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Genomes to Structure and Function Workshop Report 2022

The goal of the U.S. Department of Energy (DOE) Biological and Environmental Research (BER) Program is to achieve a predictive understanding of complex biological, earth, and environmental systems with the aim of advancing the nation’s energy and infrastructure security. (https://www.energy.gov/science/ ber/biological-and-environmental-research). To pursue this goal, collaborations among experts in diverse research areas that lead to multidisciplinary projects are indispensable. The roles of DOE’s User Facilities, which offer unique and powerful resources for such research projects, are evolving, and expectations for the facilities are increasing. To respond to Users’ needs, the Joint Genome Institute (JGI) and Environmental Molecular Sciences Laboratory (EMSL) initiated the Facilities Integrating Collaborations for User Science (FICUS) program in 2014. This collaboration has grown into a popular and successful program, advancing more than 100 multidisciplinary projects to date. Similarly, the new interFacility collaborations among the JGI, EMSL, and User resources for BER structural biology and imaging at the Basic Energy Science (BES) Program’s synchrotron and neutron facilities are becoming essential for cutting-edge transdisciplinary science. To further explore the need for the BER research community to combine genomic, functional, and structural approaches to advance their research, an organizing committee was formed to develop and jointly host a 3-part workshop. The committee’s members represented seven DOE National Laboratory User Facilities (Appendix 1 lists the members). The “Genomes to Structure and Function” virtual workshop (see Appendices 2–5) was composed of three sessions. The first session, titled “Molecular Structures” (October 27– 28, 2021), highlighted diverse integrative experimental and computational approaches correlating structural data with sequencing and functional information, as well as predicting protein structures to model complex biological systems. The second session, “Intracellular Organization, and Material Synthesis and Decomposition” (December 15–16, 2021), covered imaging methods for observing, quantifying, and manipulating biosystems. The third session, “Imaging the Rhizosphere and Cellular Organization” (January 26–27, 2022) emphasized advanced and non-invasive imaging techniques applied to plant root-microbe-soil interactions.

59 BASIC BIOLOGICAL SCIENCES↗

Developing industrial participation in space - An approach for NASA

Maximizing industrial utilization of NASA's Space Transportation System (STS) requires the identification of potential STS users, determination of user needs, and initiation of integrated technical/market development efforts. With the involvement of potential end-users, R&D must be funded to demonstrate STS capabilities in technologies which have industrial potential. An integrated user development plan for NASA is discussed, emphasizing major activities and functional relationships in a user development program. Opportunities for private industry are noted. Results presented are those developed in support of a recent NASA contract intended as an initial step in the implementation by NASA of a user development program for the STS.

Madigan, J. A.↗

DBMS UTILIZATION: A Corporate Information System (CIS) development approach

The Corporate Information System (CIS), an integrated information system intended to tie the corporation together as a functioning entity, is described. In addition to being a major upgraded automated data processing system, the CIS is a management philosophy which recognizes data as a valuable corporate resource and which distinguishes between data and selected data, or information. It further recognizes that different users need different kinds of information. Plans for CIS development are discussed. It will offer its users not just after-the-fact data, but timely information in a format that is meaningful and useful to the particular user, so that the information can be applied in planning, controlling, and decision making by all levels of management. In effect, CIS will help the corporation itself to function as a total, integrated system by typing together administrative activities through information exchange. The CIS supports the operational, tactical control, and strategic planning functions of the corporation. Operational functions are the day-to-day processing necessary to support the corporation's work, such as purchasing and payroll.

Rozett, P.↗

The exploration metaphor

NASA's experience in planetary exploration has demonstrated that the desktop workstation is inadequate for many visualization situations. The primary mission displays for the unmanned Surveyor missions to the moon during the mid-1960's, for example, were environmental images assembled on the inside surfaces of spherical shells. Future exploration missions will greatly benefit from advances in digital computer and display technology, but there remain unmet user interface needs. Alternative user interfaces and metaphors are needed for planetary exploration and other interactions with complex spatial environments. These interfaces and metaphors would enable the user to directly explore environments and naturally manipulate objects in those environments. Personal simulators, virtual workstations, and telepresence user interfaces are systems capable of providing this integration of user space and task space. The Exploration Metaphor is a useful concept for guiding the design of user interfaces for virtual environments and telepresence. To apply the Exploration Metaphor is to assert that computing is like exploration, and to support objects, operations, and contexts comparable to those encountered in the exploration of natural environments. The Exploration Metaphor, under development for user interfaces in support of NASA's planetary exploration missions and goals, will also benefit other applications where complex spatial information must be visualized. Visualization methods and systems for planetary exploration are becoming increasingly integrated and interactive as computing technology improves. These advances will benefit from virtual environment and telepresence interface technology. A key development has been the processing of multiple images and other sensor data to create detailed digital models of the planets and moons. Data from images of the Earth, Mars, and Miranda, for example, have been converted into 3D models, and dynamic virtual fly-overs have been computed as demonstrations. Similar processing of lower altitude photography and the use of computer aided design tools promise to produce very detailed models in the future.

