LipiDex: An Integrated Software Package for High-Confidence Lipid Identification
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Hutchins, Paul D. (ORCID:0000000266835735)↗
SEARCH · Engineering Papers
Results for “software integration”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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An Integrated Software Package to Enable Predictive Simulation Capabilities
The power grid is increasing in complexity due to the deployment of smart grid technologies. Such technologies vastly increase the size and complexity of power grid systems for simulation and modeling. This increasing complexity necessitates not only the use of high-performance-computing (HPC) techniques, but a smooth, well-integrated interplay between HPC applications. This paper presents a new integrated software package that integrates HPC applications and a web-based visualization tool based on a middleware framework. This framework can support the data communication between different applications. Case studies with a large power system demonstrate the predictive capability brought by the integrated software package, as well as the better situational awareness provided by the web-based visualization tool in a live mode. Test results validate the effectiveness and usability of the integrated software package.
Chen, Yousu↗
MixPI: Mixed-time slicing path integral software for quantized molecular dynamics simulations
We introduce the MixPI software to implement path integral molecular dynamics (PIMD) simulations for the study of condensed phase systems where nuclear quantum effects (NQEs) are important. In contrast to existing PIMD simulation software, MixPI enables the implementation of mixed quantum–classical path integral simulations where only a subset of system degrees of freedom (dofs) are treated quantum mechanically in an extended phase space while the remaining dofs are described classically. We expect this software to be particularly useful for simulations of electron and proton transfer in condensed phase systems, as well as for the study of biological and material systems where only a handful of dofs contribute significantly to the observed NQEs. We demonstrate the use of MixPI in two different systems. The first is a simple water model where we implement a set of mixed quantum–classical simulations to compute average energy and radial distribution functions. We use these simulations to benchmark the effectiveness of MixPI and to demonstrate how it enables systematic investigation into the origin of observed NQEs. We then compute radial distribution functions for a system where MixPI is essential: a solvated metal (M 2+ ) cation described using an explicit quantized electron localized on an M 3+ ion in water.
chemical physics↗
Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools
Background: MicroRNAs (miRNAs) are noncoding RNAs that direct post-transcriptional regulation of protein coding genes. Recent studies have shown miRNAs are important for controlling many biological processes, including nervous system development, and are highly conserved across species. Given their importance, computational tools are necessary for analysis, interpretation and integration of high-throughput (HTP) miRNA data in an increasing number of model species. The Bioinformatics Resource Manager (BRM) v2.3 is a software environment for data management, mining, integration and functional annotation of HTP biological data. In this study, we report recent updates to BRM for miRNA data analysis and cross-species comparisons across datasets. Results: BRM v2.3 has the capability to query predicted miRNA targets from multiple databases, retrieve potential regulatory miRNAs for known genes, integrate experimentally derived miRNA and mRNA datasets, perform ortholog mapping across species, and retrieve annotation and cross-reference identifiers for an expanded number of species. Here we use BRM to show that developmental exposure of zebrafish to 30 uM nicotine from 6–48 hours post fertilization (hpf) results in behavioral hyperactivity in larval zebrafish and alteration of putative miRNA gene targets in whole embryos at developmental stages that encompass early neurogenesis. We show typical workflows for using BRM to integrate experimental zebrafish miRNA and mRNA microarray datasets with example retrievals for zebrafish, including pathway annotation and mapping to human ortholog. Functional analysis of differentially regulated (p<0.05) gene targets in BRM indicates that nicotine exposure disrupts genes involved in neurogenesis, possibly through misregulation of nicotine-sensitive miRNAs. Conclusions: BRM provides the ability to mine complex data for identification of candidate miRNAs or pathways that drive phenotypic outcome and, therefore, is a useful hypothesis generation tool for systems biology. The miRNA workflow in BRM allows for efficient processing of multiple miRNA and mRNA datasets in a single software environment with the added capability to interact with public data sources and visual analytic tools for HTP data analysis at a systems level. BRM is developed using Java™ and other open-source technologies for free distribution (http://www.sysbio.org/dataresources/brm.stm).
