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At least 1,315 records · Page 73

HERON

HERON is a modeling toolset and plugin for RAVEN to accelerate stochastic technoeconomic assessment of the economic viability of various grid-energy system configurations, especially with application to electrical grids and integrated energy systems (IES). The frameworks enabling this toolset are INL's RAVEN and its TEAL plugin. The toolset includes automated RAVEN workflow generation tools for performing stochastic analysis and optimization driven by technoeconomic factors. The workflows generated employ RAVEN for parametric or optimizing study of grid component characteristics, and again for stochastic sampling of regulated and deregulated markets, load, and weather histories. The toolset further provides methods for economically-optimal dispatch of system components given the stochastic samples of market, load, and weather histories. The toolset allows assembling of existing and new models through the RAVEN interface to the Modelica process modeling language.

Talbot, PaulW↗

Scoreboard

Emerging HPC machines have given rise to enhanced compute power that far outstrips the machine's ability to save large scale results for post-processing. To combat this, in situ data analysis techniques are slowly being adopted. With in situ data management favoring workflows composed of multiple simulations and analyses connected in transit on heterogeneous machines, scientists and engineers need a tool that enables them to create data extracts, visualizations, and interactively monitor and steer their simulations. Scoreboard Phase II is a next generation analysis software that supports composite in transit workflows on heterogeneous architectures and restores interactivity to in situ data analysis through simulation monitoring and computational steering. Scoreboard provides a simulation dashboard with graphs of metrics over time, controls for setting custom simulation steering parameters, controls for managing the set of data extracts being produced in the simulation, as well as the ability to explore data extracts, all from a web browser. Realizing the vision outlined in this project required research into making a system that integrates end to end from simulations all the way to the user. In situ tools generally suffer from complexity and excessive software dependencies. Scoreboard, by contrast, is easy to build and integrate into simulation codes and it provides first class FORTRAN support. The Scoreboard library is capable of in situ and in transit data analysis that can produce data extracts commonly needed for Computational Fluid Dynamics (CFD) analysis. Simulations can transparently stage data in transit to a Scoreboard Endpoint program, which can accept their data and produce the requested data extracts. This lets simulations return to their work while the Endpoint works on the analysis. Efficiently staging the data at scale was a topic of this research. Scoreboard provides the means to let the user manage data extracts and monitor/steer many simulations from a web browser. This area of the research focused on discovery of in transit network components to expose and control their steering parameters within an interactive browser-based user interface that includes: system topology, gathered metrics, notifications, dynamically-generated steering controls, and exploration of visualization data products.

Whitlock, BradJoseph [Intelligent Light] (00000001↗

Mesoscale Science Data Analytics

This is software that will be used to do data analytics in experimental workflows for x-ray mesoscale science. This tool set will provide a mechanism for supporting experiments in many ways, from collecting calibration information and raw data, to managing and viewing data to extracting crystallographic and physical parameters. It will eventually include development of a fully automated workflow that will include statistical information and prediction capabilities to support the scientists in decision-making and replanning their experiments when necessary.

Sweeney, Christine↗

Auto_PDI

Protein-DNA Interaction Workflow (PDI Workflow), a pipeline that focuses on generating high-quality docking and molecular dynamics simulations for Protein-DNA complexes. This allows us to take DNA sequences with unknown tertiary structures, accurately predict their structure, dock them with the desired target protein, and then simulate their interactions using molecular dynamics simulations

Kumar, Neeraj↗

pnnl/PTMPSI

PTM-Psi is a Python 3 package that combines several capabilities to streamline the workflow to interrogate the impact of PTMs on proteins using well-established software packages. The workflow of the PTM-Psi software package includes input files and launch instances from standard packages such as AlphaFold, NWChem, GROMACS, and the Autodock Suite

Mejia-Rodriguez, Daniel↗

LLNL Automized Surface Titration Model

The LLNL Automized Surface Titration Model (L-ASTM) is a community data-driven surface complexation modeling workflow for simulating potentiometric titration of mineral surfaces. The model accepts raw experimental potentiometric titration data formatted in a findable, accessible, interoperable, and reusable (FAIR) structure. The workflow was coded in Python and coupled to PHREEQC for surface complexation modeling and PEST for data fitting and parameter estimation.

Solchan, Han↗

Clearance Tracker

The manual process of managing security clearance was cumbersome and inefficient, involving the emailing of a fillable PDF from person to person. There was no visibility into the progress of a clearance submission. Clearance Tracker provides an automated workflow with data validation and notifications to manage the clearance process. The automated workflow routes notifications to individuals when their input is required. All participants can track the progress of clearance requests.

