Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate
Please check the README file inside the metadata directory for more information about the dataset.
BL3↗
SEARCH · Engineering Papers
Results for “Directory”
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.
Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA
Please check the README file inside the metadata directory for more information about the dataset.
BL3↗
Short-Lived Intermediate in the N2O Generation by P450 NO Reductase Captured by Time-Resolved IR Spectroscopy and XFEL Crystallography
Diffraction images were collected using an MX300-HS CCD detector. For each cryoloop, 2D raster scan with 50 μm step in each direction was performed twice. In the second pass, the raster-scan grid was shifted 25 μm in each direction. In cheetah directory, - {puck_name}/{pin_id}_hits.h5 correspond to the first scan, and - {puck_name}/{pin_id}-2_hits.h5 correspond to the second scan.
BL3↗
Cantera and Cantera Electrolyte Thermodynamics Objects
Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. It is a multi-organizational effort to create and formulate high quality 0D and 1D constitutive modeling tools for reactive transport codes.Institutions involved with the effort include Sandia, MIT, Colorado School of Mines, U. Texas, NASA, and Oak Ridge National Labs. Specific to Sandia's contributions, the Cantera Electrolyte Thermo Objects (CETO) packages is comprised of add-on routines for Cantera that handle electrolyte thermochemistry and reactions within the overall Cantera package. Cantera is a C++ Cal Tech code that handles gas phase species transport, reaction, and thermodynamics. With this addition, Cantera can be extended to handle problems involving liquid phase reactions and transport in electrolyte systems, and phase equilibrium problemsinvolving concentrated electrolytes and gas/solid phases. A full treatment of molten salt thermodynamics and transport has also been implemented in CETO. The routines themselves consist of .cpp and .h files containing C++ objects that are derived from parent Cantera objects representing thermodynamic functions. They are linked unto the main Cantera libraries when requested by the user. As an addendum to the main thermodynamics objects, several utility applications are provided. The first is multiphase Gibbs free energy minimizer based on the vcs algorithm, called vcs_cantera. This code allows for the calculation of thermodynamic equilibrium in multiple phases at constant temperature and pressure. Note, a similar code capability exists already in Cantera. This version follows the same algorithm, but gas a different code-base starting point, and is used as a research tool for algorithm development. The second program, cttables, prints out tables of thermodynamic and kinetic information for thermodynamic and kinetic objects within Cantera. This program serves as a "Get the numbers out" utility for Cantera, and as such it is very useful as a verification tool. These add-on utilities are encapsulated into a directory structure named cantera_apps, whose installation uses autoconf and also utilizes Cantera's application environment (i.e., they utilize Cantera as a library).
John Hewson, HarryMoffat↗
OpenStudio® Resources [SWR-07-40]
This repository includes a suite of simulation tests that can be used to validate new OpenStudio® model objects as well as ensure that objects continue to work after they are added. Each new OpenStudio Model object should ideally have two simulation tests associated with it: - a Ruby one which verifies the Ruby API and, - an OSM one that verifies the OSM file can be loaded with future versions of OpenStudio. Both tests should result in a simulation-ready OpenStudio Model that can be simulated using EnergyPlus®. Both of these tests are located in the /model/simulationtests directory, the easiest way to add a new test is to find a related existing test and modify it. When new tests are added they must be added to the model_tests.rb file.
Benne, Kyle↗
Simulation INsight and Analysis
Sina is a tool set for modern scientific data management that provides flexible, light-weight support of non-bulk data capture for retention in and queries against SQL and noSQL data stores. HPC simulations traditionally maintain their data in files. Extracting data of interest for subsequent analysis then requires the time-consuming process of traversing directories and scraping data from files in a variety of formats. Sina facilitates capturing relevant data during execution or post-processing of simulation runs for retention in and queries from a modern data store. The tools are sufficiently general to allow for the inclusion of new fields as scientists learn more about their data. Libraries, currently in C++ and Python, and a command line interface (CLI) are provided. Sina's flexibility starts with a general schema, in JSON, for the collection of non-bulk simulation data. JSON provides a flexible, human-readable representation of the data that of interest. Sina currently has a C++ library for simulations to write data to and read from a schema-compliant file for subsequent ingestion into one of the supported data stores. However, applications are free to write their data directly into a schema-compliant file. Python packages provide data ingestion, management, query, and export capabilities. A command line interface (CLI) provides simplified access to these features. A common application programming interface (API) is used to maintain and query data in any of the supported data stores, which are currently limited to SQL and Apache Cassandra (a column store). Tutorials, demonstrations, and examples illustrate aspects of the process using scripts and Jupyter notebooks.
Pauli, EstebanT↗
PackageRedvoxToHdf5
This is a program to convert a directory of Redvox JSON packets to a single HDF5 file.
MAGANA-ZOOK, STEVENA.↗
ESS-DIVE File Level Metadata Extractor
The File-level Metadata (FLMD) parser is a lightweight python script that can produce a summary of fields based on column headers within a Comma-separated Values (CSV) file. The script enables a way to extract certain metadata fields from CSV data files. An optional configuration file can be used to select specific column headers to extract a smaller subset of values. The script can be used on a single file, or it can be given a directory to process groups of files in bulk. The FLMD parser outputs the metadata as a JSON and can be configured to updated the source file or produce an external companion file.
