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At least 73 records · Page 4

MO-FG-CAMPUS-TeP1-03: Pre-Treatment Surface Imaging Based Collision Detection

Purpose: Modern radiotherapy increasingly employs large immobilization devices, gantry attachments, and couch rotations for treatments. All of which raise the risk of collisions between the patient and the gantry / couch. Collision detection is often achieved by manually checking each couch position in the treatment room and sometimes results in extraneous imaging if collisions are detected after image based setup has begun. In the interest of improving efficiency and avoiding extra imaging, we explore the use of a surface imaging based collision detection model. Methods: Surfaces acquired from AlignRT (VisionRT, London, UK) were transferred in wavefront format to a custom Matlab (Mathworks, Natick, MA) software package (CCHECK). Computed tomography (CT) scans acquired at the same time were sent to CCHECK in DICOM format. In CCHECK, binary maps of the surfaces were created and overlaid on the CT images based on the fixed relationship of the AlignRT and CT coordinate systems. Isocenters were added through a graphical user interface (GUI). CCHECK then compares the inputted surfaces to a model of the linear accelerator (linac) to check for collisions at defined gantry and couch positions. Note, CCHECK may be used with or without a CT. Results: The nominal surface image field of view is 650 mm × 900 mm, with variance based on patient position and size. The accuracy of collision detections is primarily based on the linac model and the surface mapping process. The current linac model and mapping process yield detection accuracies on the order of 5 mm, assuming no change in patient posture between surface acquisition and treatment. Conclusions: CCHECK provides a non-ionizing method to check for collisions without the patient in the treatment room. Collision detection accuracy may be improved with more robust linac modeling. Additional gantry attachments (e.g. conical collimators) can be easily added to the model.

60 APPLIED LIFE SCIENCES↗

Fluctuating Hydrodynamics Methods for Dynamic Coarse-Grained Implicit-Solvent Simulations in LAMMPS

We present a software package integrated with the molecular dynamics software LAMMPS for fluctuating hydrodynamics simulations of fluid-structure interactions subject to thermal fluctuations. The package is motivated to provide dynamic thermostats to extend implicit-solvent coarse-grained (IS-CG) models by incorporating kinetic contributions from the solvent to facilitate their use in a wider range of applications. To capture the thermal and hydrodynamic contributions of the solvent to dynamics, we introduce momentum conserving thermostats and computational methods based on fluctuating hydrodynamics and the stochastic Eulerian Lagrangian method (SELM). SELM couples the coarse-grained microstructure degrees of freedom to continuum stochastic fields to capture both the relaxation of hydrodynamic modes and thermal fluctuations. Features of the SELM software include (i) numerical time-step integrators for SELM fluctuating hydrodynamics in inertial and quasi-steady regimes, (ii) Lees--Edwards-style methods for imposing shear, (iii) a Java-based graphical user interface (GUI) for setting up models and simulations, (iv) standardized XML formats for parametrization and data output, and (v) standardized formats VTK for continuum fields and microstructures. The SELM software package facilitates for pre-established models in LAMMPS easy adoption of the SELM fluctuating hydrodynamics thermostats. We offer here an overview of the SELM software package, computational methods, and applications.

97 MATHEMATICS AND COMPUTING↗

Sirepo for Synchrotron Radiation Workshop

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jinja, which is a secure and widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is the Synchrotron Radiation Workshop (SRW). SRW computes synchrotron radiation from relativistic electrons in arbitrary magnetic fields and propagates the radiation wavefronts through optical beamlines. SRW is open source and is primarily supported by Dr. Oleg Chubar of NSLS-II at Brookhaven National Laboratory.

Nagler, Robert↗

Sirepo - Warp

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jin-ja, which is a secure and widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is Warp. Warp is a particle-in-cell (PIC) code de-signed to simulate high-intensity charged particle beams and plasmas in both the electrostatic and electromagnetic regimes, with a wide variety of integrated physics models and diagnostics. At pre-sent, Sirepo supports a small subset of Warp’s capabilities. Warp is open source and is part of the Berkeley Lab Accelerator Simulation Toolkit.

