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All sources NASA NTRS DOE OSTI

DOE OSTI2023

Seismic Response Processing Module

The seismic response processing module is a Java based library that provides support for removing instrument response signals from seismic recordings. The response module provides support for EvalResp, PZF, PAZ, FAP, PAZFIR, PAZFAP, FIRFAP, and CSS response types and parallel processing support for transfer operations. Additionally, the response module uses the JSR-363 units of measurement specification to allow for transfer to and from a wide range of units types to represent the time-series.

Dodge, Douglas↗

DOE OSTI2023

ML for microbiomes

The software provides machine learning analysis and visualization to detect patterns in microbiome data, including topic modeling, probabilistic graphical modeling, conventional machine learning methods, and deep learning. The software is written in python and R, it uses some python and R libraries as well as big open-source libraries like sklearn, networkX, pytorch (python), pgmpy (python), and bnlearn (R). It also has a script to use for MALLET and DTM (open-source packages for topic modeling, written in Java).

Kim, Anastasiia↗

DOE OSTI2023

RadSim: Math, Utility & RTK

This package includes three parts, (1) gov.llnl.math, (2)gov.llnl.utility and (3)gov.llnl.rtk, which are utilized in the development of Radiation Detector Simulator (RadSim) project. RadSim is being developed to provide the capability to: (1) simulate radiation source emissions, (2) interpolate results from radiation transport tools into a common format to prepare incident flux, and (3) model radiation detector response to rapidly produce synthetic radiation measurement templates. RadSim is targeted for open-source release, which will enable researchers and industry partners to model gamma-ray detectors response to simulated flux from the transport tool of their choice. The techniques and implementation will be entirely transparent, which will allow for improvements and boutique modifications by future researchers beyond the lifespan of this specific project. The first tool of the package, gov.llnl.math, includes classes and functions to define and perform basic math operations. Some of the example features available in the package include defining statistical distributions and performing algebra and matrix operations, all of which are already accessible on publicly available software packages such as MATLAB and ROOT. The second package gov.llnl.utility includes tools commonly used to enable optimization and readability of various data structures such as Java lists and external xml files. Lastly, the gov.llnl.rtk package includes classes and functions to implement methods commonly used in radiation physics, such as data structures to represent and characterize photon spectra and tools to apply well-defined and published methods to calibrate a given spectra.

Cheung, Hoi Sing↗

DOE OSTI2021

Replete v. 2.0

SAND2021-15136 O Replete is a Java library that contains several common and useful utilities in a variety of categories including expression parsing, multi-threading, data pipelines, user interface, database connectivity, Unix shell emulation, information generalization, and Maven standardization. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

McClain, Jonathan↗

DOE OSTI2025

TimeStitch-Memento-Aggregator

Memento Aggregator is a Java service that federates web archives worldwide: given an Original-URL and optional datetime, it discovers mementos and exposes standards-compliant Memento TimeGate and TimeMap APIs.

Balakireva, Lyudmila↗

DOE OSTI2026

ROSE

Developed at Lawrence Livermore National Laboratory (LLNL), ROSE is an open source compiler infrastructure to build source-to-source program transformation and analysis tools for large-scale C (C89 to C23), C++ (C++98 to C++23), UPC, Fortran (Fortran4, 66, 77, 95, 2003), OpenMP, Java, Python, and Binary applications. ROSE users range from experienced compiler researchers to library and tool developers who may have minimal compiler experience. ROSE is particularly well suited for building custom tools for static analysis, program optimization, arbitrary program transformation, domain-specific optimizations, complex loop optimizations, performance analysis, and cyber-security. ROSE is: A library (and set of associated tools) to quickly and easily apply compiler techniques to one's code in order to improve application performance and developer productivity. A research and development compiler infrastructure for for writing custom source-to-source translators to perform source code transformations, analysis, and optimizations. Is

Pinnow, NathanT [Lawrence Livermore National Labor↗

DOE OSTI2021

Equatorial waves triggering extreme rainfall and floods in southwest Sulawesi, Indonesia