McNelis, Jack↗
sbang
sbang lets users run scripts with very long shebang (#!) lines. Many operating systems limit the length and number of possible arguments in shebang lines, making it hard to use interpreters that are deep in the directory hierarchy or require special arguments. To use it, a user puts the long shebang on the second line of their script, and makes sbang the interpreter, like this: #!/bin/sh /path/to/sbang #!/long/path/to/real/interpreter with arguments. sbang will run the real interpreter with the script as its argument.
Gamblin, Todd↗
slaclab/HXRSnD-Runs
This repo serves as the working directory of each HXRSnD run and as an archive of previous runs.
Ahmed, Abdullah P. Rashed↗
slaclab/Skywalker-Runs
This repo serves as the working directory of each Skywalker run and as an archive of previous runs.
Ahmed, Abdullah P. Rashed↗
DYnamic and Asynchronous Data Streamliner
DYAD aims to help sharing data files between producer and consumer job elements, especially between co-scheduled jobs or within an ensemble. DYAD provides the service by two components: a FLUX module and a I/O wraper set. DYAD transparently synchronizes file I/O between producer and consumer, and transfers data from the producer location to the consumer location managed by the service. Users only need to use the file path that is under the directory managed by the service.
Ahn, DongH↗
SSGUI v1.0
SSGUI is a web-based application that integrates the integrative genomics browser (IGV) with upstream alignment pipelines enabling rapid analysis of a batch of next-generation sequencing (NGS) samples. The input to SSGUI is an NGS file system directory that is organized by experiment and reference sequence. The output is an online dashboard containing various sequencing statistics for each sample and an integrated IGV plugin enabling rapid analysis of aligned NGS reads.
Kulawik, Mark↗
EQ_phase_detection
The EQ_phase_detection software is designed to scan continuous daily waveforms to detect earthquake phase arrivals from local to regional (150 km) events. The detections are made with a deep learning encoder-decoder model. When the model detects an earthquake in the waveforms, a second model is implemented to classify the first arriving motions. Both deep learning models are trained with the Tensorflow package using publicly available benchmark data sets. The software input is a path to a directory that contains waveforms in mseed format and the associated response files in xml format. The output is a data table of time stamped detections, signal amplitude, signal-to-noise ratio, and softmax probability of the detection in a generic format applicable to post-processing association algorithms for event locations. Additionally, the p-wave and s-wave waveforms are saved in a data table for rapid access when producing improved locations using correlation-based techniques. The software is designed for multiprocessing with multiple GPU’s for rapid processing of large data sets. The configuration file provides flexibility in the trained models implemented and allows access to multiple models trained for different sampling rates or input dimensions. This is particularly useful for regions with multiple networks that do not have the same data parameters.
Johnson, Christopher↗
Interpolation Models and Error Bounds for Verifiable Scientific Machine Learning
This repository contains python scripts and numerical data accompanying the paper: "Leveraging Interpolation Models and Error Bounds for Verifiable Scientific Machine Learning," Tyler Chang, Andrew Gillette, Romit Maulik, 2024. The following subdirectories are included: - "interpolants" contains our interpolation scripts used for all studies - "experiments" contains scripts demonstrating our experiments with synthetic data - "airfoil" contains scripts demonstrating our experiments with the publicly available UIUC airfoil dataset. Further instructions are provided in READMEs within the sub-directories.
Gillette, Andrew↗
Mesh Computing Remote Automatic Workflow
The software suite uses a microservice architecture using Docker and `docker-compose`. The microservices are as follows: 1. User interface. This interface is written in JavaScript using the Svelte framework. It exposes form elements and a 3D visualizer to prompt the user through the definition of microstructure parameters, and setting parameters for mesh generation and refinement. 2. Mesh generator. This is a container running the Python package for DREAM3D to generate a voxelized mesh that represents a microstructure defined by the user in the interface. 3. Cubit runner. This is a secure shell protocol tool that makes the submitting the DREAM mesh to an HPC instance and starts to run Cubit shell commands to smooth the grain boundaries with its `sculpt` library, applies user-defined boundary node sets, and bundles and returns the simulation-ready meshes and input files as a zipped directory.
Harris, BrennanKay↗
Role-Based Access Control for Distributed Energy Resources v.1.0
The Role-Based Access Control (RBAC) for Distributed Energy Resources (DER) software is an automated and transparent stack for RBAC administrators to interact with RBAC policy. The package includes demonstrations of centralized and decentralized RBAC implementation. Both include simulated DER entities that are stored automatically in a centralized Lightweight Directory Access Protocol (LDAP) server. It also includes a REST-API to serve the HTTP requests of the RBAC administrators. A complete front-end is included to serve the users' needs. This software may be used by industry (DER vendors/utilities) as well as the research community to determine if a centralized or decentralized solution fits better the needs of an RBAC model in a DER environment. Additionally, parts of this software may be useful for developing implementations for specific needs. 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. SAND2021-8292 O
Johnson, Jay↗