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At least 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2011

Modeling the TrueBeam linac using a CAD to Geant4 geometry implementation: Dose and IAEA-compliant phase space calculations

Purpose: To create an accurate 6 MV Monte Carlo simulation phase space for the Varian TrueBeam treatment head geometry imported from cad (computer aided design) without adjusting the input electron phase space parameters. Methods: geant4 v4.9.2.p01 was employed to simulate the 6 MV beam treatment head geometry of the Varian TrueBeam linac. The electron tracks in the linear accelerator were simulated with Parmela, and the obtained electron phase space was used as an input to the Monte Carlo beam transport and dose calculations. The geometry components are tessellated solids included in geant4 as gdml (generalized dynamic markup language) files obtained via STEP (standard for the exchange of product) export from Pro/Engineering, followed by STEP import in Fastrad, a STEP-gdml converter. The linac has a compact treatment head and the small space between the shielding collimator and the divergent arc of the upper jaws forbids the implementation of a plane for storing the phase space. Instead, an IAEA (International Atomic Energy Agency) compliant phase space writer was implemented on a cylindrical surface. The simulation was run in parallel on a 1200 node Linux cluster. The 6 MV dose calculations were performed for field sizes varying from 4 x 4 to 40 x 40 cm{sup 2}. The voxel size for the 60x60x40 cm{sup 3} water phantom was 4x4x4 mm{sup 3}. For the 10x10 cm{sup 2} field, surface buildup calculations were performed using 4x4x2 mm{sup 3} voxels within 20 mm of the surface. Results: For the depth dose curves, 98% of the calculated data points agree within 2% with the experimental measurements for depths between 2 and 40 cm. For depths between 5 and 30 cm, agreement within 1% is obtained for 99% (4x4), 95% (10x10), 94% (20x20 and 30x30), and 89% (40x40) of the data points, respectively. In the buildup region, the agreement is within 2%, except at 1 mm depth where the deviation is 5% for the 10x10 cm{sup 2} open field. For the lateral dose profiles, within the field size for fields up to 30x30 cm{sup 2}, the agreement is within 2% for depths up to 10 cm. At 20 cm depth, the in-field maximum dose difference for the 30x30 cm{sup 2} open field is within 4%, while the smaller field sizes agree within 2%. Outside the field size, agreement within 1% of the maximum dose difference is obtained for all fields. The calculated output factors varied from 0.938{+-}0.015 for the 4x4 cm{sup 2} field to 1.088{+-}0.024 for the 40x40 cm{sup 2} field. Their agreement with the experimental output factors is within 1%. Conclusions: The authors have validated a geant4 simulated IAEA-compliant phase space of the TrueBeam linac for the 6 MV beam obtained using a high accuracy geometry implementation from cad. These files are publicly available and can be used for further research.

43 PARTICLE ACCELERATORS↗
DOE OSTI2014

SU-E-T-544: A Radiation Oncology-Specific Multi-Institutional Federated Database: Initial Implementation

Purpose: To implement a common database structure and user-friendly web-browser based data collection tools across several medical institutions to better support evidence-based clinical decision making and comparative effectiveness research through shared outcomes data. Methods: A consortium of four academic medical centers agreed to implement a federated database, known as Oncospace. Initial implementation has addressed issues of differences between institutions in workflow and types and breadth of structured information captured. This requires coordination of data collection from departmental oncology information systems (OIS), treatment planning systems, and hospital electronic medical records in order to include as much as possible the multi-disciplinary clinical data associated with a patients care. Results: The original database schema was well-designed and required only minor changes to meet institution-specific data requirements. Mobile browser interfaces for data entry and review for both the OIS and the Oncospace database were tailored for the workflow of individual institutions. Federation of database queries--the ultimate goal of the project--was tested using artificial patient data. The tests serve as proof-of-principle that the system as a whole--from data collection and entry to providing responses to research queries of the federated database--was viable. The resolution of inter-institutional use of patient data for research is still not completed. Conclusions: The migration from unstructured data mainly in the form of notes and documents to searchable, structured data is difficult. Making the transition requires cooperation of many groups within the department and can be greatly facilitated by using the structured data to improve clinical processes and workflow. The original database schema design is critical to providing enough flexibility for multi-institutional use to improve each institution s ability to study outcomes, determine best practices, and support research. The project has demonstrated the feasibility of deploying a federated database environment for research purposes to multiple institutions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

