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NASA NTRSDate not supplied

DAAC Collaboration Overview for AGU

The Atmospheric Science Data Center (ASDC), Goddard Earth Sciences Data and Information Systems Center (GES DISC), Socioeconomic Data and Applications Center (SEDAC), Oak Ridge National Laboratory (ORNL), Land Processes DAAC, Alaska Satellite Facility (ASF), as well as NASA Global Imagery Browse Service (GIBS), Earth Science Data Systems (ESDS) Geographic Information Systems Team (EGIST), Earthdata Content Delivery Team, ArcGIS Online Governance Team, and the Systematic Data Transformation ACCESS team have come together to establish the ArcGIS DAAC Collaboration. This coalition of participants will demonstrate their use of the ArcGIS Enterprise to support Earth science research, applied science, and outreach using Earth Observing System Data and Information System (EOSDIS) data. This includes the use of web services to fuse data products across space and time through services (e.g. ArcGIS Image Services, Open Geospatial Consortium (OGC) Web Coverage Service (WCS), and OGC Web Mapping Services (WMS)) for analysis in Jupyter notebooks, desktop tools, and web based applications.

Matthew Steven Tisdale↗

NASA NTRS2020

LaRC SmartLab Apps For Instrument Control And Data Processing: Optical Micrometer Data Visualizer

The LaRC Smart Lab applications are a series of software tools to greatly enhance researcher efficiency by streamlining and automating workflows. Python scripts and applications are increasingly being used in scientific workflows, including for instrument control and data processing. Interactive Python scripting environments such as Jupyter Lab provide powerful tools for using Python. In some use cases, the development of standalone applications with dedicated graphical user interfaces (GUIs) can enhance the utility of the code and open it up to more users, including non-programmers. Here, we describe a GUI based optical micrometer data visualization application developed as part of the LaRC SmartLab project. We highlight its use in visualizing experimental data and briefly discuss its implementation to give pointers to programmers who wish develop work based on this application's or similar co de.

LaRC SmartLab↗

NASA NTRS2021

VESIcal Part I: An open-source thermodynamic model engine for mixed volatile (H2O-CO2) solubility in silicate melts

Thermodynamics has been fundamental to the interpretation of geologic data and modeling of geologic systems for decades. However, more recent advancements in computational capabilities and a marked increase in researchers’ accessibility to computing tools has outpaced the functionality and extensibility of currently available modeling tools. Here we present VESIcal (Volatile Equilibria and Saturation Identification calculator): the first comprehensive modeling tool for H 2 O, CO 2 , and mixed (H 2 O-CO 2 ) solubility in silicate melts that: a) allows users access to seven commonly used models, plus easy inter-comparison between models; b) provides universal functionality for all models (e.g., functions for calculating saturation pressures, degassing paths, etc.); c) can process large datasets (1,000’s of samples) automatically; d) can output computed data into an excel spreadsheet for simple post-modeling analysis; e) integrates advanced plotting capabilities directly within the tool; and f) provides all of these within the framework of a python library, making the tool extensible by the user and allowing any of the model functions to be incorporated into any other code capable of calling python. The tool is presented within this manuscript, which is a Jupyter notebook containing worked examples accessible to python users with a range of skill levels. The basic functions of VESIcal can also be access via a web app (https://vesical.anvil.app). The VESIcal python library is open-source and available for download at https://github.com/kaylai/VESIcal.

