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Introduction: Cybersecurity and Software Assurance Minitrack

Modern society is dependent on software systems of remarkable scope and complexity. Yet methods for assuring their security and functionality have not kept pace. The result is persistent compromises and failures despite best efforts. Cybersecurity methods must work together for situational awareness, attack prevention and detection, threat attribution, minimization of consequences, and attack recovery. Because defective software cannot be secure, assurance technologies must play a central role in cybersecurity approaches. There is increasing recognition of the need for rigorous methods for cybersecurity and software assurance. The goal of this minitrack is to develop science foundations, technologies, and practices that can improve the security and dependability of complex systems.

Burns, Luanne↗

A Tale from the Trenches: Applying Metamorphic and Differential Testing to Bioinformatics Software

Metamorphic and differential testing have been proposed as best practices for testing software that is difficult to test, such as for programs in scientific domains. An assumption is that these approaches can be easily customized and applied to almost any domain. However, scientific software is often data-driven, and metamorphic relations may require significant domain knowledge to develop. In addition, tools are often written for ad-hoc experimentation by the scientists and often embed many assumptions about the importance and representation of different natural phenomena. In this paper, we present our experience applying both metamorphic and differential testing to a set of four computational biology tools that predict the growth of an organism. While our original goal was to evaluate these techniques to improve our system-level testing, we encountered multiple roadblocks along the way. Although we did find faults (some confirmed by developers), we also uncovered a set of challenges, including the considerable manual effort required for (a) defining domain-specific tests, (b) validating correctness, and (c) distinguishing between issues stemming from poor data and those arising from incorrect software.

Marsh, Alexis L [Iowa State University/Ames Labora↗

Virtual Framework for Development and Testing of Federation Software Stack

Softwarization of networked infrastructures combined with containerization of codes promises unprecedented computing capabilities distributed across the federations of computing systems and physical instruments. The development and testing of a software stack that implements these capabilities over an expensive physical production infrastructure is not cost-effective, and in the early stages, may potentially cause service disruptions. To address these aspects, we develop the Virtual Federated Science Instrument Environment (VFSIE), a digital twin of the physical infrastructure that emulates a multi-site federation. Each federated site is emulated using containers and virtual hosts that are connected over local-area networks, and the sites, in turn, are connected over an emulated wide-area network. We describe the framework design and implementation details. We also illustrate its application by emulating a federation of four laboratories that use Jupyter Notebook for computations and the EPICS software system for instrument control.

Al Najjar, Anees↗

Managing Software Provenance to Enhance Reproducibility in Computational Research

Scientific processes rely on software as an important tool for data acquisition, analysis, and discovery. Over the years, sustainable software development practices have made progress in being considered as an integral component of research. However, management of computation-based scientific studies is often left to individual researchers who design their computational experiments based on personal preferences and the nature of the study. Here, we believe that the quality, efficiency, and reproducibility of computation-based scientific research can be improved by explicitly creating an execution environment that allows researchers to provide a clear record of traceability. This is particularly relevant to complex computational studies in high-performance computing (HPC) environments. In this article, we review the documentation required to maintain a comprehensive record of HPC computational experiments for reproducibility. We also provide an overview of tools and practices that we have developed to perform such studies around Flash-X, a multiphysics scientific software.

97 MATHEMATICS AND COMPUTING↗

An Integrated Software Package to Enable Predictive Simulation Capabilities

The power grid is increasing in complexity due to the deployment of smart grid technologies. Such technologies vastly increase the size and complexity of power grid systems for simulation and modeling. This increasing complexity necessitates not only the use of high-performance-computing (HPC) techniques, but a smooth, well-integrated interplay between HPC applications. This paper presents a new integrated software package that integrates HPC applications and a web-based visualization tool based on a middleware framework. This framework can support the data communication between different applications. Case studies with a large power system demonstrate the predictive capability brought by the integrated software package, as well as the better situational awareness provided by the web-based visualization tool in a live mode. Test results validate the effectiveness and usability of the integrated software package.