MO-F-16A-01: Implementation of MPPG TPS Verification Tests On Various Accelerators

Purpose: To demonstrate the implementation of the Medical Physics Practice Guideline (MPPG) for dose calculation and beam parameters verification of treatment planning systems (TPS). Methods: We implemented the draft TPS MPPG for three linacs: Varian Trilogy, TomoHDA and Elekta Infinity. Static and modulated test plans were created. The static fields are different than used in commissioning. Data was collected using ion chambers and diodes in a scanning water tank, Delta4 phantom and a custom phantom. MatLab and Microsoft Excel were used to create analysis tools to compare reference DICOM dose with scan data. This custom code allowed for the interpolation, registration and gamma analysis of arbitrary dose profiles. It will be provided as open source code. IMRT fields were validated with Delta4 registration and comparison tools. The time for each task was recorded. Results: The tests confirmed the strengths, and revealed some limitations, of our TPS. The agreement between calculated and measured dose was reported for all beams. For static fields, percent depth dose and profiles were analyzed with criteria in the draft MPPG. The results reveal areas of slight mismatch with the model (MLC leaf penumbra, buildup region.) For TomoTherapy, the IMRT plan 2%/2 mm gamma analysis revealed poorest agreement in the low dose regions. For one static test plan for all 10MV Trilogy photon beams, the plan generation, scan queue creation, data collection, data analysis and report took 2 hours, excluding tank setup. Conclusions: We have demonstrated the implementation feasibility of the TPS MPPG. This exercise generated an open source tool for dose comparisons between scan data and DICOM dose data. An easily reproducible and efficient infrastructure with streamlined data collection was created for repeatable robust testing of the TPS. The tests revealed minor discrepancies in our models and areas for improvement that are being investigated.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2014

MO-F-16A-06: Implementation of a Radiation Exposure Monitoring System for Surveillance of Multi-Modality Radiation Dose Data

Purpose: We have implemented a commercially available Radiation Exposure Monitoring System (REMS) to enhance the processes of radiation dose data collection, analysis and alerting developed over the past decade at our sites of practice. REMS allows for consolidation of multiple radiation dose information sources and quicker alerting than previously developed processes. Methods: Thirty-nine x-ray producing imaging modalities were interfaced with the REMS: thirteen computed tomography scanners, sixteen angiography/interventional systems, nine digital radiography systems and one mammography system. A number of methodologies were used to provide dose data to the REMS: Modality Performed Procedure Step (MPPS) messages, DICOM Radiation Dose Structured Reports (RDSR), and DICOM header information. Once interfaced, the dosimetry information from each device underwent validation (first 15–20 exams) before release for viewing by end-users: physicians, medical physicists, technologists and administrators. Results: Before REMS, our diagnostic physics group pulled dosimetry data from seven disparate databases throughout the radiology, radiation oncology, cardiology, electrophysiology, anesthesiology/pain management and vascular surgery departments at two major medical centers and four associated outpatient clinics. With the REMS implementation, we now have one authoritative source of dose information for alerting, longitudinal analysis, dashboard/graphics generation and benchmarking. REMS provides immediate automatic dose alerts utilizing thresholds calculated through daily statistical analysis. This has streamlined our Closing the Loop process for estimated skin exposures in excess of our institutional specific substantial radiation dose level which relied on technologist notification of the diagnostic physics group and daily report from the radiology information system (RIS). REMS also automatically calculates the CT size-specific dose estimate (SSDE) as well as provides two-dimensional angulation dose maps for angiography/interventional procedures. Conclusion: REMS implementation has streamlined and consolidated the dosimetry data collection and analysis process at our institutions while eliminating manual entry error and providing immediate alerting and access to dosimetry data to both physicists and physicians. Brent Stewart has funded research through GE Healthcare.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

TH-A-19A-08: Intel Xeon Phi Implementation of a Fast Multi-Purpose Monte Carlo Simulation for Proton Therapy

