Results for “Software Construction” — Page 15

NASA NTRS1994

The development and validation of command schedules for SeaWiFS

An automated method for developing and assessing spacecraft and instrument command schedules is presented for the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) project. SeaWiFS is to be carried on the polar-orbiting SeaStar satellite in 1995. The primary goal of the SeaWiFS mission is to provide global ocean chlorophyll concentrations every four days by employing onboard recorders and a twice-a-day data downlink schedule. Global Area Coverage (GAC) data with about 4.5 km resolution will be used to produce the global coverage. Higher resolution (1.1 km resolution) Local Area Coverage (LAC) data will also be recorded to calibrate the sensor. In addition, LAC will be continuously transmitted from the satellite and received by High Resolution Picture Transmission (HRPT) stations. The methods used to generate commands for SeaWiFS employ numerous hierarchical checks as a means of maximizing coverage of the Earth's surface and fulfilling the LAC data requirements. The software code is modularized and written in Fortran with constructs to mirror the pre-defined mission rules. The overall method is specifically developed for low orbit Earth-observing satellites with finite onboard recording capabilities and regularly scheduled data downlinks. Two software packages using the Interactive Data Language (IDL) for graphically displaying and verifying the resultant command decisions are presented. Displays can be generated which show portions of the Earth viewed by the sensor and spacecraft sub-orbital locations during onboard calibration activities. An IDL-based interactive method of selecting and testing LAC targets and calibration activities for command generation is also discussed.

Woodward, Robert H.↗

DOE OSTI2023

Developing a SARS-CoV-2 main protease binding prediction random forest model for drug repurposing for COVID-19 treatment

The coronavirus disease 2019 (COVID-19) global pandemic resulted in millions of people becoming infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and close to seven million deaths worldwide. It is essential to further explore and design effective COVID-19 treatment drugs that target the main protease of SARS-CoV-2, a major target for COVID-19 drugs. In this study, machine learning was applied for predicting the SARS-CoV-2 main protease binding of Food and Drug Administration (FDA)-approved drugs to assist in the identification of potential repurposing candidates for COVID-19 treatment. Ligands bound to the SARS-CoV-2 main protease in the Protein Data Bank and compounds experimentally tested in SARS-CoV-2 main protease binding assays in the literature were curated. These chemicals were divided into training (516 chemicals) and testing (360 chemicals) data sets. To identify SARS-CoV-2 main protease binders as potential candidates for repurposing to treat COVID-19, 1188 FDA-approved drugs from the Liver Toxicity Knowledge Base were obtained. A random forest algorithm was used for constructing predictive models based on molecular descriptors calculated using Mold2 software. Model performance was evaluated using 100 iterations of fivefold cross-validations which resulted in 78.8% balanced accuracy. The random forest model that was constructed from the whole training dataset was used to predict SARS-CoV-2 main protease binding on the testing set and the FDA-approved drugs. Model applicability domain and prediction confidence on drugs predicted as the main protease binders discovered 10 FDA-approved drugs as potential candidates for repurposing to treat COVID-19. Our results demonstrate that machine learning is an efficient method for drug repurposing and, thus, may accelerate drug development targeting SARS-CoV-2.

Research & Experimental Medicine↗

DOE OSTI2018

Parallel Fenics Implementation of Block Solvers (pFibs)

This software is a Python package designed to act as an interface between FEniCS and PETSc to facilitate the construction and application of parallel block solvers/preconditioners. The original intent of this software was to help enable Battery and Wind Farm simulations for use on high performance computing systems. The code is written in Python and uses the petsc4py module to access the more advance features of the PETSc Krylov Solver. In essence, pFibs is an interface to make accessing these features more streamlined. Additionally, pFibs also provides a template for building custom Python based preconditioning algorithms.

