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At least 37 records · Page 2

Community-Driven Methods for Open and Reproducible Software Tools for Analyzing Datasets from Atom Probe Microscopy

Atom probe tomography, and related methods, probe the three-dimensional architecture of a material. The software tools that microscopists use, and how these tools are connected into workflows, makes a substantial contribution to the accuracy and precision of such a material characterization experiment. Typically, we adapt methods from other communities like mathematics, data science, computational geometry, artificial intelligence, or scientific computing. We also realize that improving on research data management is a challenge when it comes to align with the FAIR data stewardship principles. Faced with this global challenge, we are convinced that collaborating is useful. Here, we report the results and challenges with an inter-laboratory call for developing test cases for several types of atom probe software tools. The results support why defining detailed recipes of software workflows and sharing these recipes is necessary and rewarding: Open source tools and (meta)data exchange can help to make our day-to-day data processing tasks become more efficient, the training of new users and knowledge transfer become easier, and assist us with automated quantification of uncertainties to gain access to substantiated results.

36 MATERIALS SCIENCE↗

Graphics software tool for VT terminals (VTGRAPH)

VTGRAPH is a graphics software tool for using DEC/VT or VT compatible terminals. It allows the user to deal with computer environments which use VT terminals for window management and graphics systems. VTGRAPH was developed using the Re'Gis Graphics set and it was written in FORTRAN language. It provides window management and a PLOT10-like package plus color or shade capability.

Wang, Caroline↗

Software Tool Integrating Data Flow Diagrams and Petri Nets

Data Flow Diagram - Petri Net (DFPN) is a software tool for analyzing other software to be developed. The full name of this program reflects its design, which combines the benefit of data-flow diagrams (which are typically favored by software analysts) with the power and precision of Petri-net models, without requiring specialized Petri-net training. (A Petri net is a particular type of directed graph, a description of which would exceed the scope of this article.) DFPN assists a software analyst in drawing and specifying a data-flow diagram, then translates the diagram into a Petri net, then enables graphical tracing of execution paths through the Petri net for verification, by the end user, of the properties of the software to be developed. In comparison with prior means of verifying the properties of software to be developed, DFPN makes verification by the end user more nearly certain, thereby making it easier to identify and correct misconceptions earlier in the development process, when correction is less expensive. After the verification by the end user, DFPN generates a printable system specification in the form of descriptions of processes and data.

Thronesbery, Carroll↗

Parallel software tools at Langley Research Center

This document gives a brief overview of parallel software tools available on the Intel iPSC/860 parallel computer at Langley Research Center. It is intended to provide a source of information that is somewhat more concise than vendor-supplied material on the purpose and use of various tools. Each of the chapters on tools is organized in a similar manner covering an overview of the functionality, access information, how to effectively use the tool, observations about the tool and how it compares to similar software, known problems or shortfalls with the software, and reference documentation. It is primarily intended for users of the iPSC/860 at Langley Research Center and is appropriate for both the experienced and novice user.

Moitra, Stuti↗

SU-F-T-300: Impact of Electron Density Modeling of ArcCHECK Cylindricaldiode Array On 3DVH Patient Specific QA Software Tool Analysis

Purpose: 3DVH software is a patient specific quality assurance tool which estimates the 3D dose to the patient specific geometry with the help of Planned Dose Perturbation algorithm. The purpose of this study is to evaluate the impact of HU value of ArcCHECK phantom entered in Eclipse TPS on 3D dose & DVH QA analysis. Methods: Manufacturer of ArcCHECK phantom provides CT data set of phantom & recommends considering it as a homogeneous phantom with electron density (1.19 gm/cc or 282 HU) close to PMMA. We performed this study on Eclipse TPS (V13, VMS) & trueBEAM STx VMS Linac & ArcCHECK phantom (SNC). Plans were generated for 6MV photon beam, 20cm×20cm field size at isocentre & SPD (Source to phantom distance) of 86.7 cm to deliver 100cGy at isocentre. 3DVH software requires patients DICOM data generated by TPS & plan delivered on ArcCHECK phantom. Plans were generated in TPS by assigning different HU values to phantom. We analyzed gamma index & the dose profile for all plans along vertical down direction of beam’s central axis for Entry, Exit & Isocentre dose. Results: The global gamma passing rate (2% & 2mm) for manufacturer recommended HU value 282 was 96.3%. Detector entry, Isocentre & detector exit Doses were 1.9048 (1.9270), 1.00(1.0199) & 0.5078(0.527) Gy for TPS (Measured) respectively.The global gamma passing rate for electron density 1.1302 gm/cc was 98.6%. Detector entry, Isocentre & detector exit Doses were 1.8714 (1.8873), 1.00(0.9988) & 0.5211(0.516) Gy for TPS (Measured) respectively. Conclusion: Electron density value assigned by manufacturer does not hold true for every user. Proper modeling of electron density of ArcCHECK in TPS is essential to avoid systematic error in dose calculation of patient specific QA.

60 APPLIED LIFE SCIENCES↗

Evaluating Software Tools for Lipid Identification from Ion Mobility Spectrometry–Mass Spectrometry Lipidomics Data

The unambiguous identification of lipids is a critical component of lipidomics studies and greatly impacts the interpretation and significance of analyses as well as the ultimate biological understandings derived from measurements. The level of structural detail that is available for lipid identifications is largely determined by the analytical platform being used. Mass spectrometry (MS) coupled with liquid chromatography (LC) is the predominant combination of analytical techniques used for lipidomics studies, and these methods can provide fairly detailed lipid identification. More recently, ion mobility spectrometry (IMS) has begun to see greater adoption in lipidomics studies thanks to the additional dimension of separation that it provides and the added structural information that can support lipid identification. At present, relatively few software tools are available for IMS-MS lipidomics data analysis, which reflects the still limited adoption of IMS as well as the limited software support. This fact is even more pronounced for isomer identifications, such as the determination of double bond positions or integration with MS-based imaging. In this review, we survey the landscape of software tools that are available for the analysis of IMS-MS-based lipidomics data and we evaluate lipid identifications produced by these tools using open-access data sourced from the peer-reviewed lipidomics literature.