K. Iacovino↗

NASA NTRSDate not supplied

GL4U: GeneLab for Colleges and Universities

GeneLab for Colleges and Universities (GL4U) will provide space biology-relevant training in bioinformatics to the next generation of scientists through direct and indirect approaches. The GeneLab (GL) team will host two annual data processing bootcamps, one for college-level students (direct) and one for college educators (indirect – Training of Trainers), in which participants learn to analyze space-relevant omics data hosted on GL. The first bootcamp took place in early June 2021 with about 30 SJSU undergraduate students and covered space biology-specific lectures and hands-on instruction using Jupyter Notebooks (JNs) for RNA sequence (RNAseq) data analysis. All training materials including the enclosed files listed below will be made publicly available on GitHub. RNAseq Bootcamp Lectures (attached in combined file): Introduction to NASA, Space Biology, GeneLab, and the Command Line: NASA_GL_CL_Intro_FINAL.pdf - DRAFT from initial submission NASA_SB_GL_CL_Intro_FULL.pdf - FINAL version presented during the bootcamp - only minor edits from the draft version RNAseq and Data Processing Overview: RNAseq_Overview_FINAL.pdf - DRAFT from initial submission RNAseq_Overview_FULL.pdf - FINAL version presented during the bootcamp - only minor edits from the draft version Overview of the Statistics Used for RNAseq Data Analysis: SJSU_Statistics_Intro_Lecture_FINAL.pdf - DRAFT from initial submission Statistics_Overview_FULL.pdf - FINAL version presented during the bootcamp - only minor edits from the draft version Completed JNs in HTML format (attached in combined file): Unix_Intro_JN_06-2021_completed.html R_Intro_JN_06-2021_completed.html RNAseq_fastq_to_counts_JN_06-2021_completed.html RNAseq_DGE_JN_06-2021_completed.html RNAseq Bootcamp Recordings (attached): GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day1_Part_1_of_5.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day1_Part_2_of_5.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day1_Part_3_of_5.mp4 *There were issues with the part 4 recording so that is not available GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day1_Part_5_of_5.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day2_Part_1_of_3.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day2_Part_2_of_3.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day2_Part_3_of_3.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day3_Part_1_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day3_Part_2_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day3_Part_3_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day3_Part_4_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day4_Part_1_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day4_Part_2_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day4_Part_3_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day4_Part_4_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day5_Part_1_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day5_Part_2_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day5_Part_3_of_4.mp4 GL4U_RNAseq_Bootcamp_June_2021_Pilot_Day5_Part_4_of_4.mp4

GeneLab↗

NASA NTRSDate not supplied

GL4U: Training the next generation of bioinformaticians, one omics datatype at a time

Spaceflight modifies gene expression in every organism examined to date, including humans. Understanding how these gene expression changes affect physiology is crucial for the development of countermeasures to enable long-duration manned missions. NASA’s GeneLab project provides researchers open access to multi-omics data, including genetic and gene expression data, from spaceflight experiments that can be mined to understand the effects of spaceflight on biological systems. To ensure new knowledge generation through data re-use, it is important to maximize the number of scientists who utilize GeneLab data. Training students on the GeneLab platform is the best way to create long-term adopters of this NASA database and its tools. Turning students into future instructors and advocates will also accelerate the dissemination of these data and tools to the broader scientific community. Therefore, in collaboration with the GeneLab Educational Working Group (EWG), GeneLab has created GeneLab for Colleges and Universities (GL4U). GL4U provides space biology-relevant training in bioinformatics to the next generation of scientists through direct and indirect approaches. The GeneLab team plans to host two annual data processing bootcamps, one for college-level students (direct) and one for college educators (indirect – training of trainers), in which participants learn to analyze GeneLab’s space-relevant omics data. During the bootcamp, educators will receive materials and training to enable them to run the bootcamp at their home institutions or alternatively to adapt the content to implement within existing courses, thereby extending the reach of this initiative. The GL4U direct training pilot program was conducted in June 2021 in collaboration with USRA and San Jose State University (SJSU). During the pilot, SJSU students participated in a week-long bootcamp consisting of space biology-specific lectures and hands-on instruction using Jupyter Notebooks to analyze RNA sequence data. This pilot demonstrates the capacity of GL4U for training young scientists and encouraging data re-use.

Jonathan Matthew Galazka↗

NASA NTRS2021

The Atacama Cosmology Telescope: Summary of DR4 and DR5 Data Products and Data Access

Two recent large data releases for the Atacama Cosmology Telescope (ACT), called DR4 and DR5, are available for public access. These data include temperature and polarization maps that cover nearly half the sky at arcminute resolution in three frequency bands; lensing maps and component-separated maps covering ∼2100 deg 2 of sky; derived power spectra and cosmological likelihoods; a catalog of over 4000 galaxy clusters; and supporting ancillary products including beam functions and masks. The data and products are described in a suite of ACT papers; here we provide a summary. In order to facilitate ease of access to these data, we present a set of Jupyter IPython notebooks developed to introduce users to DR4, DR5, and the tools needed to analyze these data. The data products (excluding simulations) and the set of notebooks are publicly available on the NASA Legacy Archive for Microwave Background Data Analysis; simulation products are available on the National Energy Research Scientific Computing Center.

