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rcsb-api : Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs

The Protein Data Bank (PDB) was founded in 1971 as the first open-access digital data resource in biology to serve as the single global archive for three-dimensional (3D) macromolecular structure data. Current PDB holdings exceed 230,000 experimentally determined structures of proteins, nucleic acids, viruses, and macromolecular machines. The RCSB Protein Data Bank RCSB.org research-focused web portal facilitates search, analyses, and visualization of every PDB structure along with more than one million Computed Structure Models from AlphaFold DB and the ModelArchive. It is powered by a set of publicly available Application Programming Interfaces (APIs) that both support RCSB.org users and provide programmatic access to PDB data. Given the breadth and levels of granularity encompassed in this rich data collection, efficiently accessing the information programmatically may be challenging for new users. RCSB PDB has developed a Python software package, rcsb-api , that facilitates easy and efficient use of RCSB PDB APIs within a Python environment. This software tool is designed to streamline access to the extensive corpus of data housed within the PDB, enabling researchers to search, retrieve, and analyze 3D biostructure data seamlessly. Its use will accelerate research in structural biology, molecular biology and biochemistry, drug discovery, and bioinformatics by providing more efficient tools for data integration and analysis. The new toolkit is available on GitHub (github.com/rcsb/py-rcsb-api) and published to the public Python package repository (PyPI) to foster wider usage and support basic and applied research in fundamental biology, biomedicine, and the energy sciences.

FAIR principles↗

Trends in Small Satellite Presentations from 2017-2019

As the small satellite community expands and new technologies emerge, it is important to understand and interpret these changes over time. In doing so, we observe progress and aid future development within the field. During the summer of 2020 we compiled for assessment purposes, archived presentation data for years 2017-2019 from three primary sources: the CubeSat Developers Workshop, Interplanetary Small Satellite Conference, and the Small Satellite Conference. A few examples of the information we recorded and compiled were presenter names and affiliations, presentation topic, and mission progress status. Ultimately, we reviewed roughly 600 presentations between the three conferences and the data obtained therein form the basis of our trend assessment. The paper focuses on trends interpreted through the assessment of key elements available in the content of each presentation to include: SmallSat mission developers, subsystem developments and the expanded scope for small satellite destinations. Data was generalized using various forms of analysis depending on the type of information being assessed. In the end, we achieved our goal of reducing the content to its key points and major takeaways from the conference proceedings. In this presentation, the observed trends in data and our findings will be discussed. First, we will cover changes in presentation topics by categorizing them as either: science, technology, science/technology, or other. Our next topic will be about the agencies and organizations at the forefront of small satellite research and development. The following section will explain trends in subsystem developments for telecommunications, propulsion, power, and thermal management. Further discussion will highlight how the scope of interplanetary spaceflight has expanded since 2017 as new small spacecraft missions venture beyond low-Earth orbit into deep space exploration. And finally, we will observe what information was lacking in archived presentations which included but not limited to: mission’s funding source, presentation focus area, and software used.

Small Satellite↗

Trends in Small Satellite Presentations from 2017 - 2019

As the small satellite community expands and new technologies emerge, it is important to understand and interpret these changes over time. In doing so, we observe progress and aid future development within the field. During the summer of 2020 we compiled for assessment purposes, archived presentation data for years 2017-2019 from three primary sources: the CubeSat Developers Workshop, Interplanetary Small Satellite Conference, and the Small Satellite Conference. A few examples of the information we recorded and compiled were presenter names and affiliations, presentation topic, and mission progress status. Ultimately, we reviewed roughly 600 presentations between the three conferences and the data obtained therein form the basis of our trend assessment. The paper focuses on trends interpreted through the assessment of key elements available in the content of each presentation to include: SmallSat mission developers, subsystem developments and the expanded scope for small satellite destinations. Data was generalized using various forms of analysis depending on the type of information being assessed. In the end, we achieved our goal of reducing the content to its key points and major takeaways from the conference proceedings. In this presentation, the observed trends in data and our findings will be discussed. First, we will cover changes in presentation topics by categorizing them as either: science, technology, science/technology, or other. Our next topic will be about the agencies and organizations at the forefront of small satellite research and development. The following section will explain trends in subsystem developments for telecommunications, propulsion, power, and thermal management. Further discussion will highlight how the scope of interplanetary spaceflight has expanded since 2017 as new small spacecraft missions venture beyond low-Earth orbit into deep space exploration. And finally, we will observe what information was lacking in archived presentations which included but not limited to: mission’s funding source, presentation focus area, and software used.

