slaclab/smurf-processor-base-docker
This docker image, named smurf-processor-base contains smurf-processor and additional tools used by the SMuRF project. It is based on the smurf-rogue docker image and contains smurf-processor.
Vasquez, Jesus↗
SEARCH · Search NASA
Results for “Docker”
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.
slaclab/smurf2mce-docker
This docker image, named smurf2mce contains smurf2mce, firmware files (mcs and pyrogue tarball) and default configuration files for stable firmware versions. It is based on the smurf2mce-base docker image.
Vasquez, Jesus↗
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↗
Ghidra Galore
SAND2025-00232O Ghidra Galore is a software tool that provides a test harness for running an analysis script in multiple versions of Ghidra, an open-source binary disassembler, using Docker. It allows users to understand how different versions of Ghidra evolve over time by analyzing a corpus of input files. The software includes a Python script that wraps the Docker functionality, simplifying the process of running the analysis script across different Ghidra versions. 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.
Crussell, Jonathan [Sandia National Lab. (SNL-CA),↗
Distributed Resources for the Earth System Grid Advanced Management (DREAM)
The DREAM project was funded more than 3 years ago to design and implement a next-generation ESGF (Earth System Grid Federation) architecture which would be suitable for managing and accessing data and services resources on a distributed and scalable environment. In particular, the project intended to focus on the computing and visualization capabilities of the stack, which at the time were rather primitive. At the beginning, the team had the general notion that a better ESGF architecture could be built by modularizing each component, and redefining its interaction with other components by defining and exposing a well defined API. Although this was still the high level principle that guided the work, the DREAM project was able to accomplish its goals by leveraging new practices in IT that started just about 3 or 4 years ago: the advent of containerization technologies (specifically, Docker), the development of frameworks to manage containers at scale (Docker Swarm and Kubernetes), and their application to the commercial Cloud. Thanks to these new technologies, DREAM was able to improve the ESGF architecture (including its computing and visualization services) to a level of deployability and scalability beyond the original expectations. Overall, during its three-year lifespan, DREAM has undertaken innovative research work and prototyping: many of its solutions (the new containerized architecture, the Visus visualization engine, the Solr Cloud based search service) were handed over to the ESGF collaboration, which will make them operational and use them as their future software basis.
42 ENGINEERING↗
Distributed Resources for the Earth System Grid Advanced Management (DREAM). Final Report
The DREAM project was funded more than 3 years ago to design and implement a next generation ESGF (Earth System Grid Federation) architecture which would be suitable for managing and accessing data and services resources on a distributed and scalable environment. In particular, the project intended to focus on the computing and visualization capabilities of the stack, which at the time were rather primitive. At the beginning, the team had the general notion that a better ESGF architecture could be built by modularizing each component, and redefining its interaction with other components by defining and exposing a well defined API. Although this was still the high level principle that guided the work, the DREAM project was able to accomplish its goals by leveraging new practices in IT that started just about 3 or 4 years ago: the advent of containerization technologies (specifically, Docker), the development of frameworks to manage containers at scale (Docker Swarm and Kubernetes), and their application to the commercial Cloud. Thanks to these new technologies, DREAM was able to improve the ESGF architecture (including its computing and visualization services) to a level of deployability and scalability beyond the original expectations.
54 ENVIRONMENTAL SCIENCES↗
FTS3: Data Movement Service in containers deployed in OKD [Slides]
The File Transfer Service (FTS3) is a data movement service developed at CERN which is used to distribute the majority of the Large Hadron Collider's data across the Worldwide LHC Computing Grid (WLCG) infrastructure. At Fermilab, we have deployed FTS3 instances for Intensity Frontier experiments (e.g. DUNE) to transfer data in America and Europe, using a container-based strategy. In this article we summarize our experience building docker images based on work from the SLATE project (slateci.io) and deployed in OKD, the community distribution of Red Hat OpenShift. Additionally, we discuss our method of certificate management and maintenance utilizing Kubernetes CronJobs. Finally, we also report on the two different configurations currently running at Fermilab, comparing and contrasting a Docker-based OKD deployment against a traditional RPM-based deployment.