Chen, Yousu↗

An Extensible Software and Communication Platform for Distributed Energy Resource Management

This paper introduces a novel Distributed Extensible Grid Control (DEGC) software and communication platform to facilitate the control of distributed energy resources on electric grids. The DEGC software platform leverages state-of-the-art advances in secure, distributed communication and decentralized authorization and authentication. We discuss how these advances enable the kind of robust and secure communication required for a distributed grid control platform, and show how DEGC applies these technologies to the agile development and deployment of grid software through an extensible and flexible API. Here, we describe how DEGC can implement both Volt-VAR voltage magnitude control and Phasor-Based Control as sample applications and demonstrate the DEGC platform in hardware with the demanding Phasor-Based Control test case, and provide performance metrics.

24 POWER TRANSMISSION AND DISTRIBUTION↗

A Survey of Software Techniques for Using Non-Volatile Memories for Storage and Main Memory Systems

Non-volatile memory (NVM) devices, such as Flash, phase change RAM, spin transfer torque RAM, and resistive RAM, offer several advantages and challenges when compared to conventional memory technologies, such as DRAM and magnetic hard disk drives (HDDs). Here, we present a survey of software techniques that have been proposed to exploit the advantages and mitigate the disadvantages of NVMs when used for designing memory systems, and, in particular, secondary storage (e.g., solid state drive) and main memory. Furthermore, we classify these software techniques along several dimensions to highlight their similarities and differences. Given that NVMs are growing in popularity, we believe that this survey will motivate further research in the field of software technology for NVMs.

97 MATHEMATICS AND COMPUTING↗

Westinghouse waste simulation and optimization software tool

Applications for dynamic simulation can be found in virtually all areas of process engineering. The tangible benefits of using dynamic simulation can be seen in tighter design, smoother start-ups and optimized operation. Thus, proper implementation of dynamic simulation can deliver substantial benefits. These benefits are typically derived from improved process understanding. Simulation gives confidence in evidence based decisions and enables users to try out lots of 'what if' scenarios until one is sure that a decision is the right one. In radioactive waste treatment tasks different kinds of waste with different volumes and properties have to be treated, e.g. from NPP operation or D and D activities. Finding a commercially and technically optimized waste treatment concept is a time consuming and difficult task. The Westinghouse Waste Simulation and Optimization Software Tool will enable the user to quickly generate reliable simulation models of various process applications based on equipment modules. These modules can be built with ease and be integrated into the simulation model. This capability ensures that this tool is applicable to typical waste treatment tasks. The identified waste streams and the selected treatment methods are the basis of the simulation and optimization software. After implementing suitable equipment data into the model, process requirements and waste treatment data are fed into the simulation to finally generate primary simulation results. A sensitivity analysis of automated optimization features of the software generates the lowest possible lifecycle cost for the simulated waste stream. In combination with proven waste management equipments and integrated waste management solutions, this tool provides reliable qualitative results that lead to an effective planning and minimizes the total project planning risk of any waste management activity. It is thus the ideal tool for designing a waste treatment facility in an optimum manner, taking account of the detailed waste stream and specific requirements. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Software-defined quantum network switching

We present the design and implementation of a software-defined quantum networking protocol and software switch integrated with a numerical quantum channel simulator. Our protocol design leverages recent advances in the OpenFlow protocol that enable software-defined control and management of optical network traffic using side-channel metadata. We implement this design using customization of the open source vSwitch for optical network routing, and we test the implementation using a numerical simulator of the quantum channel alongside actual network traffic. Our results support the integration of quantum communication with existing optical transport methods.

