics Repository, Analysis and Visualization

At NASA Ames Research Center, the GeneLab Open Science Project is on a mission to gather all large -omics datasets relevant to space biology research. These datasets come from various organisms flown in multiple space habitats such as the International Space Station or the Space Shuttle, in addition to mimicking space-like conditions on ground. Researchers and citizen scientists all around the world have used the data and the analytical tools put together by the GeneLab team to start deciphering new biological impact of microgravity, space ionizing radiation and other space stressors.

GeneLab↗

NASA NTRS2018

EOSDIS CMR: Shifting Data Discovery & Use into a Higher Gear

Earth observation data comes in many forms, formats, and from a multitude of sources; to make the best of a very large and diverse data catalog (data from a dozen different national Distributed Active Archive Centers (DAACs) as well as international sources), NASA has created a one-stop-shop for earth data consumers to view, find, and get the data they need regardless of its original source or format, which is powered by a Common Metadata Repository (CMR). CMR is the underpinning that allows for the visualization, search, discovery, manipulation, and acquisition of a variety of datasets, and as such it is constantly evolving to do more and serve our communities better; CMR has embraced community ownership by making itself an open-source API, being compatible with Catalog Services for the Web (CSW) and OpenSearch APIs, and by encouraging the user community to make and share improvements.

CMR↗

NASA NTRSDate not supplied

Ramdb: The NASA Raman Spectral Database (version 1.00).

Given that, in most instances, minimal sample preparation is required and due to its contactless instrument design, Raman spectroscopy is one of the most versatile vibrational spectroscopic techniques for the chemical analysis of environmental and biological specimens. The diversity of applications of Raman spectroscopy ranges anywhere from art [1] to planetary science missions [2]. The advancement in the use of Raman spectroscopy in Solar System missions, notably in post-mission sample return analysis, requires a spectral library holding the broad range of specimens that could be found in Solar System sources. For this purpose, we have initiated the development of a Raman spectral database (Ramdb) at NASA Ames Research Center. Currently, the database includes experimental and theoretical Raman spectra of PAHs [3, 4], as well as laboratory Raman spectra of amino acids, carbon allotropes, minerals, and analogs relevance to Earth Sciences [5], Exobiology [6], Planetary [7], and Astrochemistry [8] to name just a few examples. Ramdb can be found on the web at www.astrochemistry.org/ramdb, where raw and processed Raman spectra can be downloaded in CSV format. The laboratory Raman spectra are measured using a laser Raman spectrometer (JASCO NRS-5500-532QRI). The Raman instrument is equipped with three excitation lasers, with wavelengths of 405, 532, and 785 nm. A clean silicon substrate is used as the internal standard for wavenumber calibration. Powdered samples were prepared (microscopic >10 um, grounded microscopic < 10 um) on glass slides. Some raw data exhibited a background signal arising as a combination of laser-induced fluorescence from the sample. To correct this background, we developed a Python pipeline that uses open-source Python libraries. Ramdb provides both raw and processed (using Python pipeline) data, which includes tabulated Raman shift transitions and other measurement details. The theoretical Raman band positions of PAHs (pyrene monomers and tetramer clusters) were computed using density functional theory (DFT) with the help of the Gaussian 16 suite of programs [9]. In the near future, Ramdb will serve as a repository of Raman spectral data from Laboratory Astrophysics and Planetary Science experiments involving the irradiation of organic compounds under simulated space and planetary conditions. In addition, online and offline tools will be developed for utilising the database for comparison to the user’s sample.

N Punnakayathil↗

NASA NTRSDate not supplied

pyQuARC: Preparing for Full Release

Metadata holds the contextual information about data and is the underlying structure for many data search portals. High quality metadata optimizes search results, allowing users to quickly retrieve the data they need. With the abundant volume and diversity of Earth observation datasets, data discovery and metadata quality are critical for end users. The Common Metadata Repository (CMR), for example, currently hosts metadata for over 9,000 Earth observation data products archived across 12 NASA Distributed Active Archive Centers (DAACs). The Analysis and Review of CMR (ARC) Team, located at Marshall Space Flight Center, assesses the completeness, correctness, and consistency of these metadata records to ensure they are accessible, usable, and discoverable. In 2021, ARC began developing pyQuARC, an open source library for Earth Observation Metadata Quality Assessment to automate this effort. The tool uses ARC’s existing metadata quality framework to provide prioritized recommendations for metadata improvement. During initial testing, pyQuARC automatically identified 58% of metadata findings when compared with a sample of manually reviewed records. Using the results from initial testing, this presentation will focus on recent advancements and improvements of the tool as the ARC team prepares for pyQuARC’s full release. It will also demonstrate pyQuARC's enrichment value, not only for the ARC team, but the broader EOSDIS metadata community as well.

