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At least 721 records · Page 40

Automated Software Development Workstation (ASDW)

Software development is a serious bottleneck in the construction of complex automated systems. An increase of the reuse of software designs and components has been viewed as a way to relieve this bottleneck. One approach to achieving software reusability is through the development and use of software parts composition systems. A software parts composition system is a software development environment comprised of a parts description language for modeling parts and their interfaces, a catalog of existing parts, a composition editor that aids a user in the specification of a new application from existing parts, and a code generator that takes a specification and generates an implementation of a new application in a target language. The Automated Software Development Workstation (ASDW) is an expert system shell that provides the capabilities required to develop and manipulate these software parts composition systems. The ASDW is now in Beta testing at the Johnson Space Center. Future work centers on responding to user feedback for capability and usability enhancement, expanding the scope of the software lifecycle that is covered, and in providing solutions to handling very large libraries of reusable components.

Fridge, Ernie↗

Technical Report Interchange Through Synchronized OAI Caches

The Technical Report Interchange project is a cooperative experimental effort between NASA Langley Research Center, Los Alamos National Laboratory, Air Force Research Laboratory, Sandia National Laboratory and Old Dominion University to allow for the integration of technical reports. This is accomplished using the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH) and having each site cache the metadata from the other participating sites. Each site also implements additional software to ingest the OAI-PMH harvested metadata into their native digital library (DL). This allows the users at each site to see an increased technical report collection through the familiar DL interfaces and tale advantage of whatever valued added are provided by the native DL.

Liu, Xiaming↗

GCAS Visualization Codebase Augmentation Migration to Modern Standards and Feature Enhancements

The Glenn Research Center Communication Analysis Suite (GCAS) includes many analysis tools that can be used to support a wide range of scenarios. It includes a visualization tool that implements the three.js graphics library to display a three-dimensional (3D) representation of its results. This software will enable researchers, engineers, and mission planners to interact intuitively with and understand the results of their analyses, which might not be apparent from raw data. With NASA’s efforts to return humans to the Moon as a part of the Artemis missions, the GCAS has been used extensively for lunar terrain and landing system development analysis, which is vital to ensuring mission achievability and safety. This has created the need to add several significant features to the visualization tool, such as the ability to display the terrain of the lunar surface accurately and to provide information demonstrating how a given region might impact mission objectives. Many of the changes made to the visualization tool can be separated into one of three general advancements: code restructuring to adhere to modern coding standards and practices, new user camera controls for first-person and third-person perspective views, and a terrain generation feature to enable rendering highly accurate terrains based on any celestial body’s digital elevation model (DEM) in GeoTIFF format. These improvements notably elevate the visualization tool's functionality, accuracy, and user interaction while providing a robust foundation for future development.

Visualization↗

SNLSimMagic v 2.0

This software is an iOS (Apple) Augmented Reality (AR) application that runs on the iPhone and iPad. It is designed to scan in a photograph or graphic and "play" an associated video. This release, SNLSimMagic, was built using Wikitude Augmented Reality (AR) software development kit (SDK) integrated into Apple iOS SDK application and the Cordova libraries. These codes enable the generation of runtime targets using cloud recognition and developer-defined target features which are then accessed by means of a custom application.

Source record↗

Sirocco Storage Server v. pre-alpha 0.1

Sirocco is a parallel storage system under development, designed for write-intensive workloads on large-scale HPC platforms. It implements a keyvalue object store on top of a set of loosely federated storage servers that cooperate to ensure data integrity and performance. It includes support for a range of different types of storage transactions. This software release constitutes a conformant storage server, along with the client-side libraries to access the storage over a network.

Curry, Matthew L.↗

Generic Fortran Containers (GFC)

The Fortran language does not provide a standard library that implements generic containers, like linked lists, trees, dictionaries, etc. The GFC software provides an implementation of generic Fortran containers natively written in Fortran 2003/2008 language. The following containers are either already implemented or planned: Stack (done), Linked list (done), Tree (done), Dictionary (done), Queue (planned), Priority queue (planned).