Mcgreevy, Michael W.↗

Organizing for low cost space operations - Status and plans

Design features of the Space Transportation System (vehicle reuse, low cost expendable components, simple payload interfaces, standard support systems) must be matched by economical operational methods to achieve low operating and payload costs. Users will be responsible for their own payloads and will be charged according to the services they require. Efficient use of manpower, simple documentation, simplified test, checkout, and flight planning are firm goals, together with flexibility for quick response to varying user needs. Status of the Shuttle hardware, plans for establishing low cost procedures, and the policy for user charges are discussed.

Lee, C.↗

Proceedings of the Workshop on Government Oil Spill Modeling

Oil spill model users and modelers were brought together for the purpose of fostering joint communication and increasing understanding of mutual problems. The workshop concentrated on defining user needs, presentations on ongoing modeling programs, and discussions of supporting research for these modeling efforts. Specific user recommendations include the development of an oil spill model user library which identifies and describes available models. The development of models for the long-term fate and effect of spilled oil was examined.

Bishop, J. M.↗

Space Station information systems

The space operations information system is defined and characterized in a wide perspective. Interactive subsets of the total system are defined and discussed. Particular attention is paid to the concept of end-to-end systems and their repetitive population within the total system. High level program goals are reviewed and related to more explicit system requirements and user needs. Emphasis is placed on the utility and cost effectiveness of data system services from a user standpoint. Productivity, as a quantitative goal, in both development and operational phases is also addressed. Critical aspects of the approach to successful development of the data management system are discussed along with recommendations important to advanced development activities. Current and planned activity in both technology and advanced development areas are reviewed with emphasis on their importance to program success.

Swingle, W. L.↗

ManiPIO - Manipulate Process I/O for Industrial Control Systems

The Manipulate Process Input/Output (IO) (ManiPIO) program allows users to develop custom scripts to execute Industrial Control System (ICS) manipulations. The driving development principles of ManiPIO are modularity and ease of use. Currently the program can utilize the Modbus TCP communication protocol, but its modular programming structure allows other protocols to be quickly and easily implemented. Additional functionality can be added to fit specific user needs, due to the usage of Python classes. The input configuration instructions are human readable and allow the user to create a complex series of control system manipulations.

97 MATHEMATICS AND COMPUTING↗

A twenty-first century perspective

The status of the NASA assets which are operated by the Office of Space Operations is briefly reviewed. These assets include the ground network, the space network, and communications and data handling facilities. The current plans for each element are examined, and a projection of each is made to meet the user needs in the 21st century. The following factors are noted: increasingly responsive support will be required by the users; operational support concepts must be cost-effective to serve future missions; and a high degree of system reliability and availability will be required to support manned exploration and increasingly complex missions.

Aller, Robert O.↗

Metrics and Benchmarks for Visualization

What is a "good" visualization? How can the quality of a visualization be measured? How can one tell whether one visualization is "better" than another? I claim that the true quality of a visualization can only be measured in the context of a particular purpose. The same image generated from the same data may be excellent for one purpose and abysmal for another. A good measure of visualization quality will correspond to the performance of users in accomplishing the intended purpose, so the "gold standard" is user testing. As a user of visualization software (or at least a consultant to such users) I don't expect visualization software to have been tested in this way for every possible use. In fact, scientific visualization (as distinct from more "production oriented" uses of visualization) will continually encounter new data, new questions and new purposes; user testing can never keep up. User need software they can trust, and advice on appropriate visualizations of particular purposes. Considering the following four processes, and their impact on visualization trustworthiness, reveals important work needed to create worthwhile metrics and benchmarks for visualization. These four processes are (1) complete system testing (user-in-loop), (2) software testing, (3) software design and (4) information dissemination. Additional information is contained in the original extended abstract.