Essence Raphael↗

NASA NTRSDate not supplied

NASA GeneLab Multi-study Visualization Portal

NASA GeneLab has helped advance the field of Space Biology by providing a public repository where researchers can store, share, analyze and visualize the results of space flight related omics experiments. The GeneLab data visualization portal allows any user, regardless of bioinformatics knowledge or access to computational resources, to interact with the experimental data, draw their own conclusions, and gain insights about the effects of space on living systems. These tools help democratize scientific research and foster the NASA Open Science initiative. The new multi-study feature of the GeneLab visualization platform allows users to mine study metadata from RNA sequencing (RNA-seq) experiments to identify samples of interest by filtering datasets based on organism, tissue, assay technology type, and/or factor. Once samples are selected from multiple datasets, users can combine and normalize the sample data, then utilize the visualization displays, including Principal Component Analysis (PCA) plots, to assess sample distributions. Finally, users can perform differential gene expression analysis on the combined data and visualize the results through PCA plots, Volcano plots, Pair plots, Heatmap, Ideogram and Gene Set Enrichment Analysis. All user-generated results and visualizations will be available for download. Here, we present a biological study using samples from multiple GeneLab RNA-seq datasets and analyzed using the multi-study visualization platform to demonstrate inter- and intra-study variability, as well as commonly differentially expressed genes between spaceflight and ground control conditions across datasets. This new feature opens a wide range of possibilities and opportunities for further development including combining other assay technology types and integration with batch effect correction techniques and machine learning applications. Overall, this tool allows users to increase the statistical power of individual experiments, validate hypothesis, identify patterns, and opens the door to new and exciting research.

space biology↗

NASA NTRS2007

Lessons Learned from Deploying an Analytical Task Management Database

Defining requirements, missions, technologies, and concepts for space exploration involves multiple levels of organizations, teams of people with complementary skills, and analytical models and simulations. Analytical activities range from filling a To-Be-Determined (TBD) in a requirement to creating animations and simulations of exploration missions. In a program as large as returning to the Moon, there are hundreds of simultaneous analysis activities. A way to manage and integrate efforts of this magnitude is to deploy a centralized database that provides the capability to define tasks, identify resources, describe products, schedule deliveries, and generate a variety of reports. This paper describes a web-accessible task management system and explains the lessons learned during the development and deployment of the database. Through the database, managers and team leaders can define tasks, establish review schedules, assign teams, link tasks to specific requirements, identify products, and link the task data records to external repositories that contain the products. Data filters and spreadsheet export utilities provide a powerful capability to create custom reports. Import utilities provide a means to populate the database from previously filled form files. Within a four month period, a small team analyzed requirements, developed a prototype, conducted multiple system demonstrations, and deployed a working system supporting hundreds of users across the aeros pace community. Open-source technologies and agile software development techniques, applied by a skilled team enabled this impressive achievement. Topics in the paper cover the web application technologies, agile software development, an overview of the system's functions and features, dealing with increasing scope, and deploying new versions of the system.

O'Neil, Daniel A.↗

NASA NTRS2023

A Community Convention for Ecological Forecasting: Output Files and Metadata Version 1.0