On the basis of detailed analysis of a case study and long-term climatology, it is shown that equatorial waves and their interactions serve as precursors for extreme rain and flood events in the central Maritime Continent region of southwest Sulawesi, Indonesia. Meteorological conditions on January 22, 2019, leading to heavy rainfall and devastating flooding in this area were studied. It is shown that a convectively coupled Kelvin wave (CCKW) and a convectively coupled Rossby wave (CCERW) embedded within the larger-scale envelope of the Madden-Julian Oscillation (MJO) enhanced convective phase, contributed to the onset of a mesoscale convective system which developed over the Java Sea. Low-Level convergence from the CCKW forced mesoscale convective organization and orographic ascent of moist air over the slopes of southwest Sulawesi. Climatological analysis shows that 92 % of December-January-February floods and 76% of extreme rain events in this region were immediately preceded by positive low-level westerly wind anomalies. It is estimated that both CCKWs and CCERWs propagating over Sulawesi double the chance of floods and extreme rain event development, which the probability of such hazardous events occurring during their combined activity is eight times greater than on a random day. While the MJO is a key component shaping tropical atmospheric variability, it is shown that its usefulness as a single factor for extreme weather-driven hazard prediction is limited.

Latos, Beata↗

DOE OSTI2019

Bioinformatics Resource Manager: A systems biology web tool for microRNA and omics data integration

Background: The Bioinformatics Resource Manager (BRM) is a web-based tool developed to facilitate identifier conversion and data integration for Homo sapiens (human), Mus musculus (mouse), Rattus norvegicus (rat), Danio rerio (zebrafish), and Macaca mulatta (macaque), as well as perform orthologous conversions among the supported species. In addition to providing a robust means of identifier conversion, BRM also incorporates a suite of miRNA-target databases upon which to query target genes or to perform reverse target lookups using gene identifiers. Results: BRM has the capability to perform cross-species identifier lookups across common identifier types, directly integrate datasets across platform or species by performing identifier retrievals in the background, and retrieve miRNA targets from multiple databases simultaneously and integrate the resulting gene targets with experimental mRNA data. Here we use workflows provided in BRM to integrate RNAseq data across species to identify common biomarkers of exposure after treatment of human lung cells and zebrafish to benzo[a]pyrene (BAP). We further use the miRNA Target workflow to experimentally determine the role of miRNAs as regulators of BAP toxicity and identify the predicted functional consequences of miRNA-target regulation in our system. The output from BRM can easily and directly be uploaded to freely available visualization tools for further analysis. From these examples, we were able to identify an important role for several miRNAs as potential regulators of BAP toxicity in human lung cells associated with cell migration, cell communication, cell junction assembly and regulation of cell death. Conclusions: Overall, BRM provides bioinformatics tools to assist biologists having minimal programming skills with analysis and integration of high-content omics’ data from various transcriptomic and proteomic platforms. BRM workflows were developed in Java and other open-source technologies and are served publicly using Apache Tomcat at https://cbb.pnnl.gov/brm/.

bioinformatics, MicroRNA, systems biology, Genomic↗

DOE OSTI2020

BinaryCIF and CIFTools—Lightweight, efficient and extensible macromolecular data management

3D macromolecular structural data is growing ever more complex and plentiful in the wake of substantive advances in experimental and computational structure determination methods including macromolecular crystallography, cryo-electron microscopy, and integrative methods. Efficient means of working with 3D macromolecular structural data for archiving, analyses, and visualization are central to facilitating interoperability and reusability in compliance with the FAIR Principles. We address two challenges posed by growth in data size and complexity. First, data size is reduced by bespoke compression techniques. Second, complexity is managed through improved software tooling and fully leveraging available data dictionary schemas. To this end, we introduce BinaryCIF, a serialization of Crystallographic Information File (CIF) format files that maintains full compatibility to related data schemas, such as PDBx/mmCIF, while reducing file sizes by more than a factor of two versus gzip compressed CIF files. Moreover, for the largest structures, BinaryCIF provides even better compression—factor ten and four versus CIF files and gzipped CIF files, respectively. Herein, we describe CIFTools, a set of libraries in Java and TypeScript for generic and typed handling of CIF and BinaryCIF files. Together, BinaryCIF and CIFTools enable lightweight, efficient, and extensible handling of 3D macromolecular structural data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Enabling AI in synthetic biology through Construction File specification

The Construction File (CF) specification establishes a standardized interface for molecular biology operations, laying a foundation for automation and enhanced efficiency in experiment design. It is implemented across three distinct software projects: PyDNA_CF_Simulator, a Python project featuring a ChatGPT plugin for interactive parsing and simulating experiments; ConstructionFileSimulator, a field-tested Java project that showcases 'Experiment' objects expressed as flat files; and C6-Tools, a JavaScript project integrated with Google Sheets via Apps Script, providing a user-friendly interface for authoring and simulation of CF. The CF specification not only standardizes and modularizes molecular biology operations but also promotes collaboration, automation, and reuse, significantly reducing potential errors. The potential integration of CF with artificial intelligence, particularly GPT-4, suggests innovative automation strategies for synthetic biology. While challenges such as token limits, data storage, and biosecurity remain, proposed solutions promise a way forward in harnessing AI for experiment design. This shift from human-driven design to AI-assisted workflows, steered by high-level objectives, charts a potential future path in synthetic biology, envisioning an environment where complexities are managed more effectively.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

