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At least 343 records · Page 19

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 OSTI2012

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↗

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 OSTI2015

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

Background: Metagenomics is limited in its ability to link distinct microbial populations to genetic potential due to a current lack of representative isolate genome sequences. Reference-independent approaches, which exploit for example inherent genomic signatures for the clustering of metagenomic fragments (binning), offer the prospect to resolve and reconstruct population-level genomic complements without the need for prior knowledge. Results: We present VizBin, a Java™-based application which offers efficient and intuitive reference-independent visualization of metagenomic datasets from single samples for subsequent human-in-the-loop inspection and binning. The method is based on nonlinear dimension reduction of genomic signatures and exploits the superior pattern recognition capabilities of the human eye-brain system for cluster identification and delineation. We demonstrate the general applicability of VizBin for the analysis of metagenomic sequence data by presenting results from two cellulolytic microbial communities and one human-borne microbial consortium. The superior performance of our application compared to other analogous metagenomic visualization and binning methods is also presented. Conclusions: VizBin can be applied de novo for the visualization and subsequent binning of metagenomic datasets from single samples, and it can be used for the post hoc inspection and refinement of automatically generated bins. Due to its computational efficiency, it can be run on common desktop machines and enables the analysis of complex metagenomic datasets in a matter of minutes. The software implementation is available at https://claczny.github.io/ VizBin under the BSD License (four-clause) and runs under Microsoft Windows™, Apple Mac OS X™ (10.7 to 10.10), and Linux.

97 MATHEMATICS AND COMPUTING↗

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 OSTI2016

CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites

High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. Cis SERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. Cis SERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, Cis SERS utilizes the REBASE enzyme database. Results from Cis SERSenable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. Cis SERS is a java based graphical user interface built around a perl backbone. Several of the applications of Cis SERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool Cis SERSand results from in-silico and corresponding wet-lab analyses demonstrating that Cis SERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.

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 OSTI2016

GeoTess: A generalized Earth model software utility

GeoTess is a model parameterization and software support library that manages the construction, population, storage, and interrogation of data stored in 2D and 3D Earth models. Here, the software is available in Java and C++, with a C interface to the C++ library.

58 GEOSCIENCES↗

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 OSTI2013

Sequential Projection Pursuit Principal Component Analysis – Dealing with Missing Data Associated with New -Omics Technologies

We present a new version of sequential projection pursuit Principal Component Analysis (sppPCA) that has the capability to perform PCA on large multivariate datasets that contain non-random missing values. We demonstrate that sppPCA generates more robust and informative low-dimensional representations of the data than imputation-based approaches and improved downstream statistical analyses, such as clustering or classification. A Java program to run sppPCA is freely available at https://www.biopilot.org/docs/Software/sppPCA.

Webb-Robertson, Bobbie-Jo M.↗

DOE OSTI2012

Summary Report for the SINBAD Search Tool Project

The Shielding Integral Benchmark Archive Database (SINBAD) Search Tool has been developed to serve as an interface with the SINBAD database to facilitate a simple and quick means of searching for information related to experimental benchmark problems. The Search Tool is written in Java and provides a better and efficient way to retrieve information from the SINBAD database. Searches can be performed quickly and easily. With regard to improvements, users are no longer required to know the name of the benchmarks to search the database. Instead, a search can be performed by specifying the experimental facility, constituents of the experimental benchmark, etc. In summary, a new powerful database search tool has been developed for SINBAD.

Cunha Da Silva, Alice↗

DOE OSTI2012

Provenance-Enabling DOE Visualization Applications

VisTrails, Inc.’s goal main charter has been to develop provenance management solutions for software tools. As the use of computation increases, keeping track of computational processes and the data they consume and derive is essential for many applications. Provenance (also referred to as audit trail, lineage, and pedigree) captures information about the steps used to generate a given data product. Such information provides important documentation that is key to preserving the data, to determining the data’s quality and authorship, and to reproducing as well as validating the results. Given the growing complexity of the computational processes and the volume of data they manipulate, manual approaches to maintaining provenance are both tedious and error-prone. At VisTrails, Inc., we have implemented infrastructure that can be used to provenance-enable existing tools. We have developed a series of plugins for specific applications, including ParaView and VisIt, which enable these applications to capture provenance. While developing these plugins, we identified general patterns across different applications, and these were used to inform the design of a general framework: the VisTrails Provenance Software Development Kit (SDK). The SDK encapsulates a set of core functionality including methods for capture, navigation, analysis and re-use of provenance. It allows application or plugin developers to more effectively provide provenance support: they can use the core functionality and write code only to handle application specific components. The SDK includes features that can be used in any application, for example, a refined interface for browsing the intermediate and final results captured. While the application-specific plugins were written in Python, the SDK was written from scratch in C++. This has led not only to substantial gains in performance but also the ability to integrate the SDK with applications written in other languages, including Java. To ensure that the SDK supported all of the functionality in the application-specific plugins, we have rewritten some of the existing plugins using the SDK. The SDK can be downloaded from www.vistrals.com/sdk.html.

97 MATHEMATICS AND COMPUTING↗