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At least 415 records · Page 23

Tracking Community Building in Open Science

Open Science is enabled by a vibrant community of researchers who regularly engage with the data, from its production to its organization, curation, archiving, dissemination, analysis, and publication. This presentation will examine community building in open science. The NASA Open Science Data Repository (OSDR) makes data available to the public following the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles. OSDR takes open science further with the OS Analysis Working Groups (AWGs) that facilitate community development and promotion. The primary activity of each AWG is to establish and validate analytical processes to generate higher-order data from data housed in OSDR. There are a number of these groups on various topics, including the Animal AWG, Plant AWG, Microbial AWG, Multi-Omics AWG, AI/ML AWG, and the Ames Life Sciences Data Archive (ALSDA) AWG. The international volunteers participating in these AWGs come from academia, citizen science initiatives, industry, and government. They include researchers, principal investigators, professors, trained hobbyists, and students from various domains and disciplines. Anyone may request to join the AWGs, and membership requests are vetted monthly by the group organizers before granting admission. Core to membership is demonstrated expertise through records of training, integrity, work in the professed domain(s), and good community standing. Regular virtual meetings are held for each AWG, with a varying cadence depending on the group's needs and goals. AWG communities share their expertise in research including cutting edge tools, software, frameworks, data formats, and libraries accelerating research collectively. This collaborative approach helps community members cross technology gaps and identify emerging challenges. These diverse communities encompass a wide range of individuals hailing from various sectors within the Science Mission Directorate and beyond. They serve as a means to promote and enhance transparency, accessibility, and inclusion. An annual AWG Symposium brings contributors together in person. Participation in AWGs can be synchronous or asynchronous, with some groups performing most of their work in off hours. Participants gain valuable skills and connections that allow them to add value to their communities and new organizations that they join, resulting in an expanded return on investment for the space life science community. Open science is increasingly a federal mandate and initiatives like NASA's Transform to Open Science and instruments like the Decadal Survey of Biological and Physical Sciences in Space demonstrate the need to carefully consider best practices in this domain. Here, we present greater detail about the makeup and participation metrics of the various AWGs affiliated with OSDR and details of successful peer-reviewed publication campaigns.

Christina M Johnson↗

Tracking Community Building in Open Science

Open Science is enabled by a vibrant community of researchers who regularly engage with the data, from its production to its organization, curation, archiving, dissemination, analysis, and publication. This presentation will examine community building in open science. The NASA Open Science Data Repository (OSDR) makes data available to the public following the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles. OSDR takes open science further with the OS Analysis Working Groups (AWGs) that facilitate community development and promotion. The primary activity of each AWG is to establish and validate analytical processes to generate higher-order data from data housed in OSDR. There are a number of these groups on various topics, including the Animal AWG, Plant AWG, Microbial AWG, Multi-Omics AWG, AI/ML AWG, and the Ames Life Sciences Data Archive (ALSDA) AWG. The international volunteers participating in these AWGs come from academia, citizen science initiatives, industry, and government. They include researchers, principal investigators, professors, trained hobbyists, and students from various domains and disciplines. Anyone may request to join the AWGs, and membership requests are vetted monthly by the group organizers before granting admission. Core to membership is demonstrated expertise through records of training, integrity, work in the professed domain(s), and good community standing. Regular virtual meetings are held for each AWG, with a varying cadence depending on the group's needs and goals. AWG communities share their expertise in research including cutting edge tools, software, frameworks, data formats, and libraries accelerating research collectively. This collaborative approach helps community members cross technology gaps and identify emerging challenges. These diverse communities encompass a wide range of individuals hailing from various sectors within the Science Mission Directorate and beyond. They serve as a means to promote and enhance transparency, accessibility, and inclusion. An annual AWG Symposium brings contributors together in person. Participation in AWGs can be synchronous or asynchronous, with some groups performing most of their work in off hours. Participants gain valuable skills and connections that allow them to add value to their communities and new organizations that they join, resulting in an expanded return on investment for the space life science community. Open science is increasingly a federal mandate and initiatives like NASA's Transform to Open Science and instruments like the Decadal Survey of Biological and Physical Sciences in Space demonstrate the need to carefully consider best practices in this domain. Here, we present greater detail about the makeup and participation metrics of the various AWGs affiliated with OSDR and details of successful peer-reviewed publication campaigns.