Short, RickyD↗

Synthetic Biology PacBio/JAWS QC Analysis (PBJ) v3.0

This software was designed as a sequence validation tool for the assembly of synthetic constructs. It analyzes FASTQ files against a list of reference sequences, combining the results from eight sequencing libraries to generate a summary, and the files needed to view the results in the Integrative Genomics Viewer (IGV) application for manual verification. This was developed for FASTQ files generated by PacBio sequencing, but could be used on any FASTQ files that do not have paired end reads. It can be used to analyze one - eight libraries at a time, and assumes that each construct sequence in the reference will be in each pool, however, this is not a requirement. This is used to identify which libraries of pooled sequences contains a perfect match, or fixable match to the reference file. This pipeline uses many freely available open source libraries, the value added is that in our application the steps of the pipeline are defined in Workflow Description Language (WDL) and run through the Cromwell workflow engine in Docker containers, for easy distribution and set up, as well as the user friendly html summary that is generated.

Simirenko, Lisa↗

SynBio QC Dual Barcode QC (DBC) v1.0

This software was designed as a sequence validation tool for the assembly of synthetic constructs, where the constructs have a high degree of similarity and thus are barcoded prior to the sequencing library prep. It demultiplexes each FASTQ file for each barcode, then analyzes the resulting FASTQ files against a list of reference sequences for that barcode/library, combining the results from eight sequencing libraries to generate a summary, and the files needed to view the results in the Integrative Genomics Viewer (IGV) application for manual verification. This was developed for FASTQ files generated by PacBio sequencing, but could be used on any FASTQ files that do not have paired end reads. It can be used to analyze one - eight libraries at a time. Each construct is independently analyzed with only the sequences with the same barcode, in the same pooled library. Then the results are combined into a user friendly summary. This is used to identify which libraries of pooled sequences contains a perfect match, or fixable match to the reference file. This pipeline uses many freely available open source libraries, the value added is that in our application the steps of the pipeline are defined in Workflow Description Language (WDL) and run through the Cromwell workflow engine in Docker containers, for easy distribution and set up, as well as the user friendly html summary that is generated.

Simirenko, Lisa↗

Tardigrade-examples V0.1.0

Tardigrade-examples is a repository of computational workflows that exercise the Tardigrade software package. The Tardigrade software package is an implementation of Eringen’s micromorphic continuum theory with capabilities to support multiscale material modeling. These capabilities include homogenization through the Micromorphic Filter, calibration of micromorphic material models, and macroscale simulation in Tardigrade-MOOSE. This repository investigates continuum upscaling of various direct numerical simulations (DNS) conducted in Abaqus finite element (FE), Ratel FE, and GEOS material point method (MPM) software. Verification of the upscaling workflow is first investigated by considering DNS of trivial stress states for homogeneous materials, results of which indicate that classical continuum behavior is recovered as expected. DNS of heterogeneous materials are then considered.

Allard, Thomas↗

LowFive v1.0

LowFive is a new data transport layer based on the HDF5 data model, for in situ workflows. Executables using LowFive can communicate in situ (using in-memory data and MPI message passing), reading and writing traditional HDF5 files to physical storage, and combining the two modes. Minimal and often no source-code modification is needed for programs that already use HDF5. LowFive maintains deep copies or shallow references of datasets, configurable by the user. More than one task can produce (write) data, and more than one task can consume (read) data, accommodating fan-in and fan-out in the workflow task graph. LowFive supports data redistribution from n producer processes to m consumer processes.

Morozov, Dmitriy↗

SynBio QC-Library QC (LibQC) v2.0.0

This software is a pipeline used to identify the distribution of user-specified sequences in oligo pools that have been sequenced on the MiSeq platform for quality control purposes. The software counts instances of user-specified sequences (inserts or spacers) identified in sequencing data, returning the distribution of sequences in each pool and the length distribution of all the sequences. Among other types similar types of projects, this can be used to assess the quality of a guideRNA library once it has been inserted into the vector of choice to ensure that there is an even distribution of all the individual protospacers in the pool. This pipeline uses many freely available open source libraries, the value added is that in our application the steps of the pipeline are defined in Workflow Description Language (WDL) and run through the Cromwell workflow engine in Docker containers, for easy distribution and set up.

Simirenko, Lisa↗

IMG Annotation Pipeline (IMGAP) v5.1.13

The IMG Annotation Pipeline is a collection of Bash and Python scripts to control a workflow for structural and functional annotation of prokaryotic genomes, metagenomes, and metatranscriptomes. The bash scripts in general control the overall workflow and are wrappers around 3rd party executables (not included in repo) that predict features or functions. Whereas the Python scripts do post-processing of raw output in terms of filtering or format transformation and in some cases contain some logic for picking the correct predictions or resolving overlaps. The pipeline is tailored to produce results required by IMG (https://img.jgi.doe.gov/) and is executed on every dataset submitted to IMG via https://img.jgi.doe.gov/submit. These consist of internal genomes, metagenomes and metatranscriptomes sequenced and assembled at the JGI, as well as datasets submitted by external users (non-lab/JGI affiliates).