Purpose: Recent studies have demonstrated the capability of graphics processing units (GPUs) to compute dose distributions using Monte Carlo (MC) methods within clinical time constraints. However, GPUs have a rigid vectorial architecture that favors the implementation of simplified particle transport algorithms, adapted to specific tasks. Our new, fast, and multipurpose MC code, named MCsquare, runs on Intel Xeon Phi coprocessors. This technology offers 60 independent cores, and therefore more flexibility to implement fast and yet generic MC functionalities, such as prompt gamma simulations. Methods: MCsquare implements several models and hence allows users to make their own tradeoff between speed and accuracy. A 200 MeV proton beam is simulated in a heterogeneous phantom using Geant4 and two configurations of MCsquare. The first one is the most conservative and accurate. The method of fictitious interactions handles the interfaces and secondary charged particles emitted in nuclear interactions are fully simulated. The second, faster configuration simplifies interface crossings and simulates only secondary protons after nuclear interaction events. Integral depth-dose and transversal profiles are compared to those of Geant4. Moreover, the production profile of prompt gammas is compared to PENH results. Results: Integral depth dose and transversal profiles computed by MCsquare and Geant4 are within 3%. The production of secondaries from nuclear interactions is slightly inaccurate at interfaces for the fastest configuration of MCsquare but this is unlikely to have any clinical impact. The computation time varies between 90 seconds for the most conservative settings to merely 59 seconds in the fastest configuration. Finally prompt gamma profiles are also in very good agreement with PENH results. Conclusion: Our new, fast, and multi-purpose Monte Carlo code simulates prompt gammas and calculates dose distributions in less than a minute, which complies with clinical time constraints. It has been successfully validated with Geant4. This work has been financialy supported by InVivoIGT, a public/private partnership between UCL and IBA.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2015

SU-E-J-127: Implementation of An Online Replanning Tool for VMAT Using Flattening Filter-Free Beams

Purpose: This is to report the implementation of an online replanning tool based on segment aperture morphing (SAM) for VMAT with flattening filter free (FFF) beams. Methods: Previously reported SAM algorithm modified to accommodate VMAT with FFF beams was implemented in a tool that was interfaced with a treatment planning system (Monaco, Elekta). The tool allows (1) to output the beam parameters of the original VMAT plan from Monaco, and (2) to input the apertures generated from the SAM algorithm into Monaco for the dose calculation on daily CT/CBCT/MRI in the following steps:(1) Quickly generating target contour based on the image of the day, using an auto-segmentation tool (ADMIRE, Elekta) with manual editing if necessary; (2) Morphing apertures based on the SAM in the original VMAT plan to account for the interfractional change of the target from the planning to the daily images; (3) Calculating dose distribution for new apertures with the same numbers of MU as in the original plan; (4) Transferring the new plan into a record & verify system (MOSAIQ, Elekta); (5) Performing a pre-delivery QA based on software; (6) Delivering the adaptive plan for the fraction.This workflow was implemented on a 16-CPU (2.6 GHz dual-core) hardware with GPU and was tested for sample cases of prostate, pancreas and lung tumors. Results: The online replanning process can be completed within 10 minutes. The adaptive plans generally have improved the plan quality when compared to the IGRT repositioning plans. The adaptive plans with FFF beams have better normal tissue sparing as compared with those of FF beams. Conclusion: The online replanning tool based on SAM can quickly generate adaptive VMAT plans using FFF beams with improved plan quality than those from the IGRT repositioning plans based on daily CT/CBCT/MRI and can be used clinically. This research was supported by Elekta Inc. (Crawley, UK)

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

SU-E-T-466: Implementation of An Extension Module for Dose Response Models in the TOPAS Monte Carlo Toolkit

Purpose: To develop and verify an extension to TOPAS for calculation of dose response models (TCP/NTCP). TOPAS wraps and extends Geant4. Methods: The TOPAS DICOM interface was extended to include structure contours, for subsequent calculation of DVH’s and TCP/NTCP. The following dose response models were implemented: Lyman-Kutcher-Burman (LKB), critical element (CE), population based critical volume (CV), parallel-serials, a sigmoid-based model of Niemierko for NTCP and TCP, and a Poisson-based model for TCP. For verification, results for the parallel-serial and Poisson models, with 6 MV x-ray dose distributions calculated with TOPAS and Pinnacle v9.2, were compared to data from the benchmark configuration of the AAPM Task Group 166 (TG166). We provide a benchmark configuration suitable for proton therapy along with results for the implementation of the Niemierko, CV and CE models. Results: The maximum difference in DVH calculated with Pinnacle and TOPAS was 2%. Differences between TG166 data and Monte Carlo calculations of up to 4.2%±6.1% were found for the parallel-serial model and up to 1.0%±0.7% for the Poisson model (including the uncertainty due to lack of knowledge of the point spacing in TG166). For CE, CV and Niemierko models, the discrepancies between the Pinnacle and TOPAS results are 74.5%, 34.8% and 52.1% when using 29.7 cGy point spacing, the differences being highly sensitive to dose spacing. On the other hand, with our proposed benchmark configuration, the largest differences were 12.05%±0.38%, 3.74%±1.6%, 1.57%±4.9% and 1.97%±4.6% for the CE, CV, Niemierko and LKB models, respectively. Conclusion: Several dose response models were successfully implemented with the extension module. Reference data was calculated for future benchmarking. Dose response calculated for the different models varied much more widely for the TG166 benchmark than for the proposed benchmark, which had much lower sensitivity to the choice of DVH dose points. This work was supported by National Cancer Institute Grant R01CA140735.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