This paper summarizes the open community conventions developed by the Ecological Forecasting Initiative (EFI) for the common formatting and archiving of ecological forecasts and the metadata associated with these forecasts. Such open standards are intended to promote interoperability and facilitate forecast communication, distribution, validation, and synthesis. For output files, we first describe the convention conceptually in terms of global attributes, forecast dimensions, forecasted variables, and ancillary indicator variables. We then illustrate the application of this convention to the two file formats that are currently preferred by the EFI, netCDF (network common data form), and comma-separated values (CSV), but note that the convention is extensible to future formats. For metadata, EFI's convention identifies a subset of conventional metadata variables that are required (e.g., temporal resolution and output variables) but focuses on developing a framework for storing information about forecast uncertainty propagation, data assimilation, and model complexity, which aims to facilitate cross-forecast synthesis. The initial application of this convention expands upon the Ecological Metadata Language (EML), a commonly used metadata standard in ecology. To facilitate community adoption, we also provide a Github repository containing a metadata validator tool and several vignettes in R and Python on how to both write and read in the EFI standard. Lastly, we provide guidance on forecast archiving, making an important distinction between short-term dissemination and long-term forecast archiving, while also touching on the archiving of code and workflows. Overall, the EFI convention is a living document that can continue to evolve over time through an open community process.

Michael C. Dietze↗

NASA NTRS2016

EVA Wiki - Transforming Knowledge Management for EVA Flight Controllers and Instructors

The EVA (Extravehicular Activity) Wiki was recently implemented as the primary knowledge database to retain critical knowledge and skills in the EVA Operations group at NASA's Johnson Space Center by ensuring that information is recorded in a common, searchable repository. Prior to the EVA Wiki, information required for EVA flight controllers and instructors was scattered across different sources, including multiple file share directories, SharePoint, individual computers, and paper archives. Many documents were outdated, and data was often difficult to find and distribute. In 2011, a team recognized that these knowledge management problems could be solved by creating an EVA Wiki using MediaWiki, a free and open-source software developed by the Wikimedia Foundation. The EVA Wiki developed into an EVA-specific Wikipedia on an internal NASA server. While the technical implementation of the wiki had many challenges, the one of the biggest hurdles came from a cultural shift. Like many enterprise organizations, the EVA Operations group was accustomed to hierarchical data structures and individually-owned documents. Instead of sorting files into various folders, the wiki searches content. Rather than having a single document owner, the wiki harmonized the efforts of many contributors and established an automated revision control system. As the group adapted to the wiki, the usefulness of this single portal for information became apparent. It transformed into a useful data mining tool for EVA flight controllers and instructors, and also for hundreds of other NASA and contract employees. Program managers, engineers, astronauts, flight directors, and flight controllers in differing disciplines now have an easier-to-use, searchable system to find EVA data. This paper presents the benefits the EVA Wiki has brought to NASA's EVA community, as well as the cultural challenges it had to overcome.

Johnston, Stephanie↗

NASA NTRS2016

EVA Wiki - Transforming Knowledge Management for EVA Flight Controllers and Instructors

The EVA Wiki was recently implemented as the primary knowledge database to retain critical knowledge and skills in the EVA Operations group at NASA's Johnson Space Center by ensuring that information is recorded in a common, easy to search repository. Prior to the EVA Wiki, information required for EVA flight controllers and instructors was scattered across different sources, including multiple file share directories, SharePoint, individual computers, and paper archives. Many documents were outdated, and data was often difficult to find and distribute. In 2011, a team recognized that these knowledge management problems could be solved by creating an EVA Wiki using MediaWiki, a free and open-source software developed by the Wikimedia Foundation. The EVA Wiki developed into an EVA-specific Wikipedia on an internal NASA server. While the technical implementation of the wiki had many challenges, one of the biggest hurdles came from a cultural shift. Like many enterprise organizations, the EVA Operations group was accustomed to hierarchical data structures and individually-owned documents. Instead of sorting files into various folders, the wiki searches content. Rather than having a single document owner, the wiki harmonized the efforts of many contributors and established an automated revision controlled system. As the group adapted to the wiki, the usefulness of this single portal for information became apparent. It transformed into a useful data mining tool for EVA flight controllers and instructors, as well as hundreds of others that support the EVA. Program managers, engineers, astronauts, flight directors, and flight controllers in differing disciplines now have an easier-to-use, searchable system to find EVA data. This paper presents the benefits the EVA Wiki has brought to NASA's EVA community, as well as the cultural challenges it had to overcome.