Humble, Travis↗

SU-E-T-103: Development and Implementation of Web Based Quality Control Software

Purpose: Historically many radiation medicine programs have maintained their Quality Control (QC) test results in paper records or Microsoft Excel worksheets. Both these approaches represent significant logistical challenges, and are not predisposed to data review and approval. It has been our group's aim to develop and implement web based software designed not just to record and store QC data in a centralized database, but to provide scheduling and data review tools to help manage a radiation therapy clinics Equipment Quality control program. Methods: The software was written in the Python programming language using the Django web framework. In order to promote collaboration and validation from other centres the code was made open source and is freely available to the public via an online source code repository. The code was written to provide a common user interface for data entry, formalize the review and approval process, and offer automated data trending and process control analysis of test results. Results: As of February 2014, our installation of QAtrack+ has 180 tests defined in its database and has collected ∼22 000 test results, all of which have been reviewed and approved by a physicist via QATrack+'s review tools. These results include records for quality control of Elekta accelerators, CT simulators, our brachytherapy programme, TomoTherapy and Cyberknife units. Currently at least 5 other centres are known to be running QAtrack+ clinically, forming the start of an international user community. Conclusion: QAtrack+ has proven to be an effective tool for collecting radiation therapy QC data, allowing for rapid review and trending of data for a wide variety of treatment units. As free and open source software, all source code, documentation and a bug tracker are available to the public at https://bitbucket.org/tohccmedphys/qatrackplus/.

07 ISOTOPE AND RADIATION SOURCES↗

SU-E-T-609: Evaluation of Transit Dosimetry Software Using Heterogeneous Phantom

Purpose: The purpose of this work was to evaluate limits and capabilities in the transit dosimetry software for use with the TomoTherapy system by irradiating a heterogeneous phantom. Methods: Helical TomoTherapy plan was created using CIRS phantom (model 062M) with nine various tissue equivalent inserts (lung inhale 0.2 g/cm{sup 3}, lung exhale 0.5 g/cm{sup 3}, adipose 0.96 g/cm{sup 3}, breast 0.99 g/cm{sup 3}, water 1.01 g/cm{sup 3}, muscle 1.06 g/cm{sup 3}, liver 1.07 g/cm{sup 3}, trabecular bone 1.16 g/cm{sup 3}, and dense bone 1.53 g/cm{sup 3}). Targets were contoured within every insert. The phantom was scanned with a 50 cm field of view and 3 mm slice width. Images were imported into the TomoTherapy TPS. A plan was generated to deliver 20 Gy to every insert (2 Gy per fraction) with a jaw width of 2.5 cm, a pitch of 0.430 and an actual modulation factor of 2.621. After the radiation delivery the planning CT, the RT structure, the RT plan, and the RT dose (DICOM format) as well as the exit detector sinogram were imported into the Dosimetry Check software (Math Resolutions, LLC). The 3D delivered doses were reconstructed from the exit detector data by correcting for phantom and couch attenuation. The resulting dose distribution were compared with the TPS planned dose using gamma index. Results: Using the clinical gamma criteria, 3% and 3 mm, all tissue equivalent inserts had a passing percentage of 100% except for 0.2 g/cm{sup 3} and 0.5 g/cm{sup 3} density inserts (gamma value of 81.67% and 99.18% respectively). Conclusion: The evaluated transit dosimetry software provides an independent verification of helical TomoTherapy plans giving additional confidence in the treatment delivery, however, an overestimation of the reconstructed dose in low density materials has been revealed. Implementation of Monte Carlo algorithm for exit dose reconstruction should improve dosimetric accuracy in heterogeneous patient tissues. Agreement with Math Resolutions.

60 APPLIED LIFE SCIENCES↗

SU-F-18C-08: A Validation Study of a Commercially Available Software Package's Absorbed Dose Estimates in a Physical Phantom