Uselton, Samuel P.↗

Why Near Real-time/Low Latency is Important to Monitor the Changing World

An essential factor for remote sensing data products in impacting decision making is latency, or the time between earth observation and data are available to users. In many applications areas, latency plays an important or even decisive role where low latency earth observations help people to make timely, data-based decisions. Within the open and free NASA resources, NASA’s Land, Atmosphere Near real-time Capability for Earth Observing System (EOS) (LANCE) supports users interested in monitoring a wide variety of natural and man-made phenomena using near real-time (NRT) data products that are made available much quicker than routine processing allows. The combination of all available LANCE satellite products provides global coverage at multiple times per day, which makes it possible to meet user needs in various areas of applications including water resources, agriculture, air quality, wildland fire and many other disasters monitoring and management. As one of the prime users of LANCE, NASA’s Earth Science Applied Sciences Program promotes the use of LANCE data products to demonstrate applications in decision making and facilitates the end-user feedback to the science team to improve data products. One of the most critical applications that we expect data to be processed as close to the user as possible is wildland file response and management. User feedback indicates that LANCE NRT fire data products within 3 hours latency would meet the needs of the wildland fire community. Other examples of earth science application areas for which low latency is particularly important include detecting volcanic eruptions, early warning of disasters, tracking extreme weather events, and monitoring air quality.

Tian Yao↗

Surfer: An Extensible Pull-Based Framework for Resource Selection and Ranking

Grid computing aims to connect large numbers of geographically and organizationally distributed resources to increase computational power; resource utilization, and resource accessibility. In order to effectively utilize grids, users need to be connected to the best available resources at any given time. As grids are in constant flux, users cannot be expected to keep up with the configuration and status of the grid, thus they must be provided with automatic resource brokering for selecting and ranking resources meeting constraints and preferences they specify. This paper presents a new OGSI-compliant resource selection and ranking framework called Surfer that has been implemented as part of NASA's Information Power Grid (IPG) project. Surfer is highly extensible and may be integrated into any grid environment by adding information providers knowledgeable about that environment.

Zolano, Paul Z.↗

Benefits of a Proposed Process to Preserve Lunar Sites

Assets in lunar orbit and on the surface, whether operational or defunct, have the ability to cause inadvertent interference with proximity operations. As missions to the Moon continue to proliferate, and as more actors become involved, a mechanism is needed to bring communities together to ensure ones' actions do not inhibit the mission objectives of another. A mechanism may also be needed to determine whether any locations on the Moon or in its orbit are of high value to various users, and, pending potential decreases in this value due to interference and other concerns, warrant mitigative actions to preserve these locations. Such a mechanism could provide benefits to all those involved, including governments, industry, academia, and other interested groups. We present a notional process to aggregate community interests for lunar sites and orbits. We then consider two user needs and explore how this process could be used to identify potential alignments and misalignments across communities.

preservation↗

H2Fills™ [SWR-19-67]

H2FillS: Hydrogen Filling Simulation The Hydrogen Filling Simulation (H2FillS) software is a thermodynamic model designed to track and report on the transient change in hydrogen temperature, pressure, and mass flow when filling a fuel cell electric vehicle (FCEV). H2FillS simulates gas flow from the hydrogen station to the FCEV storage system. Using empirical fueling data sets, the model has been validated over a range of fueling conditions to match common light-duty FCEV fill profiles. Overall, it provides significant benefits to the light-duty fueling market and fill knowledge gaps of the interaction between a hydrogen station and an FCEV. Capabilities Use the comprehensive H2FillS model to: Safely design and operate a hydrogen fueling station Support code refinement with readily available data Develop system and operational improvements to reduce capital or operating costs at hydrogen stations or on-board FCEVs. How It Works H2FillS uses a "drag-and-drop" graphical user interface to simulate station and vehicle systems with preset parameters for common hydrogen station components as default values. When needed, users can define their own parameters to create their own station or vehicle components. Download H2FillS in Two Steps Read the terms of the end user software license agreement. Register to download the software. There are two versions of the model: A full-station model starts the simulation at high-pressure ground storage, runs through a dispenser, and ends at a vehicle storage system. A partial-station model starts at the dispenser breakaway and consists solely of the dispenser components and the vehicle storage system. H2FillS will automatically output fill performance data from the vehicle by tracking pressure and temperature throughout the fill. Users can input their own fill profiles into the model to run a variety of simulations.