Small Satellites↗

NASA GES DISC DAAC Satellite Data for GIS

NASA's Goddard Earth Science (GES) Data and Information Services Center (DISC) Distributed Active Archive Center (DAAC) makes available a large and continually growing collection of spatially continuous global satellite observations of environmental parameters. These products include those from the MODIS (Moderate Resolution Imaging Spectroradiometer) on both Terra and Aqua platforms, and the Tropical Rainfall Measuring Mission (TRMM). These data products are well suited for use within Geographic Information Systems (GIS), as both backdrops to cartographic products as well as spatial analysis. However, data format, file size, and other issues have limited their widespread use by traditional GIS users. To address these data usability issues, the GES DISC DAAC recently updated tools and improved documentation of conversion procedures. In addition, the GES DISC DAAC has also been working with a major GIS software vendor to incorporate the ability to read the native Hierarchial Data Format (HDF), the format in which most of the NASA data is stored. The result is the enabling of GIS users to realize the benefit of GES DISC DAAC data without a substantial expenditure in resources to incorporate these data into their GIS. Several documents regarding the potential uses of GES DISC DAAC satellite data in GIS have recently been created. These show the combinations of concurrent data from different satellite products with traditional GIS vector products for given geographic areas. These map products include satellite imagery of Hurricane Isabel and the California wildfires, and can be viewed at http://daac.gsfc.nasa.gov/MODIS/GIS/.

Nickless, Darryl↗

The System for Classification of Low-Pressure Systems (SyCLoPS): An All-In-One Objective Framework for Large-Scale Data Sets

We propose the first unified objective framework (SyCLoPS) for detecting and classifying all types of low-pressure systems (LPSs) in a given data set. We use the state-of-the-art automated feature tracking software TempestExtremes (TE) to detect and track LPS features globally in ERA5 and compute 16 parameters from commonly found atmospheric variables for classification. A Python classifier is implemented to classify all LPSs at once. The framework assigns 16 different labels (classes) to each LPS data point and designates four different types of high-impact LPS tracks, including tracks of tropical cyclone (TC), monsoonal system, subtropical storm and polar low. The classification process involves disentangling high-altitude and drier LPSs, differentiating tropical and non-tropical LPSs using novel criteria, and optimizing for the detection of the four types of high-impact LPS. A comparison of our labels with those in the International Best Track Archive for Climate Stewardship (IBTrACS) revealed an overall accuracy of 95% in distinguishing between tropical systems, extratropical cyclones, and disturbances. SyCLoPS produces a better TC detection skill compared to the previous algorithms, highlighted by an approximately 6% reduction in the false alarm rate compared to the previous TE algorithm. The vertical cross section composite of the four types of high-impact LPS we detect each shows distinct structural characteristics. Finally, we demonstrate that SyCLoPS is valuable for investigating various aspects of LPSs in climate data, such as the evolution of a single LPS track, patterns of LPS frequencies, and precipitation or wind influence associated with a particular LPS class.

54 ENVIRONMENTAL SCIENCES↗

NASA's Scientific Visualization Studio

Since 1988, the Scientific Visualization Studio(SVS) at NASA Goddard Space Flight Center has produced scientific visualizations of NASA s scientific research and remote sensing data for public outreach. These visualizations take the form of images, animations, and end-to-end systems and have been used in many venues: from the network news to science programs such as NOVA, from museum exhibits at the Smithsonian to White House briefings. This presentation will give an overview of the major activities and accomplishments of the SVS, and some of the most interesting projects and systems developed at the SVS will be described. Particular emphasis will be given to the practices and procedures by which the SVS creates visualizations, from the hardware and software used to the structures and collaborations by which products are designed, developed, and delivered to customers. The web-based archival and delivery system for SVS visualizations at svs.gsfc.nasa.gov will also be described.