Johnston, Stephanie S.↗

NASA NTRS2016

EVA Wiki - Transforming Knowledge Management for EVA Flight Controllers and Instructors

The EVA Wiki was recently implemented as the primary knowledge database to retain critical knowledge and skills in the EVA Operations group at NASA's Johnson Space Center by ensuring that information is recorded in a common, easy to search repository. Prior to the EVA Wiki, information required for EVA flight controllers and instructors was scattered across different sources, including multiple file share directories, SharePoint, individual computers, and paper archives. Many documents were outdated, and data was often difficult to find and distribute. In 2011, a team recognized that these knowledge management problems could be solved by creating an EVA Wiki using MediaWiki, a free and open-source software developed by the Wikimedia Foundation. The EVA Wiki developed into an EVA-specific Wikipedia on an internal NASA server. While the technical implementation of the wiki had many challenges, one of the biggest hurdles came from a cultural shift. Like many enterprise organizations, the EVA Operations group was accustomed to hierarchical data structures and individually-owned documents. Instead of sorting files into various folders, the wiki searches content. Rather than having a single document owner, the wiki harmonized the efforts of many contributors and established an automated revision controlled system. As the group adapted to the wiki, the usefulness of this single portal for information became apparent. It transformed into a useful data mining tool for EVA flight controllers and instructors, as well as hundreds of others that support EVA. Program managers, engineers, astronauts, flight directors, and flight controllers in differing disciplines now have an easier-to-use, searchable system to find EVA data. This paper presents the benefits the EVA Wiki has brought to NASA's EVA community, as well as the cultural challenges it had to overcome.

Johnston, Stephanie S.↗

NASA NTRSDate not supplied

NASA CARA Tools

The NASA Conjunction Assessment Risk Analysis (CARA) team has created and posted to GitHub a set of MATLAB software tools for collision assessment (CA) analysis. The software is provided to the public under a NASA Open-Source Software Agreement and is maintained/updated by the CARA Analysis team. Capabilities provided within the toolset include algorithms in assessing probability of collision (Pc), collision consequence, covariance realism, Orbit Determination (OD) quality assessment, and single covariance max Pc. Additionally, a set of utilities are provided for astrodynamics topics closely related to CA, such as: Conjunction Data Message (CDM) parsing, covariance transformations, coordinate system transformations, etc. The repository is regularly updated on a monthly basis and new functionality will be added as algorithms are approved for public release. This presentation will provide a brief introduction to the toolset, highlight some of the key components which can be used in operations, and will present information on algorithms that are in the release pipeline and can be expected soon. This software will enable operators to independently perform CA calculations using the same core algorithms that CARA uses in operations.

L. Baars↗

NASA NTRSDate not supplied

NASA CARA Tools

Luis Baars↗

NASA NTRS2016

GeneLab Phase 2: Integrated Search Data Federation of Space Biology Experimental Data

The GeneLab project is a science initiative to maximize the scientific return of omics data collected from spaceflight and from ground simulations of microgravity and radiation experiments, supported by a data system for a public bioinformatics repository and collaborative analysis tools for these data. The mission of GeneLab is to maximize the utilization of the valuable biological research resources aboard the ISS by collecting genomic, transcriptomic, proteomic and metabolomic (so-called omics) data to enable the exploration of the molecular network responses of terrestrial biology to space environments using a systems biology approach. All GeneLab data are made available to a worldwide network of researchers through its open-access data system. GeneLab is currently being developed by NASA to support Open Science biomedical research in order to enable the human exploration of space and improve life on earth. Open access to Phase 1 of the GeneLab Data Systems (GLDS) was implemented in April 2015. Download volumes have grown steadily, mirroring the growth in curated space biology research data sets (61 as of June 2016), now exceeding 10 TB/month, with over 10,000 file downloads since the start of Phase 1. For the period April 2015 to May 2016, most frequently downloaded were data from studies of Mus musculus (39) followed closely by Arabidopsis thaliana (30), with the remaining downloads roughly equally split across 12 other organisms (each 10 of total downloads). GLDS Phase 2 is focusing on interoperability, supporting data federation, including integrated search capabilities, of GLDS-housed data sets with external data sources, such as gene expression data from NIHNCBIs Gene Expression Omnibus (GEO), proteomic data from EBIs PRIDE system, and metagenomic data from Argonne National Laboratory's MG-RAST. GEO and MG-RAST employ specifications for investigation metadata that are different from those used by the GLDS and PRIDE (e.g., ISA-Tab). The GLDS Phase 2 system will implement a Google-like, full-text search engine using a Service-Oriented Architecture by utilizing publicly available RESTful web services Application Programming Interfaces (e.g., GEO Entrez Programming Utilities) and a Common Metadata Model (CMM) in order to accommodate the different metadata formats between the heterogeneous bioinformatics databases. GLDS Phase 2 completion with fully implemented capabilities will be made available to the general public in September 2017.