Liakh, Dmitry↗

Model Data Archive Associated with Manuscript "Fire-altered Carbon Pools Create Disturbance Memory in Stream Dissolved Organic Carbon"

This data package supports the publication “Fire-altered Carbon Pools Create Disturbance Memory in Stream Dissolved Organic Carbon” by Li et al. (2026). The package contains processed model inputs, configuration files, restart files, simulation outputs, scripts, and visualization products used to evaluate post-fire dissolved organic carbon (DOC) dynamics in the Naches River Watershed, Washington, USA, following the 2021 Schneider Springs Fire. The modeling workflow couples ELM-BGC, the biogeochemistry-enabled Energy Exascale Earth System Model Land Model; ATS, the Advanced Terrestrial Simulator for integrated surface-subsurface hydrology; and PFLOTRAN, a reactive transport model for multicomponent aqueous geochemistry. Together, these models simulate how wildfire-induced changes in vegetation, litter, coarse woody debris, and soil organic matter influence DOC production, transport, and reaction from burned hillslopes to stream networks. The archive includes preprocessed meteorological, geospatial, hydrologic, and biogeochemical forcing data; ELM-BGC-derived DOC source terms; ATS mesh files; PFLOTRAN reactive-transport inputs; model configuration files; spin-up and transient restart files; watershed-scale diagnostic outputs; stream concentration time series; and figures or visualization files used to inspect and reproduce key results. File types include Hierarchical Data Format 5 (HDF5) files for gridded forcing and model-coupling data, model input and configuration files for ELM-BGC, ATS, and PFLOTRAN, restart and simulation-output files generated by the modeling workflow, tabular or time-series diagnostic outputs, scripts for post-processing and figure generation, and image or visualization products associated with the manuscript. Use of the package depends on the intended task. Re-running the simulations requires the relevant modeling software, including ELM-BGC, ATS, and PFLOTRAN as ATS's geochemical engine. Inspecting outputs and reproducing figures requires Python with scientific plotting libraries such as Matplotlib, and three-dimensional model outputs may be viewed with ParaView. Geographic information system files or maps may be inspected with ArcGIS Pro or comparable GIS software. The data package is intended to enable traceability, reuse, and partial reproduction of the coupled land-to-watershed hydro-biogeochemical modeling workflow used to test how wildfire disturbance affects terrestrial carbon pools and downstream DOC dynamics.

ATS↗

Blackbird: Object-Oriented Planning, Simulation, and Sequencing Framework Used by Multiple Missions

Every JPL flight mission relies on activity planning and sequence generation software to perform operations. Most such tools in use at JPL and elsewhere use attribute-based schemas or domain-specific languages (DSLs) to define activities. This reliance poses user training, software maintenance, performance, and other challenges. To solve this problem for future missions, a new software called Blackbird was developed which allows engineers to specify behavior in standard Java. The new code base has over an order of magnitude fewer lines of code than other JPL planning software, since no DSL or schema interpreter is needed. The use of Java for defining activities also allows mission adapters to debug their code in an integrated development environment, seamlessly call external libraries, and set up truly multimission models. These efficiency gains have significantly reduced the amount of development effort required to support the software. This paper discusses Blackbird’s design, principles, and use cases.

Lawler, Christopher↗

Monitoring Astronaut Health with DNA Sequencing

In recent years microbe a plethora of microbe populations have been identified onboard the ISS (International Space Station). Approaches for real-time tracking of microbes for routine housekeeping and food/water safety monitoring will be critical for mission safety and crew health on future longer duration missions to the Moon or Mars. This work is a proof-of-concept study demonstrating an end-to-end phylogenetic identification and full genome sequencing effort of multiple microbial populations. Our methodology utilized the ISS flight-certified WetLab-2 molecular toolbox and the Biomolecule Sequencer projects for real-time end-to-end on-orbit microbial biological samples processing and molecular analysis with real time results generated utilizing only field "offline" analytic software. For this experiment we colony-cultured several ISS isolated microorganisms before generation of the pre-sequencing library via the automated VolTRAX device which enabled high library turnover with little wet-bench activity or potential future costly astronaut time. The pre-sequencing library is diluted in loading buffer and injected into the MinION sample port, drawn into the nanopore window by capillary action, and sequenced using the MinKnown. 16S and full genome alignment, nucleotide matching, gene identification, and phylogenetic sorting was accomplished utilizing the Epi2me software and the offline NCBI Blast viral, microbiome, and human somatic databases. In short, the methodologies developed herein replace the myriad of specific, often highly targeted microbiological tests used in the clinical laboratory, which would be difficult if not impossible to currently implement aboard the ISS or in deep space, with a single metagenomics test.