Allen, Jeffery↗

NASA NTRS1994

A toolbox and record for scientific models

Computational science presents a host of challenges for the field of knowledge-based software design. Scientific computation models are difficult to construct. Models constructed by one scientist are easily misapplied by other scientists to problems for which they are not well-suited. Finally, models constructed by one scientist are difficult for others to modify or extend to handle new types of problems. Construction of scientific models actually involves much more than the mechanics of building a single computational model. In the course of developing a model, a scientist will often test a candidate model against experimental data or against a priori expectations. Test results often lead to revisions of the model and a consequent need for additional testing. During a single model development session, a scientist typically examines a whole series of alternative models, each using different simplifying assumptions or modeling techniques. A useful scientific software design tool must support these aspects of the model development process as well. In particular, it should propose and carry out tests of candidate models. It should analyze test results and identify models and parts of models that must be changed. It should determine what types of changes can potentially cure a given negative test result. It should organize candidate models, test data, and test results into a coherent record of the development process. Finally, it should exploit the development record for two purposes: (1) automatically determining the applicability of a scientific model to a given problem; (2) supporting revision of a scientific model to handle a new type of problem. Existing knowledge-based software design tools must be extended in order to provide these facilities.

Ellman, Thomas↗

NASA NTRS2009

Deriving Safety Cases from Automatically Constructed Proofs

Formal proofs provide detailed justification for the validity of claims and are widely used in formal software development methods. However, they are often complex and difficult to understand, because the formalism in which they are constructed and encoded is usually machine-oriented, and they may also be based on assumptions that are not justified. This causes concerns about the trustworthiness of using formal proofs as arguments in safety-critical applications. Here, we present an approach to develop safety cases that correspond to formal proofs found by automated theorem provers and reveal the underlying argumentation structure and top-level assumptions. We concentrate on natural deduction style proofs, which are closer to human reasoning than resolution proofs, and show how to construct the safety cases by covering the natural deduction proof tree with corresponding safety case fragments. We also abstract away logical book-keeping steps, which reduces the size of the constructed safety cases. We show how the approach can be applied to the proofs found by the Muscadet prover.

Basir, Nurlida↗

NASA NTRS1986

An empirical study of flight control software reliability

The results of a laboratory experiment in flight control software reliability are reported. The experiment tests a small sample of implementations of a pitch axis control law for a PA28 aircraft with over 14 million pitch commands with varying levels of additive input and feedback noise. The testing which uses the method of n-version programming for error detection surfaced four software faults in one implementation of the control law. The small number of detected faults precluded the conduct of the error burst analyses. The pitch axis problem provides data for use in constructing a model in the prediction of the reliability of software in systems with feedback. The study is undertaken to find means to perform reliability evaluations of flight control software.

Dunham, J. R.↗

DOE OSTI2012

Internal Fiducial Markers and Susceptibility Effects in MRI-Simulation and Measurement of Spatial Accuracy

Background: It is well-known that magnetic resonance imaging (MRI) is preferable to computed tomography (CT) in radiotherapy target delineation. To benefit from this, there are two options available: transferring the MRI delineated target volume to the planning CT or performing the treatment planning directly on the MRI study. A precondition for excluding the CT study is the possibility to define internal structures visible on both the planning MRI and on the images used to position the patient at treatment. In prostate cancer radiotherapy, internal gold markers are commonly used, and they are visible on CT, MRI, x-ray, and portal images. The depiction of the markers in MRI are, however, dependent on their shape and orientation relative the main magnetic field because of susceptibility effects. In the present work, these effects are investigated and quantified using both simulations and phantom measurements. Methods and Materials: Software that simulated the magnetic field distortions around user defined geometries of variable susceptibilities was constructed. These magnetic field perturbation maps were then reconstructed to images that were evaluated. The simulation software was validated through phantom measurements of four commercially available gold markers of different shapes and one in-house gold marker. Results: Both simulations and phantom measurements revealed small position deviations of the imaged marker positions relative the actual marker positions (<1 mm). Conclusion: Cylindrical gold markers can be used as internal fiducial markers in MRI.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2021