CO2-SCREEN

CO2 Storage prospeCtive Resource Estimation Excel aNalysis (CO2-SCREEN) is a tool which was developed by the Department of Energy’s National Energy Technology Laboratory (DOE-NETL) to screen saline formations for prospective CO2 storage resources. CO2-SCREEN applies U.S. DOE methods and equations for estimating prospective CO2 storage resources for saline formations. This provides a dependable method for calculating prospective CO2 storage resources which allows for consistent comparison of results between different research efforts. CO2-SCREEN latest version (v5.0) is a python application that utilizes a Java front end user interface. The 3.0 version consists of an Excel spreadsheet containing geologic inputs and outputs, linked to a GoldSim Player model that calculates prospective CO2 storage resources via Monte Carlo simulation. https://www.youtube.com/watch?v=lhakk-HYfOI

CO2 Storage Resource,Prospective Storage,Screening↗

DOE OSTI2018

System Advisor Model (SAM) General Description (Version 2017.9.5)

This document describes the capabilities of the System Advisor Model (SAM) developed and distributed by the U.S. Department of Energy's National Renewable Energy Laboratory. The document is for potential users and others wanting to learn about the model's capabilities. SAM is a techno-economic computer model that calculates performance and financial metrics of renewable energy projects. Project developers, policy makers, equipment manufacturers, and researchers use graphs and tables of SAM results in the process of evaluating financial, technology, and incentive options for renewable energy projects. SAM simulates the performance of photovoltaic, concentrating solar power, solar water heating, wind, geothermal, biomass, and conventional power systems. The financial models are for projects that either buy and sell electricity at retail rates (residential and commercial) or sell electricity at a price determined in a power purchase agreement (PPA). SAM's simulation tools facilitate parametric and sensitivity analyses, Monte Carlo simulation and weather variability (P50/P90) studies. SAM can also read input variables from Microsoft Excel worksheets. For software developers, the SAM software development kit (SDK) makes it possible to use SAM simulation modules in their applications written in C/C plus plus, C sharp, Java, Python, MATLAB, and other languages. NREL provides both SAM and the SDK as free downloads at https://sam.nrel.gov. SAM is an open source project, so its source code is available to the public. Researchers can study the code to understand the model algorithms, and software programmers can contribute their own models and enhancements to the project. Technical support and more information about the software are available on the website.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Distributed Photovoltaic Economic Impact Analysis in Indonesia

Like other countries in the region, the Government of Indonesia aims to increase its use renewable energy in the near term from various technologies, including grid-connected distributed photovoltaics (DPV). While little DPV has been installed to date, the policy landscape has been shifting over the past few years with recent pronouncements from the state-run utility Perusahaan Listrik Negara (PLN) and the Ministry of Energy and Mines (MEMR) that have begun to provide a more supportive policy framework for the deployment of DPV. Nonetheless, many questions remain as to how DPV impacts customers, the utility, and the economy as a whole. This report presents a holistic view of DPV economic impacts in the Java-Bali region of Indonesia by assessing customer economic impacts, utility revenue impacts, and jobs and economic development impacts.

14 SOLAR ENERGY↗

DOE OSTI2020

Language Independent Static Analysis (LISA)

Software is becoming increasingly important in nearly every aspect of global society and therefore in nearly every aspect of national security as well. While there have been major advancements in recent years in formally proving properties of program source code during development, such approaches are still in the minority among development teams, and the vast majority of code in this software explosion is produced without such properties. In these cases, the source code must be analyzed in order to establish whether the properties of interest hold. Because of the volume of software being produced, automated approaches to software analysis are necessary to meet the need. However, this software boom is not occurring in just one language. There are a wide range of languages of interest in national security spaces, including well-known languages such as C, C++, Python, Java, Javascript, and many more. But recent years have produced a wide range of new languages, including Nim, (2008), Go (2009), Rust (2010), Dart (2011), Kotlin (2011), Elixir (2011), Red (2011), Julia (2012), Typescript (2012), Swift (2014), Hack (2014), Crystal (2014), Ballerina (2017) and more. Historically, automated software analyses are implemented as tools that intermingle both the analysis question at hand with target language dependencies throughout their code, making re-use of components for different analysis questions or different target languages impractical. This project seeks to explore how mission-relevant, static software analyses can be designed and constructed in a language-independent fashion, dramatically increasing the reusability of software analysis investments.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Expanded Capabilities and Opportunities for Virtual Beamline Code