Purpose: This study assesses the accuracy of the absorbed dose estimates from CT scans generated by Monte Carlo (MC) simulation using a commercially available radiation dose monitoring software program. Methods: Axial CT studies of an anthropomorphic abdomen phantom with dose bores at a central location and 4 peripheral locations were conducted using a fixed tube current at 120 kV. A 100 mm ion chamber and a 0.6 cc ion chamber calibrated at diagnostic energy levels were used to measure dose in the phantom at each of the 5 dose bore locations. Simulations using the software program's Monte Carlo engine were run using a mathematical model of the anthropomorphic phantom to determine conversion coefficients between the CTDIvol used for the study and the dose at the location of the dose bores. Simulations were conducted using both the software's generic CT beam model and a refined model generated using HVL and bow tie filter profile measurements made on the scanner used for the study. Results: Monte Carlo simulations completed using the generalized beam model differed from the measured conversion factors by an absolute value average of 13.0% and 13.8% for the 100 mm and 0.6 cc ion chamber studies, respectively. The MC simulations using the scanner specific beam model generated conversion coefficients that differed from the CTDIvol to measured dose conversion coefficients by an absolute value average of 7.3% and 7.8% for the 100 mm and 0.6 cc ion chamber cases, respectively. Conclusion: A scanner specific beam model used in MC simulations generates more accurate dose conversion coefficients in an anthropomorphic phantom than those generated with a generalized beam model. Agreement between measured conversion coefficients and simulated values were less than 20% for all positions using the universal beam model.

07 ISOTOPE AND RADIATION SOURCES↗

TU-C-17A-03: An Integrated Contour Evaluation Software Tool Using Supervised Pattern Recognition for Radiotherapy

Purpose: Radiotherapy (RT) contours delineated either manually or semiautomatically require verification before clinical usage. Manual evaluation is very time consuming. A new integrated software tool using supervised pattern contour recognition was thus developed to facilitate this process. Methods: The contouring tool was developed using an object-oriented programming language C# and application programming interfaces, e.g. visualization toolkit (VTK). The C# language served as the tool design basis. The Accord.Net scientific computing libraries were utilized for the required statistical data processing and pattern recognition, while the VTK was used to build and render 3-D mesh models from critical RT structures in real-time and 360° visualization. Principal component analysis (PCA) was used for system self-updating geometry variations of normal structures based on physician-approved RT contours as a training dataset. The inhouse design of supervised PCA-based contour recognition method was used for automatically evaluating contour normality/abnormality. The function for reporting the contour evaluation results was implemented by using C# and Windows Form Designer. Results: The software input was RT simulation images and RT structures from commercial clinical treatment planning systems. Several abilities were demonstrated: automatic assessment of RT contours, file loading/saving of various modality medical images and RT contours, and generation/visualization of 3-D images and anatomical models. Moreover, it supported the 360° rendering of the RT structures in a multi-slice view, which allows physicians to visually check and edit abnormally contoured structures. Conclusion: This new software integrates the supervised learning framework with image processing and graphical visualization modules for RT contour verification. This tool has great potential for facilitating treatment planning with the assistance of an automatic contour evaluation module in avoiding unnecessary manual verification for physicians/dosimetrists. In addition, its nature as a compact and stand-alone tool allows for future extensibility to include additional functions for physicians’ clinical needs.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Methods, software and datasets to verify DVH calculations against analytical values: Twenty years late(r)