Mitchell, Horace G.↗

Attitude Design for the LADEE Mission

The Lunar Atmosphere and Dust Environment Explorer (LADEE) satellite successfully completed its 148-day science investigation in a low-altitude, near-equatorial lunar orbit on April 18, 2014. The LADEE spacecraft was built, managed and operated by NASA's Ames Research Center (ARC). The Mission Operations Center (MOC) was located at Ames and was responsible for activity planning, command sequencing, trajectory and attitude design, orbit determination, and spacecraft operations. The Science Operations Center (SOC) was located at Goddard Space Flight Center and was responsible for science planning, data archiving and distribution. This paper details attitude design and operations support for the LADEE mission. LADEE's attitude design was shaped by a wide range of instrument pointing requirements that necessitated regular excursions from the baseline one revolution per orbit "Ram" attitude. Such attitude excursions were constrained by a number of flight rules levied to protect instruments from the Sun, avoid geometries that would result in simultaneous occlusion of LADEE's two star tracker heads, and maintain the spacecraft within its thermal and power operating limits. To satisfy LADEE's many attitude requirements and constraints, a set of rules and conventions was adopted to manage the complexity of this design challenge and facilitate the automation of ground software that generated pointing commands spanning multiple days of operations at a time. The resulting LADEE Flight Dynamics System (FDS) that was developed used Visual Basic scripts that generated instructions to AGI's Satellite Tool Kit (STK) in order to derive quaternion commands at regular intervals that satisfied LADEE's pointing requirements. These scripts relied heavily on the powerful "align and constrain" capability of STK's attitude module to construct LADEE's attitude profiles and the slews to get there. A description of the scripts and the attitude modeling they embodied is provided. One particular challenge analysts faced was in the design of LADEE maneuver attitudes. A flight rule requiring pre-maneuver verification of in-flight maneuver conditions by ground operators prior to burn execution resulted in the need to accommodate long periods in the maneuver attitude. This in turn complicated efforts to satisfy star tracker interference and communication constraints in lunar orbit. In response to this challenge, a graphical method was developed and used to survey candidate rotation angles about the thrust vector. This survey method is described and an example of its use on a particular LADEE maneuver is discussed. Finally, the software and methodology used to satisfy LADEE's attitude requirements are also discussed in the context of LADEE's overall activity planning effort. In particular, the way in which strategic schedules of instrument and engineering activities were translated into actual attitude profiles at the tactical level, then converted into precise quaternion commands to achieve those pointing goals is explained. In order to reduce the risk of time-consuming re-planning efforts, this process included the generation of long-term projections of constraint violation predictions for individual attitude profiles that could be used to establish keep-out time-frames for particular attitude profiles. The challenges experienced and overall efficacy of both the overall LADEE ground system and the attitude components of the Flight Dynamics System in meeting LADEE's varied pointing requirements are discussed.

LADEE↗

Accessing and Understanding MODIS Data

The National Aeronautics and Space Administration (NASA) launched the Terra satellite in December 1999, as part of the Earth Science Enterprise promotion of interdisciplinary studies of the integrated Earth system. Aqua, the second satellite from the series of EOS constellation, was launched in May 2002. Both satellites carry the MODerate resolution Imaging Spectroradiometer (MODIS) instrument. MODIS data are processed at the Goddard Space Flight Center, Greenbelt, MD, and then archived and distributed by the Distributed Active Archive Centers (DAACs). Data products from the MODIS sensors present new challenges to remote sensing scientists due to specialized production level, data format, and map projection. MODIS data are distributed as calibrated radiances and as higher level products such as: surface reflectance, water-leaving radiances, ocean color and sea surface temperature, land surface kinetic temperature, vegetation indices, leaf area index, land cover, snow cover, sea ice extent, cloud mask, atmospheric profiles, aerosol properties, and many other geophysical parameters. MODIS data are stored in HDF- EOS format in both swath format and in several different map projections. This tutorial guides users through data set characteristics as well as search and order interfaces, data unpacking, data subsetting, and potential applications of the data. A CD-ROM with sample data sets, and software tools for working with the data will be provided to the course participants.

