SALSA3D Software Tools for Model Interrogation Event Location and Travel-time Computation - Poster preview.
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Poster for the 2024 NETL Resource Sustainability Meeting. The poster presents a new project award by the Office of Technology Transitions to accelerate application and commercial utilization of an NETL-developed technology to rapidly characterize critical mineral occurrences within secondary and/or unconventional feedstocks, such as coal refuse or waste impoundments.
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Writing software is difficult. However, writing complex, well tested and designed, and functionally correct software is incredibly difficult. An entire field of study is devoted to the validation and verification of software to address this problem, and in this paper we analyze the landscape of currently available third party software. We have divided our analyses into three separate subsections with regards to software validation: formal methods, static analysis, and test generation. Formal verification is the most complex method in which to validate software correctness, but also the most thorough as it truly validates the mathematical validity of the source code. Static analysis generally is relegated to abstract syntax tree traversal techniques to find errors related to faulty software such as memory leaks or stack overflow issues. Automatic test generation is similar in implementation to static analysis, but pushes a bit further in verifying the boundedness of function inputs and outputs with regards to annotated or parsed criteria. The crux of this report is to analyze and describe the software tools that implement these techniques to validate and verify software. Pros and cons related to installation, utilization, and capabilities of the frameworks are described, and reproducible examples are provided with a focus on usability. The initial survey concluded that the most interesting tools of note are Z3, Isabelle/HOL, and TLA+ with regards to formal verification; and Infer, Frama-C, and SonarQube with regards to static analysis. With these tools in mind, a final conjecture is provided that describes future avenues of utilizing these tools for developing a verification framework to assist in validating existing software at Sandia National Laboratories.
Software for recording machining tracks in abrasive lapping is described. The software permits prediction of the shape and magnitude of the tool’s surface wear at the stage of process design, on the basis of the dimensions of the workpiece and the lap, their relative velocity, and the machining trajectory.
The commercial and industrial sectors account for nearly half of the total U.S. energy consumption. To help these sectors reduce their energy intensity, the U.S. Department of Energy (DOE) designed the Better Buildings, Better Plants Initiative. Through this initiative, more than 900 industrial, commercial, public and residential organizations commit to long-term sustainability goals and share their proven energy efficiency strategies, which inspire others to tap into the continued potential for energy efficiency. Collectively, these organizations have saved 2.5 quadrillion BTUs of energy, equivalent to US$15.3 billion, and 155 million metric tons of carbon dioxide. Within the initiative, the Better Plants side of the program focuses specifically on the industrial sector. More than 270 industrial partners have taken advantage of the unique selection of resources offered including workforce development programs, information sharing, peer-to-peer networking, diagnostic tool loans and software tools. One of the most powerful tools off ered is a revitalization of the legacy DOE software tools used by industry for decades. These have been transformed into a new, free, opensource software tool suite: MEASUR (Manufacturing Energy Assessment Software for Utility Reduction)
Research was undertaken to gain an understanding of the interplay between cyber security professionals and the software tools utilized in performing their jobs. Substantial investments are devoted to purchasing and developing software tools targeting cyber security operations. However, development is largely based on anecdotal knowledge concerning the work processes, cognitive demands, and the needs and requirements of cyber security analysts. The current study first characterized the workflow of a Cyber Security Incidence Response (CSIRT) team, including their use of software tools, and instantiated this workflow within a simulation model. Next, data was collected during cyber security training exercises reflecting the use of software tools. It was discovered that while cyber security professionals rely heavily on specialized software tools, their jobs require that they effectively integrate the use of specialized software tools with the use of general- purpose software tools.
Discrete dynamical systems are used to model various realistic systems in network science, from social unrest in human populations to regulation in biological networks. A common approach is to model the agents of a system as vertices of a graph, and the pairwise interactions between agents as edges. Agents are in one of a finite set of states at each discrete time step and are assigned functions that describe how their states change based on neighborhood relations. Full characterization of state transitions of one system can give insights into fundamental behaviors of other dynamical systems. In this work, we describe a discrete graph dynamical systems (GDSs) application called GDSCalc for computing and characterizing system dynamics. It is an open access system that is used through a web interface. We provide an overview of GDS theory. This theory is the basis of the web application; i.e., an understanding of GDS provides an understanding of the software features, while abstracting away implementation details. We present a set of illustrative examples to demonstrate its use in education and research. Finally, we compare GDSCalc with other discrete dynamical system software tools. Our perspective is that no single software tool will perform all computations that may be required by all users; tools typically have particular features that are more suitable for some tasks. We situate GDSCalc within this space of software tools.
Purpose: Physics second-checks for external beam radiation therapy are performed, in-part, to verify that the machine parameters in the Record-and-Verify (R&V) system that will ultimately be sent to the LINAC exactly match the values initially calculated by the Treatment Planning System (TPS). While performing the second-check, a large portion of the physicists’ time is spent navigating and arranging display windows to locate and compare the relevant numerical values (MLC position, collimator rotation, field size, MU, etc.). Here, we describe the development of a software tool that guides the physicist by aggregating and succinctly displaying machine parameter data relevant to the physics second-check process. Methods: A data retrieval software tool was developed using Python to aggregate data and generate a list of machine parameters that are commonly verified during the physics second-check process. This software tool imported values from (i) the TPS RT Plan DICOM file and (ii) the MOSAIQ (R&V) Structured Query Language (SQL) database. The machine parameters aggregated for this study included: MLC positions, X&Y jaw positions, collimator rotation, gantry rotation, MU, dose rate, wedges and accessories, cumulative dose, energy, machine name, couch angle, and more. Results: A GUI interface was developed to generate a side-by-side display of the aggregated machine parameter values for each field, and presented to the physicist for direct visual comparison. This software tool was tested for 3D conformal, static IMRT, sliding window IMRT, and VMAT treatment plans. Conclusion: This software tool facilitated the data collection process needed in order for the physicist to conduct a second-check, thus yielding an optimized second-check workflow that was both more user friendly and time-efficient. Utilizing this software tool, the physicist was able to spend less time searching through the TPS PDF plan document and the R&V system and focus the second-check efforts on assessing the patient-specific plan-quality.
Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.
Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a powerful surface analysis tool, which can simultaneously provide elemental, isotopic, and molecular information with part per million (ppm) sensitivity. However, each spectrum may be composed of hundreds of ion signals, which makes the spectra data complex. Principal component analysis (PCA) is a multivariate analysis technique that has been widely used to figure out the variances among samples in ToF-SIMS spectra data analysis and is showing great success in the explanation of complex ToF-SIMS spectra. So far, several software tools have been developed for PCA of ToF-SIMS spectra; however, none of them are freely available. Such a situation leads to some difficulties in extending applications of PCA to various research fields. More importantly, it has long been challenging for common researchers to understand PCA plots and extract chemical differences among samples. In this work, we developed a new and flexible software tool (named “advanced spectra pca toolbox”) based on python for PCA of complex ToF-SIMS spectra along with an easy-to-read manual. It can generate data analysis reports automatically to explain chemical differences among samples, allowing less experienced researchers to easily understand tricky PCA results. Moreover, it is expandable and compatible with artificial intelligence/machine learning functions. Pure goethite and different lignin adsorbed goethite samples were used as a model system to demonstrate our new software tool, proving that our software tool can be readily used in complex spectra data processing. Our new software tool is open-source, convenient, flexible, and expandable. We expect this open-source tool will benefit the ToF-SIMS community.
The mission of this CRADA with Agilent was to couple powerful MS platforms (QQQ, IM-QTOF-MS) with Agilent’s novel Ultra-High-Performance Liquid Chromatography (UHPLC) fast metabolomic workflows and perform ABF Machine Learning (ML) to generated datasets. Agilent transferred UHPLC methods to PNNL and LBNL and methods were implemented and demonstrated in both labs, achieving total acquisition times of < 10 min. Metabolites analyzed using Agilent’s shared methods included metabolites from central carbon metabolism, common across hosts, and metabolites unique to engineered strains. Standards were acquired in an UHPLC-Drift Tube Ion Mobility Mass Spectrometer (DTIMS) system for the first time within the context of ABF and methods were optimized based on Agilent’s protocols. Samples from ABF hosts Pseudomonas putida, Aspergillus pseudoterreus, Aspergillus niger and Rhodosporidium toruloides were analyzed using the UHPLC-DTIMS platform for a total of 276 runs. A data analysis workflow compatible with the Experimental Data Depot (EDD) and completely shareable was developed for the acquired UHPLC-DTIMS data. Samples were analyzed using a Data Independent Acquisition Approach (DIA), which for most of the standards provided more transitions therefore increasing detection confidence. Using the data acquired by PNNL, LBNL, and Agilent’s specifications from previous ML projects, SNL applied an ensemble ML strategy to pick the best performing model for automated LC-method selection. Finally, with the contribution of the participant labs and Agilent, SNL developed an Automated Method Selection (AMS) software tool to predict the best liquid chromatography method for analysis of any new molecules of interest. Samples with novel pathways and new metabolite targets of interest are generated at a high pace in the ABF. Therefore, our accomplishment in this CRADA improved the efficiency and accuracy of strain testing by developing and implementing fast analytical methods, robust processing tools, and software for predicting the best methods for UHPLC analysis.
NREL has developed a software tool to enable Renewance to estimate the degradation of batteries from basic information such as the type of battery and the application of that battery during its first life, so that used batteries may be evaluated for potential repurposing at low cost. This software tool utilizes NREL's BLAST-Lite battery degradation modeling code, which was updated with additional models for commercially produced lithium-ion batteries as a part of this CRADA. The software tool enables users to input details such as battery type and application so that lifetime estimates can be made without any programming or expert battery knowledge. The application input loads in saved values for parameters such as cycles per year, depth-of-discharge, and other battery operating parameters from a file defined by Renewance. These parameters may be modified to refine simulations for specific batteries. The software tool also incorporates a degradation model optimization tool, whereby existing battery degradation models may be tuned according to measured battery health. This ensures that new models still predict degradation behaviors expected from a certain battery chemistry, but with the overall degradation rate tuned to a specific battery make and model. The new model can then be saved for estimating the degradation of other similar batteries. An additional task was planned to utilize machine-learning to enable battery health diagnosis from rapid EIS measurements to accelerate the screening of used batteries. This task was not completed due to lack of available data for training a machine-learning model. CRADA benefit to DOE, Participant, and US Taxpayer: Further development of open-source software tool BLAST-Lite for predicting the lifetime of commercially produced Lithium-ion batteries (NREL SWR-22-69).
The LMDT software automates the process of the load composite model data preparation in the format supported by the major power system software vendors (GE and Siemens). Proper representation of the load composite model in power system dynamic analysis is very important. Software tools for power system simulation like GE PSLF and Siemens PSSE already include algorithms for the load composite modeling. However, these tools require that the input information on composite load to be provided in custom formats. Preparation of this data is time consuming and requires multiple manual operations. The LMDT software enables to automate this process. Software is designed to generate composite load model data. It uses the default load composition data, motor information, and bus information as an input. Software processes the input information and produces load composition model. Generated model can be stored in .dyd format supported by GE PSLF package or .dyr format supported by Siemens PSSE package.