Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “pipeline”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19

Integrase-On-Demand-Pipeline Data Set

Files needed to run the Integrase-On-Demand-Pipeline, a program designed to provide users with a list of putative attachment site and integrase pairs for a prokaryotic genome of interest. isles.pkl: Serialized python-object file, containing a dictionary of attachment site sequences and reference genomic island information extracted from the Genomic island database ints.gff: Gene format file containing annotations for all integrases referenced in isles.pkl. The source genome, gene coordinates, integrase name, protein IDs and amino acid sequence included. reps.msh: Binary file containing 1000 128-bit MurmurHash3 hashes for >80,000 genomes

McClain, Hannah Marie [Sandia National Laboratorie↗

Drug Target and Chemotype Identification Pipeline

The TargetID pipeline enables rapid identification and characterization of binding sites in SARS-CoV-2 proteins as well as the core chemical components with which these sites interact.

Sandholtz, SarahH↗

GAPs (Geospatial Analysis Pipelines)

Geospatial Analysis Pipelines (GAPs) is a framework designed to scale single-location geospatial models to a High-Performance Computing (HPC) environment.

Pinchuk, Pavlo (Paul)↗

Machine Learning Automation Pipeline

Machine Learning Automation Pipeline (MLAP) is a package to perform machine learning (ML) analysis in a step by step manner, starting with data extraction until analysis and prediction. The scripts provide the users option to chose an action such as "Extract", "Prep", and "Train" and numerous cases can be launched with just a single command. The inputs for each case are provided using a JSON file. The simulation results of several cases can be assessed using an automated process and analyzed for various metrics pertinent to ML analysis.

Jha, Pankaj↗

Disclosure of the XRD pipeline software

The XRD pipeline software is a program to reduce 2D X-ray diffraction data from area detectors with advanced algorithms on automatic masking and image segmentation, which help characterization of multiple phases recorded in the data and facilitate data analysis.SF-25-114

XU, WENQIAN [Argonne National Laboratory (ANL), Ar↗

PIPES (Pipeline for Integrated Projects in Energy Systems) [SWR-24-89]

The Pipeline for Integrated Projects in Energy Systems (PIPES) is a comprehensive project, data, and workflow management tool designed for integrated modeling teams. PIPES facilitates the management of data requirements, tasks, and progress tracking, serving as a higher-level integration layer that works across various data and modeling software. This tool integrates models, data, and tools to perform large-scale, integrated analysis work at scale. PIPES is designed to streamline integrated modeling projects, enhance collaboration, and ensure the quality and efficiency of data management and workflow processes. https://github.com/nrel-pipes/pipes-api https://github.com/nrel-pipes/pipes-web https://github.com/nrel-pipes/nrel-pipes

Gu, Jianli↗

POWER DATA PIPELINE

SF-25-081 Utility software for creating high-performance data pipelines to extract, load, and transform raw electric power systems measurements. For use with anomaly detection models training workflows. The software supports the project: Adaptive Cybersecurity for DER: A Game-Theoretic and Machine Learning approach for Real-Time Threat Detection and Mitigation

Plathottam, Silby Jose [Argonne National Laborator↗

NLR Data Processing Pipeline for MADIS [SWR-26-050]

The NLR Data Processing Pipeline for MADIS software package is for downloading, processing, and performing QA/QC on MADIS data. Designed to handle the following steps: 1) Download all MADIS data as compressed netcdf files for a given time period. 2) Unpack netcdf files into timeseries csvs for each coordinate within the given bounding box. 3) Process the csvs to filter according to quality control checks and convert variables to correct units. 4) Write processed csvs to a single nc file.