genomics↗

hypredrive: high-level interface for solving linear systems with hypre

This software introduces a high-level interface designed to simplify solving linear systems using hypre, a renowned library for such computational challenges. It is crafted to be accessible and user-friendly, making the powerful capabilities of hypre available to a broader audience without requiring in-depth technical knowledge. The interface is characterized by its use of YAML for input, a format celebrated for its structured yet straightforward readability. This choice ensures that users can easily configure the software to meet their specific needs. Additionally, the software boasts an intuitive API that encapsulates hypre's functionalities, making it easier for users to interact with the process of solving linear systems. It is particularly beneficial for prototyping, offering a quick and efficient means to test various solver and preconditioner configurations. Furthermore, the software allows for the creation of an offline testing framework in which predefined linear systems are read from files and benchmarked with user-defined solution strategies. This makes it an invaluable tool for developers and researchers exploring and validating their computational models. Overall, the software serves as a bridge, bringing the advanced computational capabilities of hypre closer to users who may need more specialized technical expertise, thereby facilitating innovation and exploration in the field of numerical linear algebra.

Paludetto Magri, Victor↗

JPL's Foundry Furnace: Web-Based Concurrent Engineering for Formulation

The Jet Propulsion Laboratory’s Innovation Foundry is an enterprise tasked with shepherding space mission concepts through the formulation lifecycle. It oversees a number of “virtual teams” for the various stages of formulation. Among these is Team X, which has had considerable success over its more than 20-year history. In a Team X study, domain experts (including engineers devoted to the various spacecraft subsystems) work concurrently and collaboratively over several days to arrive at a feasible point design with a reasonable cost estimate. They use a set of linked Excel workbooks, each developed and approved by a responsible “line organization” within JPL. This toolset has served Team X well over the years, and has evolved since its inception. At the same time, the Innovation Foundry’s portfolio of formulation teams has expanded, and so has the scope of the design challenges they face. The A-Team runs workshop-like architecture studies to focus science investigations, generate mission concepts, assess feasibility, and explore trade spaces. Team Xc performs rapid point design in the style of Team X, but for CubeSats and small spacecraft, using a different toolset. Proposal teams further mature concepts to the point where they can be proposed. Recognizing the importance of trade space modeling combined with new IT services for providing and integrating data, JPL is developing the Foundry Furnace web-based software infrastructure. It will support A-Team, Team Xc, and Team X, providing study management, a catalog of hardware components, a library of re-usable analyses, and a design environment. It is a modernization of JPL’s concurrent engineering infrastructure, embracing the core concepts of Model-Based Systems Engineering, and built with modern software design philosophies.

Murphy, Jonathan↗

Rapid and Robust Cross-Correlation-Based Seismic Signal Identification Using an Approximate Nearest Neighbor Method

The matched filtering technique that uses the cross correlation of a waveform of interest with archived signals from a template library has proven to be a powerful tool for detecting events in regions with repeating seismicity. However, waveform correlation is computationally expensive and therefore impractical for large template sets unless dedicated distributed computing hardware and software are used. In this paper, we introduce an approximate nearest neighbor (ANN) approach that enables the use of very large template libraries for waveform correlation. Our method begins with a projection into a reduced dimensionality space, based on correlation with a randomized subset of the full template archive. Searching for a specified number of nearest neighbors for a query waveform is accomplished by iteratively comparing it with the neighbors of its immediate neighbors. We used the approach to search for matches to each of ~2300 analyst-reviewed signal detections reported in May 2010 for the International Monitoring System station MKAR. The template library in this case consists of a data set of more than 200,000 analyst-reviewed signal detections for the same station from February 2002 to July 2016 (excluding May 2010). Of these signal detections, 73% are teleseismic first P and 17% regional phases (Pn, Pg, Sn, and Lg). Finally, the analyses performed on a standard desktop computer show that the proposed ANN approach performs a search of the large template libraries about 25 times faster than the standard full linear search and achieves recall rates greater than 80%, with the recall rate increasing for higher correlation thresholds.