97 MATHEMATICS AND COMPUTING↗
BLOC Site - ASSIST Thermodynamic Retrievals TROPoe v0.18 / Derived Data
This dataset contains daily files with thermodynamic profiles retrieved with the optimal estimation physical retrieval TROPoe (Turner and Löhnert 2014; Turner and Blumberg 2019; Turner and Löhnert 2021). This is a post-processed dataset and recommended for use. The profiles are retrieved every 10 minutes from instantaneous radiances observed with an Atmospheric Sounder Spectrometer by Infrared Spectral Technology (ASSIST, Michaud-Belleau et al. 2025) operated by NOAA Physical Sciences Laboratory (PSL) on Block Island for WFIP3. The spectral bands used in the retrieval are in the wavenumber range from 612 - 905.4 cm-1 and are specified in Turner and Löhnert (2021). Additional input data in TROPoe are cloud base height from a collocated ceilometer operated by NOAA GML and temperature, water vapor mixing ratio, and pressure from a collocated surface tower operated by NOAA PSL. In addition to these temporally resolved input data, TROPoe requires an a priori dataset (prior) that provides mean climatological estimates of thermodynamic profiles and specifies how temperature and humidity covary with height as an input (for details see, e.g., Djalalova et al. 2022). The prior is a key component of the retrieval and provides a constraint on the ill-posed inversion problem. A monthly prior was computed from operational radiosonde launches at Upton, NY. The TROPoe docker container (version 0.18) is available from Docker Hub at https://hub.docker.com/r/davidturner53/tropoe/tags, and the source code code is available in the GitHub repository https://github.com/OAR-atmospheric-observations/TROPoe.
17 WIND ENERGY↗
NANT Site - ASSIST Thermodynamic Retrievals TROPoe v0.18 / Derived Data
This dataset contains daily files with thermodynamic profiles retrieved with the optimal estimation physical retrieval TROPoe (Turner and Löhnert 2014; Turner and Blumberg 2019; Turner and Löhnert 2021). This is a post-processed dataset and recommended for use. The profiles are retrieved every 10 minutes from instantaneous radiances observed with an Atmospheric Sounder Spectrometer by Infrared Spectral Technology (ASSIST, Michaud-Belleau et al. 2025) operated by NOAA Physical Sciences Laboratory (PSL) on Nantucket Island for WFIP3. The spectral bands used in the retrieval are in the wavenumber range from 612 - 905.4 cm-1 and are specified in Turner and Löhnert (2021). Additional input data in TROPoe are cloud base height from a collocated ceilometer operated by NOAA GML and temperature, water vapor mixing ratio, and pressure from a collocated surface tower operated by NOAA PSL. In addition to these temporally resolved input data, TROPoe requires an a priori dataset (prior) that provides mean climatological estimates of thermodynamic profiles and specifies how temperature and humidity covary with height as an input (for details see, e.g., Djalalova et al. 2022). The prior is a key component of the retrieval and provides a constraint on the ill-posed inversion problem. A monthly prior was computed from operational radiosonde launches at Upton, NY. The TROPoe docker container (version 0.18) is available from Docker Hub at https://hub.docker.com/r/davidturner53/tropoe/tags, and the source code code is available in the GitHub repository https://github.com/OAR-atmospheric-observations/TROPoe.
17 WIND ENERGY↗
FTS3: Data Movement Service in containers deployed in OKD
The File Transfer Service (FTS3) is a data movement service developed at CERN which is used to distribute the majority of the Large Hadron Collider's data across the Worldwide LHC Computing Grid (WLCG) infrastructure. At Fermilab, we have deployed FTS3 instances for Intensity Frontier experiments (e.g. DUNE) to transfer data in America and Europe, using a container-based strategy. In this article we summarize our experience building docker images based on work from the SLATE project (slateci.io) and deployed in OKD, the community distribution of Red Hat OpenShift. Additionally, we discuss our method of certificate management and maintenance utilizing Kubernetes CronJobs. Finally, we also report on the two different configurations currently running at Fermilab, comparing and contrasting a Docker-based OKD deployment against a traditional RPM-based deployment.
Lobato Pardavila, Lorena↗
Auto-MuRCiS: a streamlined software package for analysis of multiplex, randomized CRISPR interference sequencing data
Multiplex, randomized CRISPR interference sequencing (MuRCiS) allows for the simultaneous identification of multiple gene knockouts that together influence microbial processes. Here, we report on an updated analysis tool called Auto-MuRCiS that utilizes Docker to make the analysis of these data rapid and more user-friendly.