Purpose: The authors designed data, methods, and metrics that can serve as a standard, independent of any software package, to evaluate dose-volume histogram (DVH) calculation accuracy and detect limitations. The authors use simple geometrical objects at different orientations combined with dose grids of varying spatial resolution with linear 1D dose gradients; when combined, ground truth DVH curves can be calculated analytically in closed form to serve as the absolute standards. Methods: DICOM RT structure sets containing a small sphere, cylinder, and cone were created programmatically with axial plane spacing varying from 0.2 to 3 mm. Cylinders and cones were modeled in two different orientations with respect to the IEC 1217 Y axis. The contours were designed to stringently but methodically test voxelation methods required for DVH. Synthetic RT dose files were generated with 1D linear dose gradient and with grid resolution varying from 0.4 to 3 mm. Two commercial DVH algorithms—PINNACLE (Philips Radiation Oncology Systems) and PlanIQ (Sun Nuclear Corp.)—were tested against analytical values using custom, noncommercial analysis software. In Test 1, axial contour spacing was constant at 0.2 mm while dose grid resolution varied. In Tests 2 and 3, the dose grid resolution was matched to varying subsampled axial contours with spacing of 1, 2, and 3 mm, and difference analysis and metrics were employed: (1) histograms of the accuracy of various DVH parameters (total volume, D{sub max}, D{sub min}, and doses to % volume: D99, D95, D5, D1, D0.03 cm{sup 3}) and (2) volume errors extracted along the DVH curves were generated and summarized in tabular and graphical forms. Results: In Test 1, PINNACLE produced 52 deviations (15%) while PlanIQ produced 5 (1.5%). In Test 2, PINNACLE and PlanIQ differed from analytical by >3% in 93 (36%) and 18 (7%) times, respectively. Excluding D{sub min} and D{sub max} as least clinically relevant would result in 32 (15%) vs 5 (2%) scored deviations for PINNACLE vs PlanIQ in Test 1, while Test 2 would yield 53 (25%) vs 17 (8%). In Test 3, statistical analyses of volume errors extracted continuously along the curves show PINNACLE to have more errors and higher variability (relative to PlanIQ), primarily due to PINNACLE’s lack of sufficient 3D grid supersampling. Another major driver for PINNACLE errors is an inconsistency in implementation of the “end-capping”; the additional volume resulting from expanding superior and inferior contours halfway to the next slice is included in the total volume calculation, but dose voxels in this expanded volume are excluded from the DVH. PlanIQ had fewer deviations, and most were associated with a rotated cylinder modeled by rectangular axial contours; for coarser axial spacing, the limited number of cross-sectional rectangles hinders the ability to render the true structure volume. Conclusions: The method is applicable to any DVH-calculating software capable of importing DICOM RT structure set and dose objects (the authors’ examples are available for download). It includes a collection of tests that probe the design of the DVH algorithm, measure its accuracy, and identify failure modes. Merits and applicability of each test are discussed.

60 APPLIED LIFE SCIENCES↗

SU-E-T-76: A Software System to Monitor VMAT Plan Complexity in a Large Radiotherapy Centre

Purpose: To develop a system that analyses and reports the complexity of Volumetric Modulated Arc Therapy (VMAT) plans to aid in the decision making for streamlining patient specific dosimetric quality assurance (QA) tests. Methods: A software system, Delcheck, was developed in-house to calculate VMAT plan and delivery complexity using the treatment delivery file. Delcheck has the functionality to calculate multiple plan complexity metrics including the Li-Xing Modulation Index (LI-MI), multiplicative combination of Leaf Travel and Modulation Complexity Score (LTMCSv), Monitor Units per prescribed dose (MU/D) and the delivery complexity index (MIt) that incorporates the modulation of dose rate, leaf speed and gantry speed. Delcheck includes database functionality to store and compare plan metrics for a specified treatment site. The overall plan and delivery complexity is assessed based on the 95% conformance limit of the complexity metrics as Similar, More or Less complex. The functionality of the software was tested using 42 prostate conventional, 10 prostate SBRT and 15 prostate bed VMAT plans generated for an Elekta linear accelerator. Results: The mean(σ) of LI-MI for conventional, SBRT and prostate bed plans were 1690(486), 3215.4(1294) and 3258(982) respectively. The LTMCSv of the studied categories were 0.334(0.05), 0.325(0.07) and 0.3112(0.09). The MU/D of the studied categories were 2.4(0.4), 2.7(0.7) and 2.5(0.5). The MIt of the studied categories were 21.6(3.4), 18.2(3.0) and 35.9(6.6). The values of the complexity metrics show that LI-MI appeared to resolve the plan complexity better than LTMCSv and MU/D. The MIt value increased as the delivery complexity increased. Conclusion: The developed software was shown to be working as expected. In studied treatment categories Prostate bed plans are more complex in both plan and delivery and SBRT is more complex in plan and less complex in delivery as demonstrated by LI-MI and MIt. This project was funded through a Cancer Council NSW Project Grant (RG14-11)