TU-C-201-00: Clinical Implementation of HDR Brachytherapy

Recent use of HDR has increased while planning has become more complex often necessitating 3D image-based planning. While many guidelines for the use of HDR exist, they have not kept pace with the increased complexity of 3D image-based planning. Furthermore, no comprehensive document exists to describe the wide variety of current HDR clinical indications. This educational session aims to summarize existing national and international guidelines for the safe implementation of an HDR program. A summary of HDR afterloaders available on the market and their existing applicators will be provided, with guidance on how to select the best fit for each institution’s needs. Finally, the use of checklists will be discussed as a means to implement a safe and efficient HDR program and as a method by which to verify the quality of an existing HDR program. This session will provide the perspective of expert HDR physicists as well as the perspective of a new HDR user. Learning Objectives: Summarize national and international safety and staffing guidelines for HDR implementation Discuss the process of afterloader and applicator selection for gynecologic, prostate, breast, interstitial, surface treatments Learn about the use of an audit checklist tool to measure of quality control of a new or existing HDR program Describe the evolving use of checklists within an HDR program.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

TU-C-201-01: Clinical Implementation of HDR: A New User’s Perspective

Recent use of HDR has increased while planning has become more complex often necessitating 3D image-based planning. While many guidelines for the use of HDR exist, they have not kept pace with the increased complexity of 3D image-based planning. Furthermore, no comprehensive document exists to describe the wide variety of current HDR clinical indications. This educational session aims to summarize existing national and international guidelines for the safe implementation of an HDR program. A summary of HDR afterloaders available on the market and their existing applicators will be provided, with guidance on how to select the best fit for each institution’s needs. Finally, the use of checklists will be discussed as a means to implement a safe and efficient HDR program and as a method by which to verify the quality of an existing HDR program. This session will provide the perspective of expert HDR physicists as well as the perspective of a new HDR user. Learning Objectives: Summarize national and international safety and staffing guidelines for HDR implementation Discuss the process of afterloader and applicator selection for gynecologic, prostate, breast, interstitial, surface treatments Learn about the use of an audit checklist tool to measure of quality control of a new or existing HDR program Describe the evolving use of checklists within an HDR program.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

WE-E-304-02: Implementing SBRT Protocols: A NRG CIRO Perspective

SBRT is having a dramatic impact on radiation therapy of early-stage, locally advanced cancers. A number of national protocols have been and are being developed to assess the clinical efficacy of SBRT for various anatomical sites, such as lung and spine. Physics credentialing for participating and implementation of trial protocols involve a broad spectrum of requirements from image guidance, motion management, to planning technology and dosimetric constrains. For radiation facilities that do not have extensive experiences in SBRT treatment and protocol credentialing, these complex processes of credentialing and implementation could be very challenging and, sometimes, may lead to ineffective even unsuccessful execution of these processes. In this proposal, we will provide comprehensive review of some current SBRT protocols, explain the requirements and their underline rationales, illustrate representative failed and successful experiences, related to SBRT credentialing, and discuss strategies for effective SBRT credentialing and implementation. Learning Objectives: Understand requirements and challenges of SBRT credentailing and implentation Discuss processes and strategies of effective SBRT credentailing Discuss practical considerations, potential pitfalls and solutions of SBRT implentation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