Christina M Johnson↗

LAVA Voronoi Mesher for Wall-Modeled Large-Eddy Simulations

The unstructured Voronoi mesher currently being developed within the Launch, Ascent, and Vehicle Aerodynamics (LAVA) software framework at NASA Ames Research Center is described in detail. The discussions include, but are not limited to, the strategies used in the seeding and smoothing phases to ensure a high-quality mesh for Wall-Modeled Large-Eddy Simulations (WMLES), the methods behind the cell clipping algorithm responsible for conforming the mesh to a complex geometry, and the approach to create a global mesh from the distinct Voronoi cells. Applications and benefits of the Voronoi meshing approach are also presented. The automated meshing paradigm introduced was able to significantly reduce the time necessary to create a high-quality mesh around a complex geometry when compared against the current LAVA curvilinear overset meshing standard. For example, the task of generating a single mesh around the high-lift common research model requires the full dedication of a mesh generation expert for a period between one and two months. A family of meshes with different refinement levels up to six hundred million cells can be generated by a single engineer in a day or two. This technology has the potential for decreasing the turnaround time for conducting WMLES around complex geometries, as well as facilitating comprehensive mesh refinement studies.

Victor C B Sousa↗

SoMo: Fast and Accurate Simulations of Continuum Robots in Complex Environments

Engineers and scientists often rely on their intuition and experience when designing soft robotic systems. The development of performant controllers and motion plans for these systems commonly requires time-consuming iterations on hardware. We present the SoMo (Soft Motion) toolkit, a software framework that makes it easy to instantiate and control typical continuum manipulators in an accurate physics simulator. SoMo introduces a standardized and human-readable description format for continuum manipulators. It leverages this description format and the Bullet physics engine to enable fast and accurate simulations of soft and soft-rigid hybrid robots in environments with complex contact interactions. This allows users to vary design and control parameters across simulations with minimal effort. We compare the capabilities of SoMo to other physics simulators and highlight the benefits and accuracy of SoMo by demonstrating the agreement between simulation and real-world experiments on several examples; these include an in-hand manipulation task with continuum fingers, an automated exploration of how to design soft fingers for precision grasping, and a brief snake locomotion study. Overall, SoMo provides an accessible way for designers of soft robotic hardware and control systems to gain access to a simulation-accelerated workflow.

Moritz A. Graule↗

Automated End-to-End Spacecraft Connectivity Across Diverse Links

An increasing variety of communications services are available to space missions. Yet varying standards between providers hinder adoption due to the complexity of managing many configurations. We present a software framework to automatically establish end-to-end communications during contacts with a provider by configuring spacecraft protocols at the physical, link, and network layers. Underlying protocols and routes are abstracted, allowing the user to simply send data to a destination with the framework ensuring its delivery. We evaluate a full implementation of the framework in laboratory experiments conducted on an emulated communications testbed. These tests demonstrate data delivery across three different services with rapid (<20s) reconfiguration as the spacecraft transitions between providers.

satellite communication↗

Accelerating the Computation of Detailed Chemical Reaction Kinetics for Simulating Combustion of Complex Fuels

Combustion of hydrocarbon fuels has been a very challenging scientific and engineering problem due to the complexity of turbulent flows and hydrocarbon reaction kinetics. There is an urgent need to develop an efficient modeling capability to accurately predict the combustion of complex fuels. Detailed chemical kinetic models for the surrogates of fuels such as gasoline, diesel and JP-8 consist of thousands of chemical species and Arrhenius reaction steps. Oxygenated fuels such as bio-fuels and heavier hydrocarbons, such as from newer fossil fuel sources, are expected to have a much more complex chemistry requiring increasingly larger chemical kinetic models. Such models are beyond current computational capability, except for homogeneous or partially stirred reactor type calculations. The advent of highly parallel multi-core processors and graphical processing units (GPUs) promises a steep increase in computational performance in the coming years. This paper will present a software framework that translates the detailed chemical kinetic models to high- performance code targeted for GPU accelerators.

02 PETROLEUM↗

Parallel Algorithms and Software for Nuclear, Energy, and Environmental Applications. Part II: Multiphysics Software

This paper is the second part of a two part sequence on multiphysics algorithms and software. The first [1] focused on the algorithms; this part treats the multiphysics software framework and applications based on it. Tight coupling is typically designed into the analysis application at inception, as such an application is strongly tied to a composite nonlinear solver that arrives at the final solution by treating all equations simultaneously. The application must also take care to minimize both time and space error between the physics, particularly if more than one mesh representation is needed in the solution process. This paper presents an application framework that was specifically designed to support tightly coupled multiphysics analysis. The Multiphysics Object Oriented Simulation Environment (MOOSE) is based on the Jacobian-free Newton-Krylov (JFNK) method combined with physics-based preconditioning to provide the underlying mathematical structure for applications. The report concludes with the presentation of a host of nuclear, energy, and environmental applications that demonstrate the efficacy of the approach and the utility of a well-designed multiphysics framework.