Space Biology↗

NASA NTRSDate not supplied

The Radiation Biology Ontology: A New Tool Supporting FAIR Principles Across Radiation Biology Facilitating Data Discovery and Integration

Development of the Radiation Biology Ontology (RBO) was motivated by the need for a comprehensive, well-structured ontology for encoding radiation biology metadata. The primary use-cases were archiving data in the STORE database (https://www.storedb.org/), the repository for the RadoNorm Project, and in GeneLab (https://genelab.nasa.gov), NASA’s ‘omics database. The scope of radiobiology research ranges from physics to radiation oncology to socio-legal studies; no existing ontology has the necessary breadth or depth. In addition, a formal ontology has the advantage of being usable for machine learning and, importantly, for tasks like data integration, knowledge extraction from the scientific literature and for query extension and data classification. Standardisation of metadata is one of the primary objectives of the FAIR principles for open data; RBO is an important landmark for FAIR radiation biology data.

ontology↗

NASA NTRS1992

The IDL astronomy user's library

IDL (Interactive Data Language) is a commercial programming, plotting, and image display language, which is widely used in astronomy. The IDL Astronomy User's Library is a central repository of over 400 astronomy-related IDL procedures accessible via anonymous FTP. The author will overview the use of IDL within the astronomical community and discuss recent enhancements at the IDL astronomy library. These enhancements include a fairly complete I/O package for FITS images and tables, an image deconvolution package and an image mosaic package, and access to IDL Open Windows/Motif widgets interface. The IDL Astronomy Library is funded by NASA through the Astrophysics Software and Research Aids Program.

Landsman, W. B.↗

NASA NTRSDate not supplied

Kamodo – An Adaptable Tool to Obtain and Compare Observations and Modeling Results

What is Kamodo? -Official NASA open-source project written in Python. -Building upon the functionalization of datasets. -It is a CCMC developed and maintained software tool for access, interpolation, and visualization of space weather models and data. -It allows model developers to represent simulation results as mathematical functions which may be manipulated directly by end users. -It handles unit conversion transparency and supports interactive science discovery through jupyter notebooks with minimal coding. -All Kamodo tools are accessible through Python, and all source code is publicly available on the Kamodo NASA GitHub repositories. -Kamodo does not generate model outputs. Users need to acquire the desired model outputs before they can be functionalized by Kamodo.

Kamodo↗

NASA NTRS1993

The Database Query Support Processor (QSP)

The number and diversity of databases available to users continues to increase dramatically. Currently, the trend is towards decentralized, client server architectures that (on the surface) are less expensive to acquire, operate, and maintain than information architectures based on centralized, monolithic mainframes. The database query support processor (QSP) effort evaluates the performance of a network level, heterogeneous database access capability. Air Force Material Command's Rome Laboratory has developed an approach, based on ANSI standard X3.138 - 1988, 'The Information Resource Dictionary System (IRDS)' to seamless access to heterogeneous databases based on extensions to data dictionary technology. To successfully query a decentralized information system, users must know what data are available from which source, or have the knowledge and system privileges necessary to find out this information. Privacy and security considerations prohibit free and open access to every information system in every network. Even in completely open systems, time required to locate relevant data (in systems of any appreciable size) would be better spent analyzing the data, assuming the original question was not forgotten. Extensions to data dictionary technology have the potential to more fully automate the search and retrieval for relevant data in a decentralized environment. Substantial amounts of time and money could be saved by not having to teach users what data resides in which systems and how to access each of those systems. Information describing data and how to get it could be removed from the application and placed in a dedicated repository where it belongs. The result simplified applications that are less brittle and less expensive to build and maintain. Software technology providing the required functionality is off the shelf. The key difficulty is in defining the metadata required to support the process. The database query support processor effort will provide quantitative data on the amount of effort required to implement an extended data dictionary at the network level, add new systems, adapt to changing user needs, and provide sound estimates on operations and maintenance costs and savings.

Source record↗