59 BASIC BIOLOGICAL SCIENCES↗
A Centralized AI Lakehouse Framework for Brain Tumor MRI Classification and Segmentation, University KPI Forecasting, and Water Potability Prediction
In many university and healthcare projects, models are built for very different data types such as tables, institutional time series, and medical images, but they are deployed as separate applications. In this work, that separation made testing and maintenance difficult because each module had its own pipeline and runtime requirements. This paper presents an integrated AI lakehouse-style implementation that runs three model pipelines inside one containerized backend. For medical imaging, we used MRI datasets from IEEE DataPort: a four-class classification set with 7012 images (5708 train/1304 test) and a segmentation set with 3063 image–mask pairs. The classification model (ResNet50 transfer learning) is evaluated using a proper train–validation–test protocol across multiple splits (80/10/10, 70/10/20, 60/10/30, and 10/30/60), achieving a test accuracy of 99.00% under the standard 80/10/10 split. Additionally, a patient-level evaluation is conducted using an external glioma dataset to provide a more realistic assessment without data leakage. The segmentation model (DeepLabV3-ResNet50) achieved 83.09% validation mIoU and 88.79% Dice score. For university KPI forecasting, we used annual IPEDS and NSF HERD data from 2010 to 2023 for three universities (BSU, EOU, and UAB). To examine the effect of preprocessing on forecasting performance, two case studies are conducted. In the first case, linear interpolation is applied to generate semester-level data. In the second case, the original annual data is used directly without interpolation. Random Forest regression and ARIMA models are evaluated using MAE, RMSE, MAPE, and R 2 . The results showed that interpolation improved apparent forecasting performance due to smoothing, while evaluation on the original annual data provided a more realistic assessment of model behavior. To further validate the framework on a larger dataset, an additional case study is conducted using a student dropout dataset. For water potability, we trained and compared multiple tabular classifiers on a large dataset (1,048,575 samples). A Random Forest model (100 trees, max depth 10) achieved 85.86% test accuracy and high recall for unsafe samples (0.8447). All modules are served via FastAPI and deployed together using Docker, with workflow automation routing requests to the correct endpoint. System-level benchmarking indicates that the backend maintains stable throughput and latency under concurrent requests.
97 MATHEMATICS AND COMPUTING↗
Smart connected worker edge platform for smart manufacturing: Part 1—Architecture and platform design
Abstract The challenge of sustainably producing goods and services for healthy living on a healthy planet requires simultaneous consideration of economic, societal, and environmental dimensions in manufacturing. Enabling technology for data driven manufacturing paradigms like Smart Manufacturing (a.k.a. Industry 4.0) serve as the technological backbone from which sustainable approaches to manufacturing can be implemented. Unfortunately, these technologies are typically associated with broader and deeper factory automation that is often too expensive and complex for the small and medium sized manufacturers (SMMs) that comprise the majority of manufacturing business in the USA and for whom their most valuable asset are the people whose jobs automation while replace. This paper describes an edge intelligent platform to integrate internet‐of‐things technologies with computing hardware, software, computational workflows for machine learning, and data ingestion, enabling SMMs to transition into smart manufacturing paradigms by leveraging the intelligence of their people. The platform leverages consumer grade electronics and sensors (affordable and portable), customized software with open source software packages (accessible), and existing communication network infrastructures (scalable). The software systems are implemented via Kubernetes orchestration of Docker containerization to ensure scalability and programmability. The platform is adaptive via computational workflow engines that produce information from data by processing with low‐cost edge computing devices while efficiently accessing resources of cloud servers as needed. The proposed edge platform connects workers to technological resources that provide computational intelligence (i.e., silicon‐based sensing and computation for data collection and contextualization) to enable decision making at the edge of advanced manufacturing.
Kim, Yoon G.↗
Digitalization of an experimental electrochemical reactor via the smart manufacturing innovation platform
The exponential increase in data produced over the last two decades has revolutionized the way we collect, store, process, analyze, model, and interpret information to improve profitability. Manufacturing is no exception. How- ever, Smart Manufacturing, the digital practice, organization, workforce, and infrastructure transformation for collection and deployment of data and models at scale and at all levels of manufacturing, is a complex, costly, and labor-intensive journey that is still seeing slow adoption. The Clean Energy Smart Manufacturing Innovation Institute (CESMII), a national Manufacturing USA public-private partnership sponsored by the Department of Energy, is addressing this scaled use of data and modeling in manufacturing. CESMII has focused on how to col- lect and use operating data for numerous applications that improve productivity, precision, and performance of manufacturing operations from factory floor to supply chain using process simulation, predictive analytics, mon- itoring and control, and real-time optimization. Because contextualized data are key, CESMII has developed the Smart Manufacturing Innovation Platform (SMIP) to lower the barriers to the data that are needed to accelerate data-based model building, improve data visualization, and more quickly gain insights. Reusable, standards-based ways of doing data collection, ingestion, and contextualization are particularly important for scaling access and use of data. The SMIP uses a standards-based definition and construct for reusable information models called an SM Profile. When an SM Profile is used in conjunction with the SMIP, the SMIP ensures the availability of contextualized, operational data for model building. The present work demonstrates Smart Manufacturing and the application of the SMIP for building several data-centered models for the operation and control of an ex- perimental electrochemical reactor that reduces carbon dioxide (CO 2 ) gas to valuable liquid and gas chemicals, such as alcohols, olefins, and syngas. We describe how the SMIP plays a central role in more effective model building and we demonstrate how the electochemical reactor can be controlled and optimized for the desired products. Use of the SMIP involves the transmission of real-time sensor measurements to a cloud resource so that the operating data are available to all model building experts. The data collection and transmission process is fully automated to greatly reduce the need for manual manipulation of the data. Data-driven machine learning models are used for advanced real-time state estimation, real-time optimization, and model-based feedback control for the reactor. The application models are implemented as a system to monitor the data flow and control the electrochemical reactor with a single visualization interface. SM Profiles are used to demonstrate reusability of the information models for the reactor and the instrumentation. The application packages, algorithms, and user interfaces developed are cast as Docker images in a library to facilitate reusability of the application models.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Software stewardship and advancement of a high-performance computing scientific application: QMCPACK
Here, we provide an overview of the software engineering efforts and their impact in QMCPACK, a production-level ab-initio Quantum Monte Carlo open-source code targeting high-performance computing (HPC) systems. Aspects included are: (i) strategic expansion of continuous integration (CI) targeting CPUs, using GitHub Actions own runners, and NVIDIA and AMD GPUs used in pre-exascale systems, (ii) incremental reduction of memory leaks using sanitizers, (iii) incorporation of Docker containers for CI and reproducibility, and (iv) refactoring efforts to improve maintainability, testing coverage, and memory lifetime management. We quantify the value of these improvements by providing metrics to illustrate the shift towards a predictive, rather than reactive, maintenance approach. Our goal, in documenting the impact of these efforts on QMCPACK, is to contribute to the body of knowledge on the importance of research software engineering (RSE) for the stewardship and advancement of community HPC codes to enable scientific discovery at scale.