Huntemann, Marcel↗

Deeplynx Airflow Provider Package

The DeepLynx Airflow Provider Package is a python package used to interact with the data warehouse DeepLynx when using the workflow orchestration tool Apache Airflow. This python package is packaged together using the airflow package standard so that it can be easily installed and used in any Apache Airflow environment. This package is meant to encapsulate the DeepLynx API for use in Airflow so that any interactions with DeepLynx that a user may want to use in their Airflow workflow can be easily accomplished using this provider package. This allows us to develop, implement, and test our DeepLynx-Airflow interactions in one provider package repository, and then easily install and use this package in any airflow instance. This DeepLynx Airflow Provider Package will be used extensively by the DeepLynx DAG repository.

Cavaluzzi, JackM↗

AiiDA-INQ plugin

The AiiDA-INQ plugin will allow the INQ code developed at the lab to utilize the AiiDA workflow manager which enables high-throughput workflows. This includes provenance tracking, restart capabilities, job calculators, and other capabilities

Keilbart, NathanD↗

test-grid-buildouts [SWR-23-112]

Test-grid-buildouts is a set of notebooks for creating buildouts of synthetic transmission grids with various levels of renewable energy. Workflows can be used to augment various test grid with varying levels of wind/solar generation. Aggregated renewable energy time series (actuals and scenarios) at grid buses can then be used for various transmission grid operation problems. Highly customizable workflow consists of parsing of synthetic grid files, setting up SAM & reV simulations, application of exclusion masks, creating of custom renewable generators on the grid, aggregating of power time series, and writing of modified grid description files.

Satkauskas, Ignas↗

ESnet-JLab FPGA Accelerated Transport (data plane) [EJFAT (udplb)] v1.0

The ESnet-JLab FPGA Accelerated Transport system is a solution for streaming high-speed scientific measurement data from Data Acquisition Systems (DAQs) to high-performance computing facilties. It is generally compatible with many science workflows, and makes no assumptions about the specifics of any particular experiment. This program (udplb) implements the data plane portion of the EJFAT system. It is an FPGA design that rewrites and forwards data packets from a UDP-based scientific workflow to high-performance compute nodes. It depends on another program (udplbd, disclosed separately) to implement the control system.

Bengough, Peter [Malleable Networks, Inc.]↗

Microreactor Optimization Using Simulation And Economics (mouse)

Microreactor Optimization Using Simulation and Economics (MOUSE) is a tool that integrates both nuclear microreactor design and reactor economics to provide comprehensive evaluations and optimizations. This tool enables stakeholders to explore the interplay between technical and economic variables, guiding them towards effective and competitive microreactor solutions. For the reactor core simulations, MOUSE leverages the OpenMC Monte Carlo Particle Transport Code to perform detailed core simulations for various microreactor designs. The included OpenMC models are 2D core designs of a Liquid Metal Thermal Microreactor (LMTR), a Gas-Cooled TRISO-Fueled Microreactor (GCMR), and a Heat Pipe Microreactor. Beyond core design, MOUSE includes simplified calculations for: - Calculating the masses of heat exchangers within the system. - Mechanical power of pumps. - Estimating the area occupied by various buildings within the nuclear plant. For the economic analysis, MOUSE provides detailed bottom-up cost estimates, encompassing a wide range of costs including preconstruction costs, direct costs, indirect costs, training costs, financial costs, operation & maintenance (O&M) costs, and fuel costs. These cost estimations are developed using data from the MARVEL project and additional literature sources, enabling the calculation of total capital costs and levelized cost of energy for both first-of-a-kind and nth-of-a-kind microreactors. MOUSE also enables analysis of the cost drivers and competitiveness in the electricity market. MOUSE allows users to modify a wide array of technical and economic parameters to evaluate different scenarios and their impacts. Examples of these parameters include: Fuels, coolants, or reflector materials Enrichment levels Control drum materials and geometry Fuel pin geometry and materials Moderator pin geometry and materials Reactor core and reflector dimensions Packing factor for the TRISO particles Nuclear reactor power and reactor burnup Number of sensors Shielding thickness Reactor vessel and guard vessel dimensions Operational staff requirements Number of emergency shutdowns Levelization period Interest rate Construction duration Since MOUSE is powered by the WATTS toolkit, it supports optimization studies, parametric analyses, and uncertainty calculations/propagation. The optimization techniques enable users to identify optimal design and economic configurations. The parametric analysis tools allow users to explore the sensitivity of various parameters, while uncertainty propagation helps quantify the impact of uncertainties on overall performance and cost. User Interface and Workflow: Currently, MOUSE is a command-line-based tool. Users can input various reactor design or economic parameters, modify the designs, run simulations, and visualize results through comprehensive data visualization and reporting capabilities. The typical workflow involves setting up the reactor model, defining economic parameters, running simulations, and analyzing the results to make informed decisions. By combining advanced design calculations with detailed economic modeling, MOUSE provides a robust framework for optimizing nuclear microreactor technologies, enhancing their competitiveness, and guiding stakeholders towards innovative and cost-effective solutions.

Hanna, Botros [Idaho National Laboratory (INL), Id↗