Development of the IES Plug-and-Play Framework

This report discusses the status of the flexible plug-and-play framework development currently ongoing that aims to integrate Modelica/Dymola with the Risk Analysis and Virtual ENvironment (RAVEN) software in terms of both Functional Mock-Up Interface (FMI)/Functional Mock-Up Unit (FMU) construction and repository structures that aim to ease the sharing and simulation of complex dynamic models. This report aims to provide an overview of all the performed activities resolving around the deployment of methods, software infrastructures, guidelines and workflow for the construction and usage of models, encapsulated using the FMI/FMU protocols and standards. In particular, the report is organized in three main macro-subjects, which are connected to each other: - FMI/FMU adaptors for modelica models - HYBRID repository new structure and open-source deployment - RAVEN FMI/FMU exporting capabilities and Artificial Intelligence (AI)-based analysis acceleration. The first part of the report discusses the FMI/FMU adaptors that have been created within the HYBRID repository to allow users to quickly export models, such as FMUs. Several examples are shown that highlight the step-by-step process of converting an existing Modelica model into an FMU for use within the Dymola platform. Simulation results demonstrate that, while minor differences may occur, the overall control, trends, and solution integrity are maintained between standard Modelica simulation and FMU simulation results. However, it is worth noting that, for small systems, the FMU results have a slower simulation time than the Modelica only simulation. Using this process, a company can provide models that contain proprietary information to entities without disclosing any of the information about the model that could be considered business sensitive. Such an ability would allow institutions to bypass the necessity of “whitewashing” data. In the second part of the report, the new structure of the HYBRID repository is discussed with a major focus on the series of updates that has been completed. These updates include the addition of Modelica system-level regression tests and software quality assurance documentation that ensure that modifications to the Modelica models do not alter system-level model results. The third and final part of the report aims to report the work that has been performed for the deployment of methods and workflows for the construction of RAVEN AI-based models compliant with the FMI/FMU standard. Such development represents the key for the deployment of the concept of “Flexible ecosystem” since it allows for the replacement of high-fidelity modelica models (or any other FMI/FMU compliant model) with RAVEN generated AI surrogate models. Overall, extensive work has been completed on developing FMUs and FMIs from existing models, understanding the requirements and limitations of FMUs, and open-sourcing the HYBRID repository with an integrated regression system.

42 ENGINEERING↗

DOE OSTI2021

Development of the IES Plug-and-Play Framework

This report discusses the status of the flexible plug-and-play framework development currently ongoing that aims to integrate Modelica/Dymola with the Risk Analysis and Virtual ENvironment (RAVEN) software in terms of both Functional Mock-Up Interface (FMI)/Functional Mock-Up Unit (FMU) construction and repository structures that aim to ease the sharing and simulation of complex dynamic models. This report aims to provide an overview of all the performed activities resolving around the deployment of methods, software infrastructures, guidelines and workflow for the construction and usage of models, encapsulated using the FMI/FMU protocols and standards. In particular, the report is organized in three main macro-subjects, which are connected to each other: - FMI/FMU adaptors for modelica models - HYBRID repository new structure and open-source deployment - RAVEN FMI/FMU exporting capabilities and Artificial Intelligence (AI)-based analysis acceleration. The first part of the report discusses the FMI/FMU adaptors that have been created within the HYBRID repository to allow users to quickly export models, such as FMUs. Several examples are shown that highlight the step-by-step process of converting an existing Modelica model into an FMU for use within the Dymola platform. Simulation results demonstrate that, while minor differences may occur, the overall control, trends, and solution integrity are maintained between standard Modelica simulation and FMU simulation results. However, it is worth noting that, for small systems, the FMU results have a slower simulation time than the Modelica only simulation. Using this process, a company can provide models that contain proprietary information to entities without disclosing any of the information about the model that could be considered business sensitive. Such an ability would allow institutions to bypass the necessity of “whitewashing” data. In the second part of the report, the new structure of the HYBRID repository is discussed with a major focus on the series of updates that has been completed. These updates include the addition of Modelica system-level regression tests and software quality assurance documentation that ensure that modifications to the Modelica models do not alter system-level model results. The third and final part of the report aims to report the work that has been performed for the deployment of methods and workflows for the construction of RAVEN AI-based models compliant with the FMI/FMU standard. Such development represents the key for the deployment of the concept of “Flexible ecosystem” since it allows for the replacement of high-fidelity modelica models (or any other FMI/FMU compliant model) with RAVEN generated AI surrogate models. Overall, extensive work has been completed on developing FMUs and FMIs from existing models, understanding the requirements and limitations of FMUs, and open-sourcing the HYBRID repository with an integrated regression system.