97 MATHEMATICS AND COMPUTING↗
UQpy v4.1: Uncertainty quantification with Python
This paper presents the latest improvements introduced in Version 4 of the UQpy, Uncertainty Quantification with Python, library. In the latest version, the code was restructured to conform with the latest Python coding conventions, refactored to simplify previous tightly coupled features, and improve its extensibility and modularity. To improve the robustness of UQpy, software engineering best practices were adopted. A new software development workflow significantly improved collaboration between team members, and continuous integration and automated testing ensured the robustness and reliability of software performance. Continuous deployment of UQpy allowed its automated packaging and distribution in system agnostic format via multiple channels, while a Docker image enables the use of the toolbox regardless of operating system limitations.
97 MATHEMATICS AND COMPUTING↗
CFM-ID 4.0: More Accurate ESI MS/MS Spectral Prediction and Compound Identification
In the field of metabolomics, mass spectrometry (MS) is the method most commonly used for identifying and annotating metabolites. As this typically involves matching a given MS spectrum against an experimentally acquired reference spectral library, this approach is limited by the coverage and size of such libraries (which typically number in the thousands). These experimental libraries can be greatly extended by predicting the MS spectra of known chemical structures (which number in the millions) to create computational reference spectral libraries. To facilitate the generation of predicted spectral reference libraries we developed CFM-ID, a computer program that can accurately predict ESI-MS/MS spectrum for a given compound structure. CFM-ID is one of the best-performing methods for compound-to-mass-spectrum prediction, and also one of the top tools for in silico mass-spectrum-to-compound identification. This work improves CFM-ID’s ability to predict ESI-MS/MS spectra from compounds by: (1) learning parameters from features based on the molecular topology, (2) adding a new approach to ring cleavage that models such cleavage as a sequence of simple chemical bond dissociations and (3) expanding its hand-written rule-based predictor to cover more chemical classes, including acylcarnitines, acylcholines, flavonols, flavones, flavanones, and flavonoid glycosides. We demonstrate that this new version of CFM-ID (version 4.0) is significantly more accurate than previous CFM-ID versions, in terms of both EI-MS/MS spectral prediction and compound identification. CFM-ID 4.0 is available at http://cfmid4.wishartlab.com/ as a webservice and docker images can be downloaded at https://hub.docker.com/r/wishartlab/cfmid
Wang, Fei↗
PSpecteR: A User-Friendly and Interactive Application for Visualizing Top-Down and Bottom-Up Proteomics Data in R
Visual examination of mass spectrometry data is necessary to assess data quality and to facilitate data exploration. Graphics provide the means to evaluate spectral properties, test alternative peptide/protein sequence matches, prepare annotated spectra for publication, and fine-tune parameters during wet lab procedures. Visual inspection of MS data is hindered by proprietary proteomics visualization software designed for particular workflows and academic software that lack visualization tools. We built PSpecteR, an open-source and interactive R Shiny web application to address these issues, with support for several steps of proteomics data processing, including: reading various mass spectrometry files, running open-source database search tools, labelling spectra with fragmentation patterns, testing post-translational modifications, plotting where identified fragments map to reference sequences, and visualizing algorithmic output and metadata. All figures, tables, and spectra are exportable within one easy-to-use graphical user interface. Our current software provides a flexible and modern R framework to support fast implementation of additional features. The open source code is readily available (https://github.com/EMSL-Computing/PSpecteR), and a PSpecteR Docker container (https://hub.docker.com/r/emslcomputing) is available for easy local installation.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