Nagler, Robert↗

Thermochimica

Thermochimica is a software library that determines a unique combination of phases and their compositions at thermochemical equilibrium. Thermochimica can be used for stand-alone calculations or it can be directly coupled to other codes. This release of the software does not have a graphical user interface (GUI) and it can be executed from the command line or from an Application Programming Interface (API). Also, it is not intended for thermodynamic model development or for constructing phase diagrams. The main purpose of the software is to be directly coupled with a multi-physics code to provide material properties and boundary conditions for various physical phenomena. Significant research efforts have been dedicated to enhance computational performance through advanced algorithm development, such as improved estimation techniques and non-linear solvers. Various useful parameters can be provided as output from Thermochimica, such as: determination of which phases are stable at equilibrium, the mass of solution species and phases at equilibrium, mole fractions of solution phase constituents, thermochemical activities (which are related to partial pressures for gaseous species), chemical potentials of solution species and phases, and integral Gibbs energy (referenced relative to standard state). The overall goal is to provide an open source computational tool to enhance the predictive capability of multi-physics codes without significantly impeding computational performance.

Simunovic, Srdjan↗

Protein Coverage Summarizer

The Protein Coverage Summarizer can be used to determine the percent of the residues in each protein sequence that have been identified, based on a list of identified peptides. A graphical user interface (GUI) is provided to allow the user to select the input files, set the options, and browse the coverage results.

Gibbons, Bryson↗

P Finder

P Finder is written in C# and has been tested in multiple 64-bit Windows environments (Windows 7/8/Vista). It has a user-friendly graphical user interface (GUI) that allows for intuitive RNase P RNA identification and/or annotation. The user can select from four search criteria including the use multiple threads. In addition, the user can determine what display data they wish to incorporate in the output such as: bitscore, E-value, percent ID, start location, end location, the strand in which the sequence is located, and of course the sequence itself. P Finder is the only available algorithm that is capable of not only identifying the RNase P RNA for annotation but also differentiating among the five different RNase P RNA structural types (A, B, C, M, and T) with the option to select these data types for display in the final output.

Ellis, JosephC↗

Designs for Risk Evaluation and Management

The Designs for Risk Evaluation and Management (DREAM) tool was developed as part of the effort to quantify the risk of geologic storage of carbon dioxide (CO 2 ) under the U.S. Department of Energy's National Risk Assessment Partnership (NRAP). DREAM is an optimization tool created to identify optimal monitoring schemes that minimize the time to first detection of CO 2 leakage from a subsurface storage formation. DREAM acts as a post-processer on user-provided output from subsurface leakage simulations. While DREAM was developed for CO 2 leakage scenarios, it is applicable to any subsurface leakage simulation of the same output format. The DREAM tool is comprised of three main components: (1) a Java wizard used to configure and execute the simulations, (2) a visualization tool to view the domain space and optimization results, and (3) a plotting tool used to analyze the results. A secondary Java application is provided to aid users in converting common American Standard Code for Information Interchange (ASCII) output data to the standard DREAM hierarchical data format (HDF5). DREAM employs a simulated annealing approach that searches the solution space by iteratively mutating potential monitoring schemes built of various configurations of monitoring locations and leak detection parameters. This approach has proven to be orders of magnitude faster than an exhaustive search of the entire solution space. The user's manual illustrates the program graphical user interface (GUI), describes the tool inputs, and includes an example application.

(Ruprecht) Yonkofski, Catherine↗

Building Efficiency Targeting Tool for Energy Retrofits (BETTER) Web Application (BETTER Web App) v1.0

The Building Efficiency Targeting Tool for Energy Retrofits (BETTER) V.1.0 web application identifies cost-saving energy and emissions reductions in buildings and portfolios, without site visits or complex modeling. With minimal data entry, BETTER benchmarks a building's or portfolio's energy use against peers; quantifies energy, cost, and greenhouse gas (GHG) reduction potential; and recommends energy efficiency measures for individual buildings or portfolios, targeting specific energy savings levels. The source code of BETTER's modular, cross-platform analytical engine has previously been disclosed (2019-001) and is available on GitHub and can be adopted, redeveloped, and redistributed freely under an open-source license, allowing users to incorporate BETTER's analytical capabilities into their own software platforms and tools. The BETTER V.1.0 web application, developed with the Django web-framework and the Model-View-Controller (MVC) architecture being disclosed here, provides a graphical user interface (GUI) for any user to view the software tutorials, download and upload a data entry template, configure and run the BETTER analyses, and view the final analytical reports.