Maya Mallaby-Kay↗

NASA NTRSDate not supplied

What (and How) MERRA-2 Reanalysis Data are Used in Applied Sciences

The Modern Era Retrospective-analysis for Research and Applications, Version 2 (MERRA-2) is the global atmospheric data reanalysis for the satellite era produced by NASA’s Global Modeling and Assimilation Office (GMAO), using the Goddard Earth Observing System Model (GEOS)version 5.12.4. The data are officially distributed by the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC). MERRA-2 data have been widely used by the Earth sciences and application community. Since MERRA-2 data were released in early 2016, the number of registered data users has grown steadily from 1,252 in 2016 to 6477 in 2020. By the end of October 2021, ~16 petabytes (over 360 million files) of data have been distributed to more than 18,900 users. Searching in Google Scholar (https://scholar.google.com/), we have found over 7,000 articles, published between January 2017 and May 2021, involving the use ofMERRA-2 data. The figure shows the numbers for various application areas in which theMERRA-2 data have been used, covering almost all of the application areas defined in NASA Applied Sciences (http://appliedsciences.nasa.gov). The largest number of articles are found in disaster research, with the subcategories ordered in flood, wildfires, hurricanes and cyclones, and other forms of severe weather. In this presentation, we will discuss the preliminary findings from a review of the selected literature that uses MERRA-2 data in applied sciences. The current analytic and interoperable data services at GES DISC are listed, such as the on-the-fly subset and analysis service, NASA Giovanni; THREDDS Data Server(TDS); and Python Jupyter notebooks. In addition, we will introduce two new services for supporting the open sciences: My Dashboard and Related Publications.

data management↗

NASA NTRSDate not supplied

GL4U: Bioinformatics training for students and educators using space omics data

Amanda Marie Saravia-butler↗

NASA NTRSDate not supplied

fmdtools Tutorial: Intro to Resilience Modelling, Simulation, and Visualization in Python With fmdtools

This workshop will cover the basics of using the fmdtools package for the simulation of hazardous scenarios for resilience simulation. The fmdtools simulation package is an open-source python toolkit for simulating the dynamic response of a system to internal and externally-driven hazardous scenarios, including faults and environmental conditions, that can be used to analyze the risks related to these hazards. Prior to the development of fmdtools, researchers had to either adapt an (often limited) propriety toolkit or develop their own design/simulation/analysis codes to develop their models of hazardous events, a significant technical burden to both (1) leveraging resilience modeling methodologies and (2) extending these methodologies with their own contributions. The fmdtools package provides a number of model constructs and simulation and analysis methods to enable the designer to focus to solely on their modeling case-study while still enabling a significant degree of model expressiveness and adaptability via Python-based model definition. This tutorial will present the setup of fmdtools and a high-level overview of its use, as well as some simple examples for understanding how to leverage its modelling, simulation, and analysis capabilities. Familiarity with jupyter notebook and basic python will be assumed.

Daniel Hulse↗

NASA NTRSDate not supplied

GL4U: Using Space Omics Data to Provide Bioinformatics Training for Students and Educators

NASA’s GeneLab project provides researchers open access to space-relevant experiment multi-omics data that can be mined to understand the effects of spaceflight on biological systems. To maximize the number of scientists who understand and utilize GeneLab data and data processing pipelines, GeneLab has created GeneLab for Colleges and Universities (GL4U). GL4U provides space biology-relevant training in bioinformatics to the next generation of scientists through direct and indirect approaches. The GeneLab team plans to host two annual data processing bootcamps, one for college-level students (direct) and one for college educators (indirect – training of trainers), in which participants learn to analyze GeneLab’s space-relevant omics data. The GL4U direct training pilot program was conducted in June 2021. During the pilot, students participated in a week-long bootcamp consisting of space biology-specific lectures and hands-on instruction using Jupyter Notebooks to analyze RNA sequence data. This pilot demonstrated the capacity of GL4U for training young scientists and encouraging data re-use. In June 2022, GL4U partnered with Jet Propulsion Laboratory’s (JPL) Planetary Protection Center of Excellence to conduct the indirect training pilot program by training educators at historically black colleges and universities (HBCUs) and minority serving institutions (MSIs). During the educator pilot, participants received materials, training, and will be provided the necessary compute resources to enable them to run the bootcamp at their home institutions or alternatively to adapt the content to implement within existing courses, thereby extending the reach of this initiative. The GL4U training program provides undergraduate students from underrepresented groups the opportunity to learn about NASA and Space Biology, and to enhance their career prospects by gaining hands-on experience analyzing omics data, a skillset that is highly applicable and marketable in the life sciences. Pre- and post-bootcamp surveys were completed by all participants and show the overwhelming success of the bootcamps.