Benton, Brandon [National Laboratory of the Rockie↗

HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly

Abstract Background Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large sequencing and assembly initiatives for generation of de novo assemblies in non-model organisms. Though adapter contamination filtering is routine in traditional short-read analysis pipelines, it has not been widely adopted for HiFi workflows. Results Analysis of 55 publicly available HiFi datasets revealed that a read-sanitation step to remove sequence artifacts derived from PacBio library preparation from read pools is necessary as adapter sequences can be erroneously integrated into assemblies. Conclusions Here we describe the nature of adapter contaminated reads, their consequences in assembly, and present HiFiAdapterFilt, a simple and memory efficient solution for removing adapter contaminated reads prior to assembly.

59 BASIC BIOLOGICAL SCIENCES↗

COMPILE: a GWAS computational pipeline for gene discovery in complex genomes

Abstract Background Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity. Results COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer ( Ostrinia nubilalis ). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity. Conclusions The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A high solids field-to-fuel research pipeline to identify interactions between feedstocks and biofuel production

Abstract Background Environmental factors, such as weather extremes, have the potential to cause adverse effects on plant biomass quality and quantity. Beyond adversely affecting feedstock yield and composition, which have been extensively studied, environmental factors can have detrimental effects on saccharification and fermentation processes in biofuel production. Only a few studies have evaluated the effect of these factors on biomass deconstruction into biofuel and resulting fuel yields. This field-to-fuel evaluation of various feedstocks requires rigorous coordination of pretreatment, enzymatic hydrolysis, and fermentation experiments. A large number of biomass samples, often in limited quantity, are needed to thoroughly understand the effect of environmental conditions on biofuel production. This requires greater processing and analytical throughput of industrially relevant, high solids loading hydrolysates for fermentation, and led to the need for a laboratory-scale high solids experimentation platform. Results A field-to-fuel platform was developed to provide sufficient volumes of high solids loading enzymatic hydrolysate for fermentation. AFEX pretreatment was conducted in custom pretreatment reactors, followed by high solids enzymatic hydrolysis. To accommodate enzymatic hydrolysis of multiple samples, roller bottles were used to overcome the bottlenecks of mixing and reduced sugar yields at high solids loading, while allowing greater sample throughput than possible in bioreactors. The roller bottle method provided 42–47% greater liquefaction compared to the batch shake flask method for the same solids loading. In fermentation experiments, hydrolysates from roller bottles were fermented more rapidly, with greater xylose consumption, but lower final ethanol yields and CO 2 production than hydrolysates generated with shake flasks. The entire platform was tested and was able to replicate patterns of fermentation inhibition previously observed for experiments conducted in larger-scale reactors and bioreactors, showing divergent fermentation patterns for drought and normal year switchgrass hydrolysates. Conclusion A pipeline of small-scale AFEX pretreatment and roller bottle enzymatic hydrolysis was able to provide adequate quantities of hydrolysate for respirometer fermentation experiments and was able to overcome hydrolysis bottlenecks at high solids loading by obtaining greater liquefaction compared to batch shake flask hydrolysis. Thus, the roller bottle method can be effectively utilized to compare divergent feedstocks and diverse process conditions.

09 BIOMASS FUELS↗

MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations

Abstract Background Microbes and their viruses are hidden engines driving Earth’s ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed. Results Here, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro - and microdiversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity ( π and θ ), and selective pressures (pN/pS and Tajima’s D ) within and fixation indices ( F ST ) between populations. MetaPop will also identify genes with distinct codon usage. Following rigorous validation, we applied MetaPop to the gut viromes of autistic children that underwent fecal microbiota transfers and their neurotypical peers. The macrodiversity results confirmed our prior findings for viral populations (microbial shotgun metagenomes were not available) that diversity did not significantly differ between autistic and neurotypical children. However, by also quantifying microdiversity, MetaPop revealed lower average viral nucleotide diversity ( π ) in autistic children. Analysis of the percentage of genomes detected under positive selection was also lower among autistic children, suggesting that higher viral π in neurotypical children may be beneficial because it allows populations to better “bet hedge” in changing environments. Further, comparisons of microdiversity pre- and post-FMT in autistic children revealed that the delivery FMT method (oral versus rectal) may influence viral activity and engraftment of microdiverse viral populations, with children who received their FMT rectally having higher microdiversity post-FMT. Overall, these results show that analyses at the macro level alone can miss important biological differences. Conclusions These findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tool package to explore the dual impact of macro - and microdiversity across microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗

CO2 pipeline data catalog

This "Data Catalog" is an excel spreadsheet of collected and catalogued spatial and non-spatial public datasets in relevance to and support of CO2 transport (pipelines) infrastructure development and risk modeling. Includes data associated with CO2 sources, sinks, and transportation.