14 SOLAR ENERGY↗

NASA NTRS2020

Integrating the Science Opportunity Analyzer with a Reusable Opportunity Search Framework

In our interactions with the Science Opportunity Analyzer (SOA) software, we recognized how its ability to search for geometric events in space is a need for robotic space missions in general. To satisfy this need, we propose the Tychonis framework, which is built upon the principles of: (1) separations of concerns, (2) extensibility, (3) reusability, and (4) independent verification and validation. Tychonis’ separation of concerns results in the availability of different constructs to model geometric events and search for them. These constructs can be extended by users as needed and reused across missions without changes. Given the low coupling between concerns, and the fact Tychonis can be augmented in isolation, its constructs can be validated independently from other pieces of software. This paper elaborates on these topics and presents an integration case study between Tychonis and SOA that relies on the concept of dynamic integration. Dynamic integration entails that augmentations of the framework are reflected automatically in the host application without any changes to the host application’s code. The SOA-Tychonis integration case study can be extrapolated to other tools that need to search for geometric events as the pattern repeats across implementations: (i) the manipulation of a user interface to model opportunities, (ii) the execution of algorithms to search for opportunities, and (iii) the presentation of search results to users. Overall, Tychonis’ is a story about how the application of proven software principles and good design choices can reduce risk and cost to space missions

Soria, Manel↗

NASA NTRS1992

Providing an empirical basis for optimizing the verification and testing phases of software development

Applying equal testing and verification effort to all parts of a software system is not very efficient, especially when resources are limited and scheduling is tight. Therefore, one needs to be able to differentiate low/high fault density components so that the testing/verification effort can be concentrated where needed. Such a strategy is expected to detect more faults and thus improve the resulting reliability of the overall system. This paper presents an alternative approach for constructing such models that is intended to fulfill specific software engineering needs (i.e. dealing with partial/incomplete information and creating models that are easy to interpret). Our approach to classification is as follows: (1) to measure the software system to be considered; and (2) to build multivariate stochastic models for prediction. We present experimental results obtained by classifying FORTRAN components developed at the NASA/GSFC into two fault density classes: low and high. Also we evaluate the accuracy of the model and the insights it provides into the software process.

Briand, Lionel C.↗

DOE OSTI2012

Water Usage for In-Situ Oil Shale Retorting – A Systems Dynamics Model

A system dynamic model was construction to evaluate the water balance for in-situ oil shale conversion. The model is based on a systems dynamics approach and uses the Powersim Studio 9™ software package. Three phases of an insitu retort were consider; a construction phase primarily accounts for water needed for drilling and water produced during dewatering, an operation phase includes the production of water from the retorting process, and a remediation phase water to remove heat and solutes from the subsurface as well as return the ground surface to its natural state. Throughout these three phases, the water is consumed and produced. Consumption is account for through the drill process, dust control, returning the ground water to its initial level and make up water losses during the remedial flushing of the retort zone. Production of water is through the dewatering of the retort zone, and during chemical pyrolysis reaction of the kerogen conversion. The major water consumption was during the remediation of the insitu retorting zone.

02 PETROLEUM↗

DOE OSTI2013

Benchmark Imagery Project: Selection of Real World Images for Creating Composite Images of Facilities

The "Benchmark Imagery" project is a DOE NA-22-funded effort whose three-year goal is to create a suite of imagery (both real and composite) that can be used to test geospatial algorithms used for extracting semantic content from overhead images of industrial facilities. A composite image is an image that contains both real elements such as photographic imagery and synthetic elements such as 3D models. Composite images have the advantage of being customizable and distributable, and they can contain complete ground truth. It is our goal to generate composite images which appear realistic to both human and algorithm. When generating composite images of facilities we use real overhead imagery to increase realism and decrease effort. To construct all elements with purely synthetic textures would require too much effort and still may not look as realistic as a real image. We use real time 3D rendering software "SceneWorks" for rendering composite images. In SceneWorks, a scene is constructed by placing 3D models of facility components on top of a base terrain. A base terrain is a 3D model constructed from digital elevation mapping (DEM) data and then textured with overhead orthorectified imagery. The base terrain is constructed to be geospatially accurate using a real location’s source data (DEM and Imagery.) This document outlines the selection criteria in selecting appropriate location and source data for constructing the base terrain. Imagery should have resolution equal or better than desired composite image resolution. The imagery should have no seams. Seams can occur when two or more different imagery data sets exist in a single area with neither set covering the entire area. Elevation data (DEM) resolution generally should be 1/9 arc second or better depending on the variability of elevation. The imagery must contain a flat clearing of land large enough for multiple facility types. There should be no high-rise buildings anywhere in the base terrain.