97 MATHEMATICS AND COMPUTING↗

Enforcing elemental mass and energy balances for reduced order models

Development of economically feasible gasification and carbon capture, utilization and storage (CCUS) technologies requires a variety of software tools to optimize the designs of not only the key devices involved (e., g., gasifier, CO{sub 2} adsorber) but also the entire power generation system. High-fidelity models such as Computational Fluid Dynamics (CFD) models are capable of accurately simulating the detailed flow dynamics, heat transfer, and chemistry inside the key devices. However, the integration of CFD models within steady-state process simulators, and subsequent optimization of the integrated system, still presents significant challenges due to the scale differences in both time and length, as well the high computational cost. A reduced order model (ROM) generated from a high-fidelity model can serve as a bridge between the models of different scales. While high-fidelity models are built upon the principles of mass, momentum, and energy conservations, ROMs are usually developed based on regression-type equations and hence their predictions may violate the mass and energy conservation laws. A high-fidelity model may also have the mass and energy balance problem if it is not tightly converged. Conservations of mass and energy are important when a ROM is integrated to a flowsheet for the process simulation of the entire chemical or power generation system, especially when recycle streams are connected to the modeled device. As a part of the Carbon Capture Simulation Initiative (CCSI) project supported by the U.S. Department of Energy, we developed a software framework for generating ROMs from CFD simulations and integrating them with Process Modeling Environments (PMEs) for system-wide optimization. This paper presents a method to correct the results of a high-fidelity model or a ROM such that the elemental mass and energy are conserved perfectly. Correction factors for the flow rates of individual species in the product streams are solved using a minimization algorithm based on Lagrangian multiplier method. Enthalpies of product streams are also modified to enforce the energy balance. The approach is illustrated for two ROMs, one based on a CFD model of an entrained-flow gasifier and the other based on the CFD model of a multiphase CO{sub 2} adsorber.

01 COAL, LIGNITE, AND PEAT↗

Performing Probabilistic Risk Assessment Through RAVEN

The Reactor Analysis and Virtual control ENviroment (RAVEN) code is a software tool that acts as the control logic driver and post-processing engine for the newly developed Thermal-Hydraulic code RELAP-7. RAVEN is now a multi-purpose Probabilistic Risk Assessment (PRA) software framework that allows dispatching different functionalities: Derive and actuate the control logic required to simulate the plant control system and operator actions (guided procedures), allowing on-line monitoring/controlling in the Phase Space Perform both Monte-Carlo sampling of random distributed events and Dynamic Event Tree based analysis Facilitate the input/output handling through a Graphical User Interface (GUI) and a post-processing data mining module

99 GENERAL AND MISCELLANEOUS↗

Multiphysics Simulations: Challenges and Opportunities

We consider multiphysics applications from algorithmic and architectural perspectives, where "algorithmic" includes both mathematical analysis and computational complexity, and "architectural" includes both software and hardware environments. Many diverse multiphysics applications can be reduced, en route to their computational simulation, to a common algebraic coupling paradigm. Mathematical analysis of multiphysics coupling in this form is not always practical for realistic applications, but model problems representative of applications discussed herein can provide insight. A variety of software frameworks for multiphysics applications have been constructed and refined within disciplinary communities and executed on leading-edge computer systems. We examine several of these, expose some commonalities among them, and attempt to extrapolate best practices to future systems. From our study, we summarize challenges and forecast opportunities.

99 GENERAL AND MISCELLANEOUS↗

Simulating Microbial Community Patterning Using Biocellion

Mathematical modeling and computer simulation are important tools for understanding complex interactions between cells and their biotic and abiotic environment: similarities and differences between modeled and observed behavior provide the basis for hypothesis forma- tion. Momeni et al. [5] investigated pattern formation in communities of yeast strains engaging in different types of ecological interactions, comparing the predictions of mathematical modeling and simulation to actual patterns observed in wet-lab experiments. However, simu- lations of millions of cells in a three-dimensional community are ex- tremely time-consuming. One simulation run in MATLAB may take a week or longer, inhibiting exploration of the vast space of parameter combinations and assumptions. Improving the speed, scale, and accu- racy of such simulations facilitates hypothesis formation and expedites discovery. Biocellion is a high performance software framework for ac- celerating discrete agent-based simulation of biological systems with millions to trillions of cells. Simulations of comparable scale and accu- racy to those taking a week of computer time using MATLAB require just hours using Biocellion on a multicore workstation. Biocellion fur- ther accelerates large scale, high resolution simulations using cluster computers by partitioning the work to run on multiple compute nodes. Biocellion targets computational biologists who have mathematical modeling backgrounds and basic C++ programming skills. This chap- ter describes the necessary steps to adapt the original Momeni et al.'s model to the Biocellion framework as a case study.