Leptoukh, Gregory↗

JMISR INteractive eXplorer

MISR (Multi-angle Imaging SpectroRadiometer) INteractive eXplorer (MINX) is an interactive visualization program that allows a user to digitize smoke, dust, or volcanic plumes in MISR multiangle images, and automatically retrieve height and wind profiles associated with those plumes. This innovation can perform 9-camera animations of MISR level-1 radiance images to study the 3D relationships of clouds and plumes. MINX also enables archiving MISR aerosol properties and Moderate Resolution Imaging Spectroradiometer (MODIS) fire radiative power along with the heights and winds. It can correct geometric misregistration between cameras by correlating off-nadir camera scenes with corresponding nadir scenes and then warping the images to minimize the misregistration offsets. Plots of BRF (bidirectional reflectance factor) vs. camera angle for points clicked in an image can be displayed. Users get rapid access to map views of MISR path and orbit locations and overflight dates, and past or future orbits can be identified that pass over a specified location at a specified time. Single-camera, level-1 radiance data at 1,100- or 275- meter resolution can be quickly displayed in color using a browse option. This software determines the heights and motion vectors of features above the terrain with greater precision and coverage than previous methods, based on an algorithm that takes wind direction into consideration. Human interpreters can precisely identify plumes and their extent, and wind direction. Overposting of MODIS thermal anomaly data aids in the identification of smoke plumes. The software has been used to preserve graphical and textural versions of the digitized data in a Web-based database.

Nelson, David L.↗

SPE (trademark) Oxygen Generator Assembly (OGA). (Refurbishment of the technology demonstrator LFSPE oxygen generation subsystem)

The SPE Oxygen Generator Assembly (OGA) has been modified to correct operational deficiencies present in the original system, and to effect changes to the system hardware and software such that its operating conditions are consistent with the latest configuration requirements for the International Space Station Alpha (ISSA). The effectiveness of these changes has recently been verified through a comprehensive test program which saw the SPE OGA operate for over 740 hours at various test conditions, including over 690 hours, or approximately 460 cycles, simulating the orbit of the space station. This report documents the changes made to the SPE OGA, presents and discusses the test results from the acceptance test program, and provides recommendations for additional development activities pertinent to evolution of the SPE OGA to a flight configuration. Copies of the test data from the acceptance test program are provided with this report on 3.5 inch diskettes in self-extracting archive files.

Roy, Robert J.↗

Photometric Analysis in the Kepler Science Operations Center Pipeline

We describe the Photometric Analysis (PA) software component and its context in the Kepler Science Operations Center (SOC) pipeline. The primary tasks of this module are to compute the photometric flux and photocenters (centroids) for over 160,000 long cadence (~thirty minute) and 512 short cadence (~one minute) stellar targets from the calibrated pixels in their respective apertures. We discuss the science algorithms for long and short cadence PA: cosmic ray cleaning; background estimation and removal; aperture photometry; and flux-weighted centroiding. We discuss the end-to-end propagation of uncertainties for the science algorithms. Finally, we present examples of photometric apertures, raw flux light curves, and centroid time series from Kepler flight data. PA light curves, centroid time series, and barycentric timestamp corrections are exported to the Multi-mission Archive at Space Telescope [Science Institute] (MAST) and are made available to the general public in accordance with the NASA/Kepler data release policy.

Twicken, Joseph D.↗

Photometric Analysis in the Kepler Science Operations Center Pipeline

We describe the Photometric Analysis (PA) software component and its context in the Kepler Science Operations Center (SOC) Science Processing Pipeline. The primary tasks of this module are to compute the photometric flux and photocenters (centroids) for over 160,000 long cadence (~thirty minute) and 512 short cadence (~one minute) stellar targets from the calibrated pixels in their respective apertures. We discuss science algorithms for long and short cadence PA: cosmic ray cleaning; background estimation and removal; aperture photometry; and flux-weighted centroiding. We discuss the end-to-end propagation of uncertainties for the science algorithms. Finally, we present examples of photometric apertures, raw flux light curves, and centroid time series from Kepler flight data. PA light curves, centroid time series, and barycentric timestamp corrections are exported to the Multi-mission Archive at Space Telescope [Science Institute] (MAST) and are made available to the general public in accordance with the NASA/Kepler data release policy.