CO2↗

Reduce, reuse, reinterpret: An end-to-end pipeline for recycling particle physics results

Searches for new physics at the Large Hadron Collider have constrained many models of physics beyond the Standard Model. Many searches also provide resources that allow them to be reinterpreted in the context of other models. We describe a reinterpretation pipeline that examines previously untested models of new physics using supplementary information from ATLAS Supersymmetry (SUSY) searches in a way that provides accurate constraints even for models that differ meaningfully from the benchmark models of the original analysis. The public analysis information, such as public analysis routines and serialized probability models, is combined with common event generation and simulation toolkits MADGRAPH, PYTHIA8, and DELPHES into workflows steered by TOML configuration files, and bundled into the mapyde Python package. The use of mapyde is demonstrated by constraining previously untested SUSY models with compressed sleptons and electroweakinos using ATLAS results.

Stark, Giordon↗

Partnership and Pipeline Office Overview [Slides]

Partnerships ensure a strong Laboratory and support our missions. Partnerships are critical to our success as a Laboratory: community relations, colleges and universities and technical communities, regional and national economic development through industrial partners, DOE Laboratories, and other federal agencies. The Laboratory has many tools to build and enhance partnerships. The Community Programs Office in our Northern New Mexico Region has K-12 educational programs, supports teacher professional development and retention in regional elementary, middle and high schools, and provides community college engagement. The Partnerships and Pipeline Office works with the National Security Education Center (NSEC) which has broad university engagement including New Mexico universities. The Feynman Center for Innovation is involved in 'tech transfer' to innovation asset stewardship. The External Assignments Office shares LANL's technical expertise. The Student and Postdoc Program Offices build our workforce of the future.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

E-PiPEline: Quick to Market Emulated-PPE using Commonly Available Materials

The Center for Disease Control has recommended the public to wear cloth face coverings in public settings that reduce potential exposure to COVID-19 where other social distancing measures are difficult to maintain (e.g., grocery stores and pharmacies) especially in areas of significant community based transmission. These face coverings and other Emulated-Personal Protective Equipment (EPPE) can be made by using Commonly Available Materials (CAMs). As part of the Sandia COVID-19 LDRD effort (funded under the Materials Science Investment Area), the Sandia E-PiPEline task evaluated E-PPE design options for face coverings and face shields considering their effectiveness, durability, build difficulty, build cost, and comfort. Observations from this investigation are presented here to provide guidelines for home construction of E-PPE. This executive summary includes a brief roadmap of the analysis methodology, two one-page handouts geared to be distributed to the public at large (one for E-PPE face coverings and one for E-PPE face shields), and additional observations regarding the potential solutions for E-PPE face coverings and face shields included to further support the one-page handouts.

60 APPLIED LIFE SCIENCES↗

E-PiPEline: Face Shields and Face Coverings Using Commonly Available Materials

The Center for Disease Control has recommended that the public should wear cloth face coverings in public settings . Face coverings and face shields can be made by using Commonly Available Materials (CAMs). As part of the Sandia COVID - 19 LDRD effort (funded under the Materials Science Investment Area), the Sandia E - PiPEline task evaluated design options for face coverings and face shields considering their effectiveness, durability, build difficulty, build cost, and comfort. Observations from this investigation are presented here to provide guidelines for home construction of face coverings and face shields

54 ENVIRONMENTAL SCIENCES↗