42 ENGINEERING↗

NASA NTRS1991

A software development and evolution model based on decision-making

Design is a complex activity whose purpose is to construct an artifact which satisfies a set of constraints and requirements. However the design process is not well understood. The software design and evolution process is the focus of interest, and a three dimensional software development space organized around a decision-making paradigm is presented. An initial instantiation of this model called 3DPM(sub p) which was partly implemented, is presented. Discussion of the use of this model in software reuse and process management is given.

Wild, J. Christian↗

DOE OSTI2019

A Thermodynamic Model Toward the Comprehension of Ferrous Burden Softening and Melting Using FactSage Macro-Processing

The softening and melting properties of iron-bearing materials play a decisive role in the formation of the cohesive zone, which greatly affects blast furnace gas flow distribution and heat-transfer efficiency. To improve the understanding regarding the evolution of condensed phases during reduction, softening, and melting, a thermodynamic model has been developed using FactSage™ thermodynamic software and macro-processing. The model was constructed using a series of equilibrium stages and splitters to determine flow directions of streams and to consider kinetic inhibitions. For all iron-bearing materials studied, the methodology proposed for modeling was capable of obtaining reduction degrees in very good agreement to its experimental data. The evolution of solid phases was qualitatively comparable to the available literature, with Fayalite, Kirschsteinite, Melilite, and FeO as the main solid phases in equilibrium before slag formation. The comparison between the profiles of the calculated slag mass fraction and the experimental pressure drop showed a close relation between these properties. Moreover, the level of heterogeneity of each raw material may play a significant role in the interpretation of its results.

36 MATERIALS SCIENCE↗

DOE OSTI2014

Extending particle tracking capability with Delaunay triangulation

Here, particle tracking, the analysis of individual moving elements in time series of microscopic images, enables burgeoning new applications, but there is need to better resolve conformation and dynamics. Here we describe the advantages of Delaunay triangulation to extend the capabilities of particle tracking in three areas: (1) discriminating irregularly shaped objects, which allows one to track items other than point features; (2) combining time and space to better connect missing frames in trajectories; and (3) identifying shape backbone. To demonstrate the method, specific examples are given, involving analyzing the time-dependent molecular conformations of actin filaments and λ-DNA. The main limitation of this method, shared by all other clustering techniques, is the difficulty to separate objects when they are very close. This can be mitigated by inspecting locally to remove edges that are longer than their neighbors and also edges that link two objects, using methods described here, so that the combination of Delaunay triangulation with edge removal can be robustly applied to processing large data sets. As common software packages, both commercial and open source, can construct Delaunay triangulation on command, the methods described in this paper are both computationally efficient and easy to implement.

36 MATERIALS SCIENCE↗

DOE OSTI2024

A Microservices Architecture Toolkit for Interconnected Science Ecosystems

Microservices architecture is a promising approach for developing reusable scientific workflow capabilities for inte- grating diverse resources, such as experimental and observational instruments and advanced computational and data management systems, across many distributed organizations and facilities. In this paper, we describe how the INTERSECT Open Architec- ture leverages federated systems of microservices to construct interconnected science ecosystems, review how the INTERSECT software development kit eases microservice capability develop- ment, and demonstrate the use of such capabilities for deploying an example multi-facility INTERSECT ecosystem.

Brim, Michael↗

DOE OSTI2016

A frequentist approach to computer model calibration

The paper considers the computer model calibration problem and provides a general frequentist solution. Under the framework proposed, the data model is semiparametric with a non-parametric discrepancy function which accounts for any discrepancy between physical reality and the computer model. In an attempt to solve a fundamentally important (but often ignored) identifiability issue between the computer model parameters and the discrepancy function, the paper proposes a new and identifiable parameterization of the calibration problem. It also develops a two-step procedure for estimating all the relevant quantities under the new parameterization. This estimation procedure is shown to enjoy excellent rates of convergence and can be straightforwardly implemented with existing software. For uncertainty quantification, bootstrapping is adopted to construct confidence regions for the quantities of interest. As a result, the practical performance of the methodology is illustrated through simulation examples and an application to a computational fluid dynamics model.

97 MATHEMATICS AND COMPUTING↗