58 GEOSCIENCES↗

SQMBox: Interfacing a semiempirical integral library to modular ab initio electronic structure enables new semiempirical methods

Ab initio and semiempirical electronic structure methods are usually implemented in separate software packages or use entirely different code paths. As a result, it can be time-consuming to transfer an established ab initio electronic structure scheme to a semiempirical Hamiltonian. Here we present an approach to unify ab initio and semiempirical electronic structure code paths based on a separation of the wavefunction ansatz and the needed matrix representations of operators. With this separation, the Hamiltonian can refer to either an ab initio or semiempirical treatment of the resulting integrals. We built a semiempirical integral library and interfaced it to the GPU-accelerated electronic structure code TeraChem. Equivalency between ab initio and semiempirical tight-binding Hamiltonian terms is assigned according to their dependence on the one-electron density matrix. The new library provides semiempirical equivalents of the Hamiltonian matrix and gradient intermediates, corresponding to those provided by the ab initio integral library. This enables the straightforward combination of semiempirical Hamiltonians with the full pre-existing ground and excited state functionality of the ab initio electronic structure code. We demonstrate the capability of this approach by combining the extended tight-binding method GFN1-xTB with both spin-restricted ensemble-referenced Kohn–Sham and complete active space methods. We also present a highly efficient GPU implementation of the semiempirical Mulliken-approximated Fock exchange. The additional computational cost for this term becomes negligible even on consumer-grade GPUs, enabling Mulliken-approximated exchange in tight-binding methods for essentially no additional cost.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Final Report

This final progress report describes the development of the CANDO Software package at ThirdLaw Technologies LLC (TLT) towards a software platform that will be used by its subsidiary company ThirdLaw Molecular LLC (TLM) for the development of therapeutic Spiroligomer™ molecules. ThirdLaw Molecular LLC is 95% owned by ThirdLaw Technologies LLC. TLM is developing a new therapeutics platform based on Spiroligomer™ molecules and is currently funded by the Department of Defense, Defense Threat Reduction Agency (DOD/DTRA W15QKN209C004). Spiroligomer™ molecules are complex, highly-preorganized macromolecules with programmable three-dimensional shapes. Spiroligomer™ molecules are currently synthesized by TLM in the form of large (>880,000 member) DNA-encoded libraries and screened against dangerous bacteria and viruses as part of the DOD/DTRA project. The CANDO software package is being developed to enable the computational design of Spiroligomer™ molecules for the development of therapeutic and diagnostic molecules. Towards this end, over the period of the grant we implemented software algorithms and a user interface within CANDO to enable the computational design of Spiroligomer™ molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Uncertainty Visualization of Critical Points of 2D Scalar Fields for Parametric and Nonparametric Probabilistic Models

This paper presents a novel end-to-end framework for closed-form computation and visualization of critical point uncertainty in 2D uncertain scalar fields. Critical points are fundamental topological descriptors used in the visualization and analysis of scalar fields. The uncertainty inherent in data (e.g., observational and experimental data, approximations in simulations, and compression), however, creates uncertainty regarding critical point positions. Uncertainty in critical point positions, therefore, cannot be ignored, given their impact on downstream data analysis tasks. Here, in this work, we study uncertainty in critical points as a function of uncertainty in data modeled with probability distributions. Although Monte Carlo (MC) sampling techniques have been used in prior studies to quantify critical point uncertainty, they are often expensive and are infrequently used in production-quality visualization software. We, therefore, propose a new end-to-end framework to address these challenges that comprises a threefold contribution. First, we derive the critical point uncertainty in closed form, which is more accurate and efficient than the conventional MC sampling methods. Specifically, we provide the closed-form and semianalytical (a mix of closed-form and MC methods) solutions for parametric (e.g., uniform, Epanechnikov) and nonparametric models (e.g., histograms) with finite support. Second, we accelerate critical point probability computations using a parallel implementation with the VTK-m library, which is platform portable. Finally, we demonstrate the integration of our implementation with the ParaView software system to demonstrate near-real-time results for real datasets.