In the 25 years since LLNL broke ground on the National Ignition Facility (NIF) - a cornerstone of the National Nuclear Security Administration’s Stockpile Stewardship Program - the NIF and Photon Science (NIF&PS) Directorate has steadily pushed the boundaries of laser physics, nonlinear optics, and photonics in service of inertial confinement fusion experiments, and advanced photon sources development. Beyond the 192 beamlines of the primary laser facility with its world-record energy and fusion yields, NIF&PS capabilities have expanded to include chirped-pulse amplification, kilojoule petawatt-class short-pulse systems to generate hard x-ray radiographic probes, high-average power lasers as secondary sources for generation or wake field particle acceleration along directed energy applications, and other scientific pursuits. The Computing Directorate partners with NIF&PS on numerous projects and technologies from diagnostic measurements and high performance control systems to data analysis, information technology infrastructure, and scientific simulation code development. “This strong collaboration enables cutting-edge science, particularly with regard to physics-based modeling and simulation,” says physicist Jean-Michel Di Nicola. One crucial capability for NIF&PS is the Virtual Beamline (VBL) laser simulation code. It can model all the major laser physics and technology involved in the design optimization, commissioning, and operations of advanced laser architectures from tabletop to NIF-scale. VBL provides researchers with high-fidelity models and high-resolution calculations of laser performance predictions—including for the entire NIF laser system, the Advanced Radiographic Capability, parts of the High Repetition-Rate Advanced Petawatt Laser System laser delivered to the Czech Republic, and the Optical Science Laser. After more than two decades of experimentally verified physics and computing enhancements, this unique workhorse code is wrapping up another major milestone: migration from Java to C++ with a flurry of user interface and optimization features, as well as laser physics and high-resolution enhancements thanks to parallel execution on Livermore Computing platforms.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

November 2021 Operational Highlights

Completed: 1. the initial tests of document workflows for Titan on the Red, which included standing up a software encryption capability to test data ingestion; 2. a software encryption capability in order to ingest the first data source by the end of the month; 3. a stand-alone computer for classified ontology data entry. Titan on the Red is an artificial intelligence/machine learning system to make digitizing, cataloging, and searching NSRC collections easier and more efficient. Created Online Vault backups, with one copy stored at LANL and one shipped to Lawrence Livermore National Laboratory. The Online Vault is a classified, searchable library of LANL’s nuclear weapons design and test history. Imported new Laboratory Directed Research and Development (LDRD) documents based on revised access categories. Bulk ingested nearly 10,000 documents via java-based PowerLoader. This application ingests metadata and content into the Online Vault to meet the requirements for the NSRC collections. Rehoused 300 linear feet of weapons physics documents in archival, acid-free storage folders and boxes.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2022

CO 2 Storage prospeCtive Resource Estimation Excel aNalysis (CO 2 -SCREEN) User’s Manual: Python_V4.1

This user’s manual guides the use of the National Energy Technology Laboratory’s (NETL) CO 2 Storage prospeCtive Resource Estimation Excel aNalysis (CO 2 -SCREEN) tool, which was developed to aid users in screening geologic formations for prospective CO 2 storage resources. This manual is specific to the CO 2 -SCREEN 4.1 version which is based in Python. The 4.1 version of CO 2 -SCREEN adds in newly updated storage efficiency factors for saline formations. CO 2 -SCREEN applies U.S. Department of Energy (DOE) methods and equations for estimating prospective CO 2 storage resources for saline formations, shale formations, and residual oil zones (ROZ). CO 2 -SCREEN was developed to be substantive and user-friendly and provide a consistent method for calculating prospective CO 2 storage resources. CO 2 -SCREEN uses a Java- based graphical user interface (GUI) for data inputs and uses Python to calculate prospective CO 2 storage resources.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Creation of the VADER Code in SCALE [Slides]

This presentation details the creation of Validation Analysis Data Evaluation Resource (VADER) code in SCALE. This lecture highlights the USLSTATS program written in JAVA and its history. Additionally, it covers the integration of VADER with SCALE along with features and background information.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