59 BASIC BIOLOGICAL SCIENCES↗
Infrastructure for Multiphysics Software Integration in High Performance Computing-Aided Science and Engineering
The project described in this report constructed and exercised an innovative multiphysics coupling toolkit called the Illinois Rocstar MultiPhysics Application Coupling Toolkit (IMPACT). IMPACT is an open source, flexible, natively parallel infrastructure for coupling multiple uniphysics simulation codes into multiphysics computational systems. IMPACT works with codes written in several high-performance-computing (HPC) programming languages, and is designed from the beginning for HPC multiphysics code development. It is designed to be minimally invasive to the individual physics codes being integrated, and has few requirements on those physics codes for integration. The goal of IMPACT is to provide the support needed to enable coupling existing tools together in unique and innovative ways to produce powerful new multiphysics technologies without extensive modification and rewrite of the physics packages being integrated. There are three major outcomes from this project: 1) construction, testing, application, and open-source release of the IMPACT infrastructure, 2) production of example open-source multiphysics tools using IMPACT, and 3) identification and engagement of interested organizations in the tools and applications resulting from the project. This last outcome represents the incipient development of a user community and application echosystem being built using IMPACT. Multiphysics coupling standardization can only come from organizations working together to define needs and processes that span the space of necessary multiphysics outcomes, which Illinois Rocstar plans to continue driving toward. The IMPACT system, including source code, documentation, and test problems are all now available through the public gitHUB.org system to anyone interested in multiphysics code coupling. Many of the basic documents explaining use and architecture of IMPACT are also attached as appendices to this document. Online HTML documentation is available through the gitHUB site. There are over 100 unit tests provided that run through the Illinois Rocstar Application Development (IRAD) lightweight testing infrastructure that is also supplied along with IMPACT. The package as a whole provides an excellent base for developing high-quality multiphysics applications using modern software development practices. To facilitate understanding how to utilize IMPACT effectively, two multiphysics systems have been developed and are available open-source through gitHUB. The simpler of the two systems, named ElmerFoamFSI in the repository, is a multiphysics, fluid-structure-interaction (FSI) coupling of the solid mechanics package Elmer with a fluid dynamics module from OpenFOAM. This coupling illustrates how to combine software packages that are unrelated by either author or architecture and combine them into a robust, parallel multiphysics system. A more complex multiphysics tool is the Illinois Rocstar Rocstar Multiphysics code that was rebuilt during the project around IMPACT. Rocstar Multiphysics was already an HPC multiphysics tool, but now that it has been rearchitected around IMPACT, it can be readily expanded to capture new and different physics in the future. In fact, during this project, the Elmer and OpenFOAM tools were also coupled into Rocstar Multiphysics and demonstrated. The full Rocstar Multiphysics codebase is also available on gitHUB, and licensed for any organization to use as they wish. Finally, the new IMPACT product is already being used in several multiphysics code coupling projects for the Air Force, NASA and the Missile Defense Agency, and initial work on expansion of the IMPACT-enabled Rocstar Multiphysics has begun in support of a commercial company. These initiatives promise to expand the interest and reach of IMPACT and Rocstar Multiphysics, ultimately leading to the envisioned standardization and consortium of users that was one of the goals of this project.
42 ENGINEERING↗
Interactive statistical decision tools (GiSdT): An open source software integration of decision analysis and stakeholder judgment for sustainable waste management, disposal and remediation - 15650
The vast majority of remediation and waste management decisions are made without quantitative consideration of economic and socio-political factors. They are made instead based on quantitative metrics of human health risk. Sustainable decisions need to be made based on all three 'pillars of sustainability' (economics, environment and social), and require understanding and characterization of the costs and values associated with each pillar. In addition, such decisions need to conform to regulatory or other legal requirements, which often constrains the decision space of interest. Although efforts are often made to include factors across all three pillars (for example, for decisions made under CERCLA), these efforts are usually qualitative, and hence difficult to defend. They lack technical defensibility, transparency and traceability. The purpose of GiSdT (Guided Interactive Statistical Decision Tools) is to provide a quantitative framework whereby all