photocenter↗

NAE Twin Otter operations in FIFE 1989

During the summer of 1989, the National Aeronautical Establishment (Canada) Twin Otter Atmospheric Research Aircraft was flow in support of the NASA sponsored First ISLSCP (International Satellite Land Surface Climatology Project) Field Experiment called FIFE-89. Airborne measurements of the fluxes of heat, momentum, water vapor and carbon dioxide were made during 16 flow-altitude flights over the FIFE project area in central Kansas. The Twin Otter operations in FIFE are documented and details are included on the instrumentation, software, flight procedures, atmospheric conditions and analysis methods. Comparisons of Twin Otter measured fluxes are made with those determined at several surface sites and with those made by other instrumented aircraft in the FIFE-87 measurements. Airborne flux measurements are related to run length, altitude, and environmental parameters such as vegetation type, temperature, and wind speed. One night flight was run in an attempt to measure the respiration component of the CO2 flux. The use of aircraft was studied for regional observations of fluxes and to relate these to satellite radiance measurements. Run average data are presented for all 285 flux runs flown by the Twin Otter in FIFE-89. This should serve as as a working reference for scientists utilizing Twin Otter data either directly of through the FIFE data archive.

Macpherson, J. I.↗

Displaying Composite and Archived Soundings in the Advanced Weather Interactive Processing System

This presentation describes work done by the Applied Meteorology Unit (AMU) to add composite soundings to the Advanced Weather Interactive Processing System (AWIPS). This allows National Weather Service (NWS) forecasters to compare the current atmospheric state with climatology. In a previous task, the AMU created composite soundings for four rawinsonde observation stations in Florida, for each of eight flow regimes. The composite soundings were delivered to the NWS Melbourne (MLB) office for display using the NSHARP software program. NWS MLB requested that the AMU make the composite soundings available for display in AWIPS. The AMU first created a procedure to customize AWIPS so composite soundings could be displayed. A unique four-character identifier was created for each of the 32 composite soundings. The AMIU wrote a Tool Command Language/Tool Kit (TclITk) software program to convert the composite soundings from NSHARP to Network Common Data Form (NetCDF) format. The NetCDF files were then displayable by AWIPS.

Barrett, Joe H., III↗

Managing an archive of weather satellite images

The author's experiences of building and maintaining an archive of hourly weather satellite pictures at NOAO are described. This archive has proven very popular with visiting and staff astronomers - especially on windy days and cloudy nights. Given access to a source of such pictures, a suite of simple shell and IRAF CL scripts can provide a great deal of robust functionality with little effort. These pictures and associated data products such as surface analysis (radar) maps and National Weather Service forecasts are updated hourly at anonymous ftp sites on the Internet, although your local Atsmospheric Sciences Department may prove to be a more reliable source. The raw image formats are unfamiliar to most astronomers, but reading them into IRAF is straightforward. Techniques for performing this format conversion at the host computer level are described which may prove useful for other chores. Pointers are given to sources of data and of software, including a package of example tools. These tools include shell and Perl scripts for downloading pictures, maps, and forecasts, as well as IRAF scripts and host level programs for translating the images into IRAF and GIF formats and for slicing & dicing the resulting images. Hints for displaying the images and for making hardcopies are given.

Seaman, R. L.↗

Earth Observing System Data Gateway

The Earth Observing System Data Gateway (EDG) software provides a "one-stop-shopping" standard interface for exploring and ordering Earth-science data stored at geographically distributed sites. EDG enables a user to do the following: 1) Search for data according to high-level criteria (e.g., geographic location, time, or satellite that acquired the data); 2) Browse the results of a search, viewing thumbnail sketches of data that satisfy the user s criteria; and 3) Order selected data for delivery to a specified address on a chosen medium (e.g., compact disk or magnetic tape). EDG consists of (1) a component that implements a high-level client/server protocol, and (2) a collection of C-language libraries that implement the passing of protocol messages between an EDG client and one or more EDG servers. EDG servers are located at sites usually called "Distributed Active Archive Centers" (DAACs). Each DAAC may allow access to many individual data items, called "granules" (e.g., single Landsat images). Related granules are grouped into collections called "data sets." EDG enables a user to send a search query to multiple DAACs simultaneously, inspect the resulting information, select browseable granules, and then order selected data from the different sites in a seamless fashion.