Szum, Carolyn↗

Sudoku Online Testing Framework v.0.2

The Sudoku Online Testing Framework provides a configurable basis for testing user interactions to solve visualization-related problems with sudoku puzzles and games. It consists of a server, a client, and test code. The python server implements sudoku puzzle logic and board selection functions. The JavaScript client implements a graphical user interface (GUI) front-end to display the puzzles and facilitate interactions with users. Within the GUI, logical rules may be selected. Cells may be selected to “pivot” on to make a board for each possible value in the cell. 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. SAND2021-6409 O

Leger, Michelle↗

Sequential Training ToolKit - STTK

Sequential Training ToolKit, or STTK, is a software toolkit plugin for the Unity development platform that enables software developers to easily develop structured Sequential Training applications for gaming and extended reality (XR) environments. STTK is architected to easily import the toolkit as a plugin for the Unity platform and then interact with the graphical user interface (GUI) for drag-and-drop functionality. STTK also includes easy add-on plugins for Prefabs and auto-builds a State Machine. 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. SAND2021-3059 O

Klein, BrandonThorin↗

Coincidence Doppler Broadening Analysis Program

A graphical user interface (GUI) that helps analyze data from coincidence Doppler broadening positron annihilation spectroscopy. It is a quick tool to rapidly reduce large data and conveniently analyze multiple datasets.

Watkins, JosephM.↗

ISO 15118 Node-Red Dashboard

This is a graphical user interface (GUI) that can be deployed in a Node-RED environment and be configured to provide monitoring and control of an ISO 15118 EV Charger (DC or AC).

Harper, Jason↗

ORNL Slicer 2 - Open Source Copyright

ORNL Slicer 2 is a slicing program for additive manufacturing. It takes a solid body mesh object, typically as .STL file, and converts that into machine readable instructions, called g-code, that a 3D printer can use to build the object. The functionality includes loading and positioning an object, slicing it into layers, fitting toolpaths to the layers, and outputting g-code to construct the object. All of this is contained within a graphical user interface (GUI) that allows the user to define all of the settings specific to their machine and process, then preview the resultant g-code before starting the printing process.

Roschli, Alex (0000000213084632)↗

phenix v. 7.0

SAND2021-6741 O phenix is Sandia's orchestration tool that allows users to quickly deploy, un-deploy, and interact with SCEPTRE ICS environments. phenix is an orchestration tool used for managing the creation, configuration, and deployment of modeling and simulation environments. As an abstraction layer on top of an underlying virtual machine manager called minimega, phenix organizes the network, application, and scenario information for a given deployment. It allows users to create, configure, and deploy experiments in a repeatable and rapid fashion. An application framework provides the flexibility to manipulate an experiment to suit various needs and requirements. phenix also includes a web-based graphical user interface (GUI) where experiments can be created, configured, and interacted with.

Sahakian, Meghan↗

System Validation Platform Working Directories

A suite of software tools used to interface with power electronic equipment for laboratory testing and device certification. They are typically used as equipment drivers with using the System Validation Platform (SVP) graphical user interface (GUI). 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. SAND2021-1185 O

Johnson, JayT↗

Imaging Bragg Edge Analysis TooLs for Engineering Structures (iBeatles)

The Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL) provides pulsed neutrons with energies varying from epithermal to cold. In preparation for VENUS, the neutron imaging beamline to be located at beam port 10, we have performed a series of experiments focused on wavelength-dependent radiography and computed tomography for a broad range of applications, from materials science to biological tissues.One of the time-of-flight (TOF) techniques that is of interest to the scientific community is the 2-dimensional mapping of phases and average crystalline plane orientation in samples both ex-situ and during applied stresses such as tensile loading and heating. This technique is known as Bragg edgeimaging and relies on the identification of changes of transmission values, fitting of the edge to measure its displacement, and thus identify the shift in lattice parameter due to stresses. One of the challenges of TOF imaging measurements is the amount of data and the inability to observe Bragg edge shifts in real time during an experiment. Thus, we have been focusing on creating a Python-based interface that allows fast data processing and instantaneous mapping and fitting of the Bragg edges, and their evolution through time. Python libraries and Jupyter notebooks have been implemented to facilitate decision making during an experiment. The advantage of the notebooks is the possibility to guide an experiment as they can quickly process and display Bragg edge data. These notebooks can be used independently, or can be combined in a Python Graphical User Interface (GUI) tool called iBeatles. This interface permits visualization and fitting of the Bragg edges, and ultimately back-projects the fitting results onto the radiographs to display a strain map. Assuming data collection has sufficient statistics, the strain mapping analysis can be performed on a pixel-by-pixel basis. This development is a step forward toward a better user experience at the future VENUS beamline in terms of live feedback and productivity. Analysis that used to take days of switching between different applications can now be done in minutes within the

Bilheux, JeanChristophe [Oak Ridge National Labora↗