Amanda M. Saravia-Butler↗

NASA NTRSDate not supplied

GL4U: Bioinformatics Training for Students and Educators Using Space Omics Data

Amanda Marie Saravia-butler↗

NASA NTRSDate not supplied

Characterizing Wildfires in Western US.: A Cloud-based Case Study for Interdisciplinary Research using NASA Resources

This presentation will demonstrate a case study of interdisciplinary research done in the Amazon Web Services (AWS) cloud platform, in addition to in the local machine. We conduct data analysis next to data by leveraging various cloud-based data in NASA Earthdata Cloud, which are distributed by different missions/NASA Distributed Active Archive Centers (DAACs), and cloud computing resources at NASA. For instance, we directly access multiple datasets stored in the AWS Simple Storage Service (S3) buckets using a Python Jupyter notebook through a JupyterHub interface hosted in AWS (without having to download data), and conduct data analysis next to data in the cloud. We will also show how to share the research results following Open Source policy. This case study characterizes the change in wildfire events in the western United States during the past 20 years. In particular, we focus on the wildfires in California in 2021, one of the most severe wildfire years occurring in the most recent 20 years in California. We will analyze the possible causes of wildfires, such as drought conditions and climate variability, and examine the impacts of wildfires on air quality and atmospheric composition, and on land cover. We will examine the data distributed by the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC), including aerosols and meteorological data from the NASA Modern-Era Retrospective analysis for Research and Applications version 2 (MERRA-2), precipitation from the Global Precipitation Measurement (GPM) and Global Precipitation Climate Project (GPCP), and aerosol index from Ozone Monitoring Instrument (OMI). We also utilize the data distributed by the Physical Oceanography (PO) DAAC, such as Sea Surface Temperature (SST) data from the Group for High Resolution Sea Surface Temperature (GHRSST), and the data distributed by Land Processes (LP) DAAC, such as Normalized Difference Vegetation Index (NDVI).

Xiaohua Pan↗

NASA NTRSDate not supplied

The NASA Merra-2 Reanalysis Products: Data and Tools Used for Aerosol and Air Quality Studies

The NASA Modern-Era Retrospective analysis for Research and Applications Version 2 (MERRA-2) is atmospheric reanalysis data spanning 1980 to present. It has been produced by the NASA Global Modeling and Assimilation Office (GMAO) and is distributed by the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC). MERRA-2 data includes 100 collections of Earth system variables, mainly from the atmospheric model, such as aerosol fields and meteorological fields, radiation fields, and aerosol fields, guided by the assimilation of as many as six million observations every six hours. MERRA-2 has been one of the most popular datasets from NASA and is widely used in interdisciplinary research and applications, with increasing numbers of new users. For example, at least 7000 users accessed MERRA-2 data at GES DISC in the year 2021, ~1000 more users than in the year 2020. In this presentation, we will introduce the MERRA-2 datasets associated with aerosol and air quality studies and use a wildfire case study to demonstrate the data tools developed at GES DISC to analyze and visualize MERRA-2 data, such as Giovanni and the level 3 and level 4 subsetter, and Jupyter Python notebook. We will also update the status of cloud migration of the MERRA-2 data to Amazon Web Services (AWS).

Xiaohua Pan↗

NASA NTRSDate not supplied

Data Assimilation and Reanalysis

This presentation introduces the Data Assimilation and Reanalysis principle, then details the NASA Modern-Era Retrospective analysis for Research and Applications Version 2 (MERRA-2). The MERRA-2 is atmospheric reanalysis data spanning 1980 to the present. It has been produced by the NASA Global Modeling and Assimilation Office (GMAO) and is distributed by the NASA Goddard Earth Sciences Data and Information Services Center (GES DISC). In this presentation, I will introduce the MERRA-2 datasets associated with aerosol and air quality studies and use case studies to demonstrate the data tools developed at GES DISC to analyze and visualize MERRA-2 data, such as Giovanni and Jupyter Python notebook.