aspects of a decision problem, such as remediation and waste management decisions, can be addressed quantitatively, and hence, defensibly, transparently and traceably. Most decision-makers do not currently have access to useful or usable methods and approaches when are presented with choices that have significant impacts across all three pillars of sustainability. The goal of GiSdT is to provide that access by identifying or developing effective and user-friendly decision methods and approaches that empower decision-makers to explicitly and routinely incorporate all aspects of sustainability into their decision-making. To identify and develop these methods and approaches, GiSdT provides the tools needed for decision-makers and stakeholders to understand and characterize their knowledge of their current decision-making processes, and what methods and approaches they need to pro-actively and quantitatively address all aspects of sustainability in their decisions. GiSdT is an open source interactive framework program that provides the tools needed to address the relevant components of a sustainability-based decision problem, including describing the decision landscape, translating that landscape into goals and objectives, valuing the measurable attributes that describe each objective, identifying decision options and addressing the uncertainty in the attributes (e.g., human health risk, institutional controls) through appropriate probabilistic models. In addition to addressing these quantitative technical components, the GiSdT program is aimed at facilitating stakeholder involvement so that the perspectives, values and objectives are all relevant stakeholders are addressed explicitly in the decision making process. The technical underpinnings of our software program, called Guided Interactive Statistical Decision Tools (GiSdT), are described. (authors)
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Parallel time integration software
This package implements an optimal-scaling multigrid solver for the (non) linear systems that arise from the discretization of problems with evolutionary behavior. Typically, solution algorithms for evolution equations are based on a time-marching approach, solving sequentially for one time step after the other. Parallelism in these traditional time-integrarion techniques is limited to spatial parallelism. However, current trends in computer architectures are leading twards system with more, but not faster. processors. Therefore, faster compute speeds must come from greater parallelism. One approach to achieve parallelism in time is with multigrid, but extending classical multigrid methods for elliptic poerators to this setting is a significant achievement. In this software, we implement a non-intrusive, optimal-scaling time-parallel method based on multigrid reduction techniques. The examples in the package demonstrate optimality of our multigrid-reduction-in-time algorithm (MGRIT) for solving a variety of parabolic equations in two and three sparial dimensions. These examples can also be used to show that MGRIT can achieve significant speedup in comparison to sequential time marching on modern architectures.
Source record↗
Scientific Data Management Integrated Software Infrastructure Center (SDM/ISIC): Scientific Process Automation (SPA) (Final Report)
The KEPLER project has made a significant impact and established a sustained leadership in the field of scientific workflows. The open source KEPLER project started in 2003 when members of the SciDAC-SDM Center/SPA Team, sponsored by this DOE-funded project (DE-FC02-01ER25486) and members of the SEEK project (NSF/ITR awards DBI-0225674 and DBI-0533368) decided to collaborate and jointly develop a scientific workflow system based on the open source PTOLEMY II system (Ludäscher was a co-PI on both projects). In the first project phase, between 2001 and 2003, the SDSC team (Altintas, Ludäscher) worked closely with a domain scientist (Matt Coleman, LLNL) and created early versions of a Promoter Identification Workflow (PIW). Towards the end of that period, the open source PTOLEMY II system was adopted by SciDAC-SDM and SEEK as the basis for a general scientific workflow system and problem-solving environment to design and execute scientific workflows, giving rise to Kepler. Once started through SciDAC-SDM and SEEK, the KEPLER leadership team was able to attract further support from funding agencies including from DOE (as part of SciDAC-2), NSF, NIH, and the Gordon and Betty Moore Foundation. Important advances to KEPLER were made by the SciDAC/SDM-SPA team during the report period (2001–2007), in particular by the SDSC team (and after Ludäscher's move) the UC Davis team, including (i) research and development of the workflow infrastructure, (ii) library (actor) development, and (iii) development of concrete scientific workflows, in collaboration with scientists. Years later, the KEPLER system was listed as one of the prominent “Big Data” research outcomes of DOE in the White House Big Data Factsheet, announced as part of the White House Big Data press release.
97 MATHEMATICS AND COMPUTING↗
Hardware & software integration for accelerating the materials workflow.
Abstract not provided.