WE-E-304-00: Implementing SBRT Protocols

SBRT is having a dramatic impact on radiation therapy of early-stage, locally advanced cancers. A number of national protocols have been and are being developed to assess the clinical efficacy of SBRT for various anatomical sites, such as lung and spine. Physics credentialing for participating and implementation of trial protocols involve a broad spectrum of requirements from image guidance, motion management, to planning technology and dosimetric constrains. For radiation facilities that do not have extensive experiences in SBRT treatment and protocol credentialing, these complex processes of credentialing and implementation could be very challenging and, sometimes, may lead to ineffective even unsuccessful execution of these processes. In this proposal, we will provide comprehensive review of some current SBRT protocols, explain the requirements and their underline rationales, illustrate representative failed and successful experiences, related to SBRT credentialing, and discuss strategies for effective SBRT credentialing and implementation. Learning Objectives: Understand requirements and challenges of SBRT credentailing and implentation Discuss processes and strategies of effective SBRT credentailing Discuss practical considerations, potential pitfalls and solutions of SBRT implentation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-A-BRA-02: Making the Most of a One Hour Lecture with Alternative Teaching Methodologies: Implementing Project-Based and Flipped Learning

Vic Montemayor - No one has been more passionate about improving the quality and effectiveness of the teaching of Medical Physics than Bill Hendee. It was in August of 2008 that the first AAPM Workshop on Becoming a Better Teacher of Medical Physics was held, organized and run by Bill Hendee. This was followed up in July of 2010 with a summer school on the same topic, again organized by Bill. There has been continued interest in alternate approaches to teaching medical physics since those initial gatherings. The momentum established by these workshops is made clear each year in the annual Innovation in Medical Physics Education session, which highlights work being done in all forms of medical physics education, from one-on-one residencies or classroom presentations to large-scale program revisions and on-line resources for international audiences. This symposium, presented on behalf of the Education Council, highlights the work of three finalists from past Innovation in Education sessions. Each will be presenting their approaches to and innovations in teaching medical physics. It is hoped that audience members interested in trying something new in their teaching of medical physics will find some of these ideas and approaches readily applicable to their own classrooms. Rebecca Howell - The presentation will discuss ways to maximize classroom learning, i.e., increasing the amount of material covered while also enhancing students’ understanding of the broader implications of the course topics. Specifically, the presentation will focus on two teaching methodologies, project based learning and flip learning. These teaching methods will be illustrated using an example of graduate medical physics course where both are used in conjunction with traditional lectures. Additionally, the presentation will focus on our experience implementing these methods including challenges that were overcome. Jay Burmeister - My presentation will discuss the incorporation of active learning techniques into a traditional medical physics classroom course. I will describe these techniques and how they were implemented as well as student performance before and after implementation. Student feedback indicated that these course changes improved their ability to actively assimilate the course content, thus improving their understanding of the material. Shahid Naqvi - My talk will focus on ways to help students visualize crucial concepts that lie at the core of radiation physics. Although particle tracks generated by Monte Carlo simulations have served as an indispensable visualization tool, students often struggle to resolve the underlying physics from a simultaneous jumble of tracks. We can clarify the physics by “coding” the tracks, e.g., by coloring the tracks according to their “starting” or “crossing” regions. The regionally-coded tracks when overlaid with dose distributions help the students see the elusive connection between dose, kerma and electronic disequilibrium. Tracks coded according to local energy or energy-loss rate can illustrate the need for stopping power corrections in electron beams and explain the Bragg peak in a proton beam. Coding tracks according to parent interaction type and order can clarify the often misunderstood distinction between primary and scatter dose. The students can thus see the “whole” simultaneously with the “sum of the parts,” which enhances their physical insight and creates a sustainable foundation for further learning. After the presentations the speakers and moderator will be open to questions and discussion with the audience members. Learning Objectives: Be able to explain Project-Based Learning and how can it be incorporated into a Medical Physics classroom. Be able to explain Flipped Learning and how can it be incorporated into a Medical Physics classroom. Be able to explain active-learning strategies for the teaching of Medical Physics. Be able to explain how Monte Carlo simulations can be used to deepen a student’s understanding of radiation physics and dosimetry.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2016

SU-F-SPS-06: Implementation of a Back-Projection Algorithm for 2D in Vivo Dosimetry with An EPID System