metabolic interaction↗

Analysis of the Space Propulsion System Problem Using RAVEN

This paper presents the solution of the space propulsion problem using a PRA code currently under development at Idaho National Laboratory (INL). RAVEN (Reactor Analysis and Virtual control ENviroment) is a multi-purpose Probabilistic Risk Assessment (PRA) software framework that allows dispatching different functionalities. It is designed to derive and actuate the control logic required to simulate the plant control system and operator actions (guided procedures) and to perform both Monte- Carlo sampling of random distributed events and Event Tree based analysis. In order to facilitate the input/output handling, a Graphical User Interface (GUI) and a post-processing data-mining module are available. RAVEN allows also to interface with several numerical codes such as RELAP5 and RELAP-7 and ad-hoc system simulators. For the space propulsion system problem, an ad-hoc simulator has been developed and written in python language and then interfaced to RAVEN. Such simulator fully models both deterministic (e.g., system dynamics and interactions between system components) and stochastic behaviors (i.e., failures of components/systems such as distribution lines and thrusters). Stochastic analysis is performed using random sampling based methodologies (i.e., Monte-Carlo). Such analysis is accomplished to determine both the reliability of the space propulsion system and to propagate the uncertainties associated to a specific set of parameters. As also indicated in the scope of the benchmark problem, the results generated by the stochastic analysis are used to generate risk-informed insights such as conditions under witch different strategy can be followed.

97 MATHEMATICS AND COMPUTING↗

Beamline Insertions Manager at Jefferson Lab

The beam viewer system at Jefferson Lab provides operators and beam physicists with qualitative and quantitative information on the transverse electron beam properties. There are over 140 beam viewers installed on the 12 GeV CEBAF accelerator. This paper describes an upgrade consisting of replacing the EPICS-based system tasked with managing all viewers with a mixed system utilizing EPICS and high-level software. Most devices, particularly the beam viewers, cannot be safely inserted into the beam line during high-current beam operations. Software is partly responsible for protecting the machine from untimely insertions. The multiplicity of beam-blocking and beam-vulnerable devices motivates us to try a data-driven approach. The beamline insertions application components are centrally managed and configured through an object-oriented software framework created for this purpose. A rules-based engine tracks the configuration and status of every device, along with the beam status of the machine segment containing the device. The application uses this information to decide on which device actions are allowed at any given time.

43 PARTICLE ACCELERATORS↗

A Comprehensive Validation Approach Using The RAVEN Code

The RAVEN computer code , developed at the Idaho National Laboratory, is a generic software framework to perform parametric and probabilistic analysis based on the response of complex system codes. RAVEN is a multi-purpose probabilistic and uncertainty quantification platform, capable to communicate with any system code. A natural extension of the RAVEN capabilities is the imple- mentation of an integrated validation methodology, involving several different metrics, that represent an evolution of the methods currently used in the field. The state-of-art vali- dation approaches use neither exploration of the input space through sampling strategies, nor a comprehensive variety of metrics needed to interpret the code responses, with respect experimental data. The RAVEN code allows to address both these lacks. In the following sections, the employed methodology, and its application to the newer developed thermal-hydraulic code RELAP-7, is reported.The validation approach has been applied on an integral effect experiment, representing natu- ral circulation, based on the activities performed by EG&G Idaho. Four different experiment configurations have been considered and nodalized.

PRA↗

DGM Version .1.2

Software framework for forward modeling and optimization of partial differential equations using the discontinuous Galerkin method (DGM). Examples are provided for solution to generic Navier-Stokes (with and without subgrid-scale turbulence models), Euler, Burgers, Poisson, Helmholtz, Darcy, linear transport, and advection-diffusion equations.

Source record↗

Rplexos

rplexos is a R (statistical software framework; more? details below) package that processes and facilitates analysis of solution from PLEXOS. PLEXOS is a production cost model that is utilize to simulate the behavior of the power.systems and is developed and commercialized by Energy Exomplar. The intention is to make rptexos open-source so other PLEXOS users can utilize it.

Ibanez, Eduardo↗

Tusas, Version 1.0

Tusas is a general / flexible software framework for solving coupled systems of onlinear partial differential equations. Tusas was originally developed for phase-field simulation of solidification. In order for Tusas to be effective, the PDEs must be compatible with structured or unstructured Lagrange (nodal) finite element discretizations and explicit (Euler) or implicit (Euler, Trapezoid, BDF2) temporal discretizations.

Newman, Christopher K.↗