Pfister, Robin↗

Origami-based Composite Space Structures

The main objective of my internship was working on developing a new type of deployable composite for space structures and new method of deployment via use of origami, composites, UV curing resins, and shape memory polymers. My role in the project was to collect an initial literature survey on the subject including origami, the history of deployable space structures, previous issues and problems faced in the field, previous and current research being done on the structural aspect as well as the materials aspect of the subject. I presented this information to our team, where we discussed and determined our research focus and project design specs. We have been making or will make decisions on the project’s purpose, material, origami type, manufacturing method, and testing methods. I am now in charge of the protype design as we enter the design stage of our research. I am using PTC Creo software to design the structural aspects of the first protype so that we can begin small scale testing. I will perform data analysis in order to review the results with our team, so we can make the next design decisions regarding changes or iterations of the design. We hope to renew this project in the next fiscal year in order to increase the TRL of the project so that it can eventually be used in multiple functions in space such as the construction of lunar habitats. In just my brief time with NASA, I have gained so much personally and professionally. I developed my ability to search through and narrow down information when doing research. In the weekly meetings I practiced presenting information to my peers and superiors, and, just as importantly, discussing and adapting to what we were learning. I acquired experience in using technology to my advantage including remote work, new software like PTC Creo, NASA archives, and connecting with others beyond my team to gain help. I enjoyed the immense resource of knowledge that my mentors had to offer, and that they gave me a large amount of responsibility in this research. I truly felt like I was contributing to something bigger than myself and understood how directly I was involved in NASA’s work. This internship has further cemented my love for space and desire to continue in the field. I have a better understanding of the research and development process and am now considering joining a research lab with my university next year.

Composite↗

SAMZ: Satellite-Derived Management Zones

The term "satellite-derived management zones" (SAMZ) denotes agricultural management zones that are subdivisions of large fields and that are derived from images of the fields acquired by instruments aboard Earth orbiting satellites during approximately the past 15 years. "SAMZ" also denotes the methodology and the software that implements the methodology for creating such zones. The SAMZ approach is one of several products of continuing efforts to realize a concept of precision agriculture, which involves optimal variations in seeding, in application of chemicals, and in irrigation, plus decisions to farm or not to farm certain portions of fields, all in an effort to maximize profitability in view of spatial and temporal variations in the growth and health of crops and in the chemical and physical conditions of soils. As used here, "management zone" signifies, more precisely, a subdivision of a field within which the crop production behavior is regarded as homogeneous. From the perspective of precision agriculture, management zones are the smallest subdivisions between which the seeding, application of chemicals, and other management parameters are to be varied. In the SAMZ approach, the main sources of data are the archives of satellite imagery that have been collected over the years for diverse purposes. One of the main advantages afforded by the SAMZ approach is that the data in these archives can be reused for purposes of precision agriculture at low cost. De facto, these archives contain information on all sources of variability within a field, including weather, crop types, crop management, soil types, and water drainage patterns. The SAMZ methodology involves the establishment of a Web-based interface based on an algorithm that generates management zones automatically and quickly from archival satellite image data in response to requests from farmers. A farmer can make a request by either uploading data describing a field boundary to the Web site or else drawing the boundary on a reference image. Hence, a farmer can start to engage in precision farming shortly after gaining access to the Web site, without need for incurring the high costs of conventional precision-agriculture data-collection practices that include collecting soil samples, mapping electrical conductivity of soil, and compiling multi-year crop-yield data. Given the boundary of a field, a SAMZ server computes the zones within the field in a three-stage process. In the first stage, a vector-valued image of the field is constructed by assembling, from the archives, the equivalent of a stack of the available images of the field (see figure). In the second stage, the vector-valued image is analyzed by use of a wavelet transform that detects spatial variations considered significant for precision farming while suppressing small-scale heterogeneities that are regarded as insignificant. In the third stage, a segmentation algorithm assembles the zones from smaller regions that have been identified in the wavelet analysis.

Source record↗