Purpose: To implement a back-projection algorithm for 2D dose reconstructions for in vivo dosimetry in radiation therapy using an Electronic Portal Imaging Device (EPID) based on amorphous silicon. Methods: An EPID system was used to calculate dose-response function, pixel sensitivity map, exponential scatter kernels and beam hardenig correction for the back-projection algorithm. All measurements were done with a 6 MV beam. A 2D dose reconstruction for an irradiated water phantom (30×30×30 cm{sup 3}) was done to verify the algorithm implementation. Gamma index evaluation between the 2D reconstructed dose and the calculated with a treatment planning system (TPS) was done. Results: A linear fit was found for the dose-response function. The pixel sensitivity map has a radial symmetry and was calculated with a profile of the pixel sensitivity variation. The parameters for the scatter kernels were determined only for a 6 MV beam. The primary dose was estimated applying the scatter kernel within EPID and scatter kernel within the patient. The beam hardening coefficient is σBH= 3.788×10{sup −4} cm{sup 2} and the effective linear attenuation coefficient is µAC= 0.06084 cm{sup −1}. The 95% of points evaluated had γ values not longer than the unity, with gamma criteria of ΔD = 3% and Δd = 3 mm, and within the 50% isodose surface. Conclusion: The use of EPID systems proved to be a fast tool for in vivo dosimetry, but the implementation is more complex that the elaborated for pre-treatment dose verification, therefore, a simplest method must be investigated. The accuracy of this method should be improved modifying the algorithm in order to compare lower isodose curves.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

A brain-plausible neuromorphic on-the-fly learning system implemented with magnetic domain wall analog memristors

Neuromorphic computing is an approach to efficiently solve complicated learning and cognition problems like the human brain using electronics. To efficiently implement the functionality of biological neurons, nanodevices and their implementations in circuits are exploited. Here, we describe a general-purpose spiking neuromorphic system that can solve on-the-fly learning problems, based on magnetic domain wall analog memristors (MAMs) that exhibit many different states with persistence over the lifetime of the device. The research includes micromagnetic and SPICE modeling of the MAM, CMOS neuromorphic analog circuit design of synapses incorporating the MAM, and the design of hybrid CMOS/MAM spiking neuronal networks in which the MAM provides variable synapse strength with persistence. Using this neuronal neuromorphic system, simulations show that the MAM-boosted neuromorphic system can achieve persistence, can demonstrate deterministic fast on-the-fly learning with the potential for reduced circuitry complexity, and can provide increased capabilities over an all-CMOS implementation.

42 ENGINEERING↗
DOE OSTI2019

Quantum Circuits for S-Box Implementation without Ancilla Qubits

A method is presented for implementing substitutions (S-boxes) in the form of quantum circuits without ancilla qubits. Quantum circuits are presented that implement substitutions in the GOST R 34.12-2015 block cipher “Magma” on four logical qubits, and the descriptions of quantum circuits implementing AES and GOST R 34.12-2015 “Kuznechik” S-boxes on 8 logical qubits—quantum circuits with minimum number of logical qubits—are given.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Implementing and evaluating a Gaussian mixture framework for identifying gene function from TnSeq data

The rapid acceleration of microbial genome sequencing increases opportunities to understand bacterial gene function. Unfortunately, only a small proportion of genes have been studied. Recently, TnSeq has been proposed as a cost-effective, highly reliable approach to predict gene functions as a response to changes in a cell’s fitness before-after genomic changes. However, major questions remain about how to best determine whether an observed quantitative change in fitness represents a meaningful change. To address the limitation, we develop a Gaussian mixture model framework for classifying gene function from TnSeq experiments. In order to implement the mixture model, we present the Expectation-Maximization algorithm and a hierarchical Bayesian model sampled using Stan’s Hamiltonian Monte-Carlo sampler. We compare these implementations against the frequentist method used in current TnSeq literature. From simulations and real data produced by E.coli TnSeq experiments, we show that the Bayesian implementation of the Gaussian mixture framework provides the most consistent classification results.

Li, Kevin↗
DOE OSTI2016

Open SHMEM Reference Implementation

OpenSHMEM is an effort to create a specification for a standardized API for parallel programming in the Partitioned Global Address Space. Along with the specification the project is also creating a reference implementation of the API. This implementation attempts to be portable, to allow it to be deployed in multiple environments, and to be a starting point for implementations targeted to particular hardware platforms. It will also serve as a springboard for future development of the API.

Pritchard, Howard↗
DOE OSTI2013

HSE12 implementation in libxc

This piece of software is a new feature implemented inside an existing open-source library. Specifically, it is a new implementation of a density functional (HSE, short for Heyd-Scuseria-Ernzerhof) for a repository of density functionals, the libxc library. It fixes some numerical problems with existing implementations, as outlined in a scientific paper recently submitted for publication. Density functionals are components of electronic structure simulations, which model properties of electrons inside molecules and crystals.

Moussa, JonathanE.↗