Peters, Michael↗

An easy-to-use diagnostic system development shell

The Diagnostic System Development Shell (DSDS), an expert system development shell for diagnostic systems, is described. The major objective of building the DSDS is to create a very easy to use and friendly environment for knowledge engineers and end-users. The DSDS is written in OPS5 and CommonLisp. It runs on a VAX/VMS system. A set of domain independent, generalized rules is built in the DSDS, so the users need not be concerned about building the rules. The facts are explicitly represented in a unified format. A powerful check facility which helps the user to check the errors in the created knowledge bases is provided. A judgement facility and other useful facilities are also available. A diagnostic system based on the DSDS system is question driven and can call or be called by other knowledge based systems written in OPS5 and CommonLisp. A prototype diagnostic system for diagnosing a Philips constant potential X-ray system has been built using the DSDS.

Tsai, L. C.↗

A Finite Element Procedure for Calculating Fluid-Structure Interaction Using MSC/NASTRAN

This report is intended to serve two purposes. The first is to present a survey of the theoretical background of the dynamic interaction between a non-viscid, compressible fluid and an elastic structure is presented. Section one presents a short survey of the application of the finite element method (FEM) to the area of fluid-structure-interaction (FSI). Section two describes the mathematical foundation of the structure and fluid with special emphasis on the fluid. The main steps in establishing the finite element (FE) equations for the fluid structure coupling are discussed in section three. The second purpose is to demonstrate the application of MSC/NASTRAN to the solution of FSI problems. Some specific topics, such as fluid structure analogy, acoustic absorption, and acoustic contribution analysis are described in section four. Section five deals with the organization of the acoustic procedure flowchart. Section six includes the most important information that a user needs for applying the acoustic procedure to practical FSI problems. Beginning with some rules concerning the FE modeling of the coupled system, the NASTRAN USER DECKs for the different steps are described. The goal of section seven is to demonstrate the use of the acoustic procedure with some examples. This demonstration includes an analytic verification of selected FE results. The analytical description considers only some aspects of FSI and is not intended to be mathematically complete. Finally, section 8 presents an application of the acoustic procedure to vehicle interior acoustic analysis with selected results.

Chargin, Mladen↗

Modeling Atmospheric Science Knowledge from Research Publications

NASA Earth Science Data Centers contain enormous amounts of remote sensing digital data. It is often a significant challenge for users to find data suitable for their research topic in these vast archives. One of the approaches is the usage-driven dataset discovery, where users seek publications on projects similar to their intended study. For this approach to be effective, users need a clear connection between the underlying data in the publications and the study objectives; this is not often apparent to non-expert users. Tools and methodologies that can help facilitate and organize these connections are therefore valuable for creating improved knowledge mappings, which can be further used by search engines to suggest data or publications best tailored to a user’s specific research goal. As an illustration of these challenges, in this work we focus on the atmospheric chemistry processes related to Earth environmental impacts such as ozone depletion, aerosols, smog formation, acid rain, and radiative forcing. We further limit our study to publications that use data from the Microwave Limb Sounder (MLS) instrument flown on the Aura Earth Observing System. To create knowledge representations of science carried out in these publications, we use existing ontologies such as the Global Change Master Directory (GCMD) and Semantic Web for Earth and Environmental Terminology (SWEET). These ontologies together encompass term dictionaries that include measured variables, names of molecules or radicals, mission and instrument names, locations, action words, among many others. Based on these terms acknowledge graph database was populated with the terms retrieved from scientific publications that study atmospheric chemistry. These databases can be used to further enhance the automation of knowledge discovery and facilitate machine learning and artificial intelligence algorithms or applications. These tools and methods can also be extended to apply to content from other related Earth science domains.

Irina Gerasimov↗

Toward a Virtual Solar Observatory: Starting Before the Petabytes Fall

Although a few, large, space- and groundbased solar physics databases exist at selected locations, there is as yet only limited standardization or interoperability. I describe the outline of a plan to facilitate access to a distributed network of online solar data archives, both large and small. The underlying principle is that the user need not know where- the data are, only how to specify which data are desired. At the least, such an approach could considerably simplify the scientific user's access to the enormous amount of solar physics data to be obtained in the next decade. At best, it might mean the withering away of traditional data centers, and all the bureaucracy they entail. This work is supported by the Sun-Earth Connections Division of NASA Office of Space Science, thanks to an anomalous act of largess on the part of the 2001 SEC Senior Review.

Gurman, Joseph↗