Boyce, Brad↗
Modular Subsurface Sensors and Integrated Software for Advanced Subsurface Characterization and Monitoring using Unoccupied Vehicles
The advent and subsequent proliferation of autonomous airborne, waterborne, and groundbased vehicles (i.e., “drones”) promises to broadly transform the geosciences and associated industries, including fossil energy exploration and development, mineral resource exploration and development, water-resource management, and environmental remediation. For geophysical characterization and monitoring, the prospect of programming highly repeatable and low-cost drone missions for subsurface imaging will allow for deployments in hazardous and previously inaccessible areas. Coupled with autonomous workflows for data processing, management, and visualization, drone-based geophysical characterization and monitoring will enable unprecedented, real-time insight into diverse subsurface properties and processes of scientific and engineering importance. Toward this end, the objectives of this Lab Directed Research and Development (LDRD) project were to develop new (1) instrumentation for dronebased electromagnetic induction (EMI) geophysical imaging, including separated transmitter and receivers and associated electronics, (2) software for real-time data telemetry, processing, management, and visualization. Although EMI has been previously deployed using unoccupied aerial systems (UASs), these applications failed to capitalize on the game-changing capabilities of drone platforms. Whereas drone-based data acquisition allows for collection of rich, three-dimensional (3D) multi-offset/multi-angle configurations between transmitters and receivers, past efforts have relied on conventional instrumentation that was designed for ground-based data collection with the transmitter and a single receiver housed in the same unit; nor did these previous applications demonstrate real-time delivery of results to support rapid management decisions in the field. In this 1-year project, we (1) designed and constructed new lightweight independent transmitter and receiver antenna platforms that communicate with a laptop computer; (2) developed software to control data acquisition, manage/transfer data, and visualize data as its collected; and (3) demonstrated the operation of the new hardware and software systems in a ground-based field test. Our work entails major technological advances for EMI and established a foundation on which to build a new drone-based, real-time geophysical EMI imaging capability to support diverse challenges facing the nation.
47 OTHER INSTRUMENTATION↗
A CASL Multiphysics Code Coupling Primer: Software Integration 101.
Abstract not provided.
Pawlowski, Roger P↗
Infrastructure for Multiphysics Software Integration in High Performance Computing-Aided Science and Engineering
Explore the source record for details and available documents.
97 MATHEMATICS AND COMPUTING↗
Parallel time integration software
This package implements an optimal-scaling multigrid solver for the (non) linear systems that arise from the discretization of problems with evolutionary behavior. Typically, solution algorithms for evolution equations are based on a time-marching approach, solving sequentially for one time step after the other. Parallelism in these traditional time-integrarion techniques is limited to spatial parallelism. However, current trends in computer architectures are leading twards system with more, but not faster. processors. Therefore, faster compute speeds must come from greater parallelism. One approach to achieve parallelism in time is with multigrid, but extending classical multigrid methods for elliptic poerators to this setting is a significant achievement. In this software, we implement a non-intrusive, optimal-scaling time-parallel method based on multigrid reduction techniques. The examples in the package demonstrate optimality of our multigrid-reduction-in-time algorithm (MGRIT) for solving a variety of parabolic equations in two and three sparial dimensions. These examples can also be used to show that MGRIT can achieve significant speedup in comparison to sequential time marching on modern architectures.
Source record↗
Software Development Kits: A Software Integration Strategy for CSE.
Abstract not provided.
Willenbring, James Michael↗
Software Integration Challenges
Explore the source record for details and available documents.
Computer science↗
An Integrated Software Package for Studying Structure-Property-Processing Relationships in Material Systems
Explore the source record for details and available documents.
36 MATERIALS SCIENCE↗
Finite-Test-Case Development to Demonstrate Logical Integrity of Software in DRPS
Reactor protection system (RPS) in nuclear power plant (NPP) is in the process of digitalization in response to advanced features of digital systems. In this context, software integrity in the RPS becomes an important issue since it may cause common-cause failure. Therefore, to guarantee the safety of NPPs, the integrity of the software need to be properly demonstrated or assessed. There are three typical approaches for software reliability quantification: software reliability growth model (SRGM), Bayesian belief network (BBN), and test-based method. Basically, SRGM is difficult to apply to the safety-critical software because not only sufficient failure sets are unavailable but consequence of system failure is also unacceptable. Then the result obtained through the BBN model may have large uncertainty, so it produces difficulties in integrity demonstration of safety-critical software. Thus, the BBN result need to be complemented or verified by test-based method. Currently, for the integrity demonstration of safety-critical software, black-box test which feeds inputs and examines just outputs whether they succeeded or failed is considered based on trajectory-form-of-input (a series of successive values for the input variables that occur during the operation of the software over time). Usually these trajectory-inputs are randomly sampled from operational profile. In this approach, however, there are some practical difficulties. Therefore, we proposed a new test method for safety-critical software in digitalized reactor protection system (DRPS). The main contents described in this paper are about basic concepts under development of finite-test-cases by which the integrity of the software logic can be verified. It should be noted that the influence of the environments, such as operating system and other hardware, are not considered since the method focuses on software logic only. (authors)
22 GENERAL STUDIES OF NUCLEAR REACTORS↗