97 MATHEMATICS AND COMPUTING↗

MONTE for Orbit Determination

Monte is the Jet Propulsion Laboratory’s (JPL) signature astrodynamic computing platform. Its main interface is a collection of Python-language libraries that can be used either for one-o analyses or to build high-quality software applications. Perhaps nowhere is Monte’s versatility and excellence better demonstrated than in its use for operational orbit determination (OD). Over the period from 2007 to 2016, Monte was the prime OD solution for fourteen JPL flight projects, and secondary for seven non-JPL projects. These missions span the range of Solar System destinations and operational protocols, yet each were successfully serviced by Monte’s flexible OD library. This paper reviews the missions on which Monte has been used for OD, with an eye toward pointing out the di erent ways it has been deployed to solve unique problems. It also gives an outline of the main elements of the orbit determination library and how they work together to navigate flight missions.

Martin-Mur, Tomas↗

SU-F-J-72: A Clinical Usable Integrated Contouring Quality Evaluation Software for Radiotherapy

Purpose: To introduce the Auto Contour Evaluation (ACE) software, which is the clinical usable, user friendly, efficient and all-in-one toolbox for automatically identify common contouring errors in radiotherapy treatment planning using supervised machine learning techniques. Methods: ACE is developed with C# using Microsoft .Net framework and Windows Presentation Foundation (WPF) for elegant GUI design and smooth GUI transition animations through the integration of graphics engines and high dots per inch (DPI) settings on modern high resolution monitors. The industrial standard software design pattern, Model-View-ViewModel (MVVM) pattern, is chosen to be the major architecture of ACE for neat coding structure, deep modularization, easy maintainability and seamless communication with other clinical software. ACE consists of 1) a patient data importing module integrated with clinical patient database server, 2) a 2D DICOM image and RT structure simultaneously displaying module, 3) a 3D RT structure visualization module using Visualization Toolkit or VTK library and 4) a contour evaluation module using supervised pattern recognition algorithms to detect contouring errors and display detection results. ACE relies on supervised learning algorithms to handle all image processing and data processing jobs. Implementations of related algorithms are powered by Accord.Net scientific computing library for better efficiency and effectiveness. Results: ACE can take patient’s CT images and RT structures from commercial treatment planning software via direct user input or from patients’ database. All functionalities including 2D and 3D image visualization and RT contours error detection have been demonstrated with real clinical patient cases. Conclusion: ACE implements supervised learning algorithms and combines image processing and graphical visualization modules for RT contours verification. ACE has great potential for automated radiotherapy contouring quality verification. Structured with MVVM pattern, it is highly maintainable and extensible, and support smooth connections with other clinical software tools.

60 APPLIED LIFE SCIENCES↗

Information Metacatalog for a Grid

SWIM is a Software Information Metacatalog that gathers detailed information about the software components and packages installed on a grid resource. Information is currently gathered for Executable and Linking Format (ELF) executables and shared libraries, Java classes, shell scripts, and Perl and Python modules. SWIM is built on top of the POUR framework, which is described in the preceding article. SWIM consists of a set of Perl modules for extracting software information from a system, an XML schema defining the format of data that can be added by users, and a POUR XML configuration file that describes how these elements are used to generate periodic, on-demand, and user-specified information. Periodic software information is derived mainly from the package managers used on each system. SWIM collects information from native package managers in FreeBSD, Solaris, and IRX as well as the RPM, Perl, and Python package managers on multiple platforms. Because not all software is available, or installed in package form, SWIM also crawls the set of relevant paths from the File System Hierarchy Standard that defines the standard file system structure used by all major UNIX distributions. Using these two techniques, the vast majority of software installed on a system can be located. SWIM computes the same information gathered by the periodic routines for specific files on specific hosts, and locates software on a system given only its name and type.

Kolano, Paul↗