60 APPLIED LIFE SCIENCES↗

SU-E-T-211: Comparison of Seven New TrueBeam Linacs with Enhanced Beam Data Conformance Using a Beam Comparison Software Tool

Purpose: To develop an independent software tool to assist in commissioning linacs with enhanced beam conformance, as well as perform ongoing QA for dosimetrically equivalent linacs. Methods: Linac manufacturers offer enhanced beam conformance as an option to allow for clinics to complete commissioning efficiently, as well as implement dosimetrically equivalent linacs. The specification for enhanced conformance includes PDD as well as profiles within 80% FWHM. Recently, we commissioned seven Varian TrueBeam linacs with enhanced beam conformance. We developed a software tool in Visual Basic to allow us to load the reference beam data and compare our beam data during commissioning to evaluate enhanced beam conformance. This tool also allowed us to upload our beam data used for commissioning our dosimetrically equivalent beam models to compare and tweak each of our linac beams to match our modelled data in Varian’s Eclipse TPS. This tool will also be used during annual QA of the linacs to compare our beam data to our baseline data, as required by TG-142. Results: Our software tool was used to check beam conformance for seven TrueBeam linacs that we commissioned in the past six months. Using our tool we found that the factory conformed linacs showed up to 3.82% difference in their beam profile data upon installation. Using our beam comparison tool, we were able to adjust the energy and profiles of our beams to accomplish a better than 1.00% point by point data conformance. Conclusion: The availability of quantitative comparison tools is essential to accept and commission linacs with enhanced beam conformance, as well as to beam match multiple linacs. We further intend to use the same tool to ensure our beam data conforms to the commissioning beam data during our annual QA in keeping with the requirements of TG-142.

43 PARTICLE ACCELERATORS↗

TU-PIS-Exhibit Hall-2: Deformable Image Registration, Contour Propagation, and Dose Mapping inMIM Maestro - MIM Software

Brachytherapy devices and software are designed to last for a certain period of time. Due to a number of considerations, such as material factors, wear-and-tear, backwards compatibility, and others, they all reach a date when they are no longer supported by the manufacturer. Most of these products have a limited duration for their use, and the information is provided to the user at time of purchase. Because of issues or concerns determined by the manufacturer, certain products are retired sooner than the anticipated date, and the user is immediately notified. In these situations, the institution is facing some difficult choices: remove these products from the clinic or perform tests and continue their usage. Both of these choices come with a financial burden: replacing the product or assuming a potential medicolegal liability. This session will provide attendees with the knowledge and tools to make better decisions when facing these issues. Learning Objectives: Understand the meaning of “end-of-life or “life expectancy” for brachytherapy devices and software Review items (devices and software) affected by “end-of-life” restrictions Learn how to effectively formulate “end-of-life” policies at your institution Learn about possible implications of “end-of-life” policy Review other possible approaches to “end-of-life” issue.

60 APPLIED LIFE SCIENCES↗

TU-D-201-01: Definition and Purpose of End-Of-Life for Brachytherapy Devices and Software

Brachytherapy devices and software are designed to last for a certain period of time. Due to a number of considerations, such as material factors, wear-and-tear, backwards compatibility, and others, they all reach a date when they are no longer supported by the manufacturer. Most of these products have a limited duration for their use, and the information is provided to the user at time of purchase. Because of issues or concerns determined by the manufacturer, certain products are retired sooner than the anticipated date, and the user is immediately notified. In these situations, the institution is facing some difficult choices: remove these products from the clinic or perform tests and continue their usage. Both of these choices come with a financial burden: replacing the product or assuming a potential medicolegal liability. This session will provide attendees with the knowledge and tools to make better decisions when facing these issues. Learning Objectives: Understand the meaning of “end-of-life or “life expectancy” for brachytherapy devices and software Review items (devices and software) affected by “end-of-life” restrictions Learn how to effectively formulate “end-of-life” policies at your institution Learn about possible implications of “end-of-life” policy Review other possible approaches to “end-of-life” issue.

60 APPLIED LIFE SCIENCES↗