Xiaohua Pan↗

NASA NTRSDate not supplied

Microbial Optical Data Processing: A Key Step in the Metabolic Assessment of Lunar Explorer Instrument for Space Biology Applications (LEIA) and Biosentinel’s Payload Data

The BioSensor payload platform on BioSentinel and LEIA autonomously collects optical data from microbial model organisms in liquid culture. The BioSensor is designed to monitor metabolic activity using absorbance measurements of cell density and alamarBlue, a readily available colorimetric redox indicator dye. BioSentinel, a pioneering NASA CubeSat, uses yeast to study deep space radiation. LEIA investigates radiation and lunar gravity response. The experimental setup includes 16 wells equipped with three LEDs (570, 630, and 850 nm) and their corresponding photodetectors. One well is a calibration control without biology while the rest have desiccated cultures. Autonomous rehydration initiates the experiment. Data from the BioSensor are received from the flight and ground units, enabling comparison to uncover location-based metabolic rate variations. This study presents a Python Jupyter notebook developed for efficient data processing of multiple CSV files containing date and time columns, temperature, and well illumination data. It offers a user-friendly interface while maintaining computational power, automatically recognizing and iteratively processing data files in a user-input path. A Hampel filter with a short window eliminates outlier artifacts from sensor dropout. Because absorbance is a relative measurement, conversion from raw illumination requires defining a “blank” value, so the first data points are averaged to provide the necessary denominator. A cube-root function correction mitigates undesired drift caused by air pockets during the fluidic card filling phase, maintaining optical path length consistency. Beer-Lambert's law is applied to further convert absorbance values to cell and dye form concentrations, the desired science parameters. The processed data are saved and visualized as SVG plots. Future plans include extracting specific science parameters from the processed data like growth rate and metabolic rate, and identification of features corresponding to metabolic and phenotypic shifts such as starvation, shifts from aerobic to anaerobic growth, and osmotic stresses.

Space biology↗

NASA NTRSDate not supplied

GL4U: Using Space Biology Omics Data to Provide Bioinformatics Training for Students and Educators

NASA’s GeneLab project provides researchers open access to space-relevant multi-omics data via the Open Science Data Repository (OSDR) that can be mined to understand the effects of spaceflight on biological systems. To maximize the number of scientists who understand and utilize GeneLab data and data processing pipelines, GeneLab created GeneLab for Colleges and Universities (GL4U). GL4U provides space biology-relevant training in bioinformatics to the next generation of scientists through direct (training students) and indirect (training educators) approaches. The GL4U pilot programs were conducted in June 2021 (direct training) and 2022 (indirect training). During the pilots, students and educators at Historically Black Colleges and Universities (HBCUs) and Minority Serving Institutions (MSIs) participated in a week-long (direct training) or two-week-long (indirect training) bootcamp consisting of space biology-specific lectures and hands-on instruction using Jupyter Notebooks to analyze space biology RNA sequencing data from OSDR. During the educator pilot, participants received materials, training, and the necessary compute resources to enable them to run the bootcamp at their home institutions, thereby extending the reach of this initiative. In July 2023, GeneLab is partnering with JPL to expand GL4U to include amplicon sequencing (Amp-Seq) analysis training. During the GL4U Amp-Seq bootcamp, student and educator participants will receive training on how to analyze and interpret Amp-Seq data using the NASA GeneLab data processing pipeline. All bootcamp material, including instructions for requesting compute resources, will be made publicly available on GitHub for educators to teach the GL4U content in subsequent semesters. GL4U provides undergraduate students from underrepresented groups the opportunity to learn about NASA and Space Biology, and to enhance their career prospects by gaining hands-on experience analyzing omics data, a skillset that is highly applicable and marketable in the life sciences. We present results from pre- and post-training surveys completed by all participants of the Amp-Seq bootcamp.

Amanda M Saravia-Butler↗

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 NTRSDate not supplied

Enabling Analysis of Air Quality Data From Tropospheric Emissions: Monitoring of POllution (Tempo) Via Cloud-Based Tools

Launched in April 2023, the Tropospheric Emissions: Monitoring of POllution (TEMPO) instrument provides high-resolution measurements of key atmospheric pollutants, such as ozone, nitrogen dioxide, and formaldehyde. Maximizing the use and utility of this new source of air quality information requires streamlining data access for a wide variety of research, public health, and other interested users. These varied applications often require the data to be structured in different ways, e.g., specific formats, array shapes, or file sizes. To enable access to TEMPO data in different forms, the NASA Atmospheric Science Data Center (ASDC), as part of the NASA Earth Science Data and Information System (ESDIS), provides a variety of cloud-based data transformation and GIS visualization tools. This presentation demonstrates methods of accessing and working with TEMPO data through these services, while highlighting aspects of the software and algorithmic workflows that perform the necessary data transformations. Examples include data subsetting, concatenation, and visualizations accessible via Jupyter notebooks and GIS software.

Daniel Kaufman↗