59 BASIC BIOLOGICAL SCIENCES↗

Git and Software Tools for CTS

This presentation will provide an overview of the progress made helping the EDX4CCS, SMART, and NRAP projects virtualize their CO2 Transport and Storage software tools to boost their stakeholder availability through the DisCO2ver platform. This presentation will also cover helpful software development tools with a focus on researchers and developers who have not had formal training or many years of experience in software engineering best practices.

Zaengle, Dakota↗

A software tool for dataflow graph scheduling

A graph-theoretic design process and software tool is presented for selecting a multiprocessing scheduling solution for a class of computational problems. The problems of interest are those that can be described using a dataflow graph and are intended to be executed repetitively on multiple processors. The dataflow paradigm is very useful in exposing the parallelism inherent in algorithms. It provides a graphical and mathematical model which describes a partial ordering of algorithm tasks based on data precedence.

Jones, Robert L., III↗

Use of software tools in the development of real time software systems

The transformation of a preexisting software system into a larger and more versatile system with different mission requirements is discussed. The history of this transformation is used to illustrate the use of structured real time programming techniques and tools to produce maintainable and somewhat transportable systems. The predecessor system is a single ground diagnostic system; its purpose is to exercise a computer controlled hardware set prior to its deployment in its functional environment, as well as test the equipment set by supplying certain well known stimulas. The successor system (FTE) is required to perform certain testing and control functions while this hardware set is in its functional environment. Both systems must deal with heavy user input/output loads and a new I/O requirement is included in the design of the FTF system. Human factors are enhanced by adding an improved console interface and special function keyboard handler. The additional features require the inclusion of much new software to the original set from which FTF was developed. As a result, it is necessary to split the system into a duel programming configuration with high rates of interground communications. A generalized information routing mechanism is used to support this configuration.

Garvey, R. C.↗

An evaluation of software tools for the design and development of cockpit displays

The use of all-glass cockpits at the NASA Langley Research Center (LaRC) simulation facility has changed the means of design, development, and maintenance of instrument displays. The human-machine interface has evolved from a physical hardware device to a software-generated electronic display system. This has subsequently caused an increased workload at the facility. As computer processing power increases and the glass cockpit becomes predominant in facilities, software tools used in the design and development of cockpit displays are becoming both feasible and necessary for a more productive simulation environment. This paper defines LaRC requirements of a display software development tool and compares two available applications against these requirements. As a part of the software engineering process, these tools reduce development time, provide a common platform for display development, and produce exceptional real-time results.

Ellis, Thomas D., Jr.↗

Advanced software tools space station focused technology

Information is given in outline form on advanced software tools for the Space Station data management system. The Space Station data management system is identified as a highly distributed system with payload users controlling experiments and processing payload data from home facilities.

Nelson, Robert W.↗

Software Tools to Support Research on Airport Departure Planning

A simple, portable and useful collection of software tools has been developed for the analysis of airport surface traffic. The tools are based on a flexible and robust traffic-flow model, and include calibration, validation and simulation functionality for this model. Several different interfaces have been developed to help promote usage of these tools, including a portable Matlab(TM) implementation of the basic algorithms; a web-based interface which provides online access to automated analyses of airport traffic based on a database of real-world operations data which covers over 250 U.S. airports over a 5-year period; and an interactive simulation-based tool currently in use as part of a college-level educational module. More advanced applications for airport departure traffic include taxi-time prediction and evaluation of "windowing" congestion control.

Carr, Francis↗

ProZES: the methodology and software tool for assessment of assigned share of radiation in probability of cancer occurrence

ProZES is a software tool for estimating the probability that a given cancer was caused by preceding exposure to ionising radiation. ProZES calculates this probability, the assigned share, for solid cancers and hematopoietic malignant diseases, in cases of exposures to low-LET radiation, and for lung cancer in cases of exposure to radon. User-specified inputs include birth year, sex, type of diagnosed cancer, age at diagnosis, radiation exposure history and characteristics, and smoking behaviour for lung cancer. Cancer risk models are an essential part of ProZES. Linking disease and exposure to radiation involves several methodological aspects, and assessment of uncertainties received particular attention. ProZES systematically uses the principle of multi-model inference. Models of radiation risk were either newly developed or critically re-evaluated for ProZES, including dedicated models for frequent types of cancer and, for less common diseases, models for groups of functionally similar cancer sites. The low-LET models originate mostly from the study of atomic bomb survivors in Hiroshima and Nagasaki. Risks predicted by these models are adjusted to be applicable to the population of Germany and to different time periods. Adjustment factors for low dose rates and for a reduced risk during the minimum latency time between exposure and cancer are also applied. The development of the methodology and software was initiated and supported by the German Federal Ministry for the Environment, Nature Conservation and Nuclear Safety (BMU) taking up advice by the German Commission on Radiological Protection (SSK, Strahlenschutzkommission). These provide the scientific basis to support decision making on compensation claims regarding malignancies following occupational exposure to radiation in Germany.

97 MATHEMATICS AND COMPUTING↗

Constructing an advanced software tool for planetary atmospheric modeling

A prototype is described that can serve as a scientific-modeling software tool to facilitate the development of useful scientific models. The prototype is developed for applications to planetary modeling, and specific examples are given that relate to the atmosphere of Titan. The scientific modeling tool employs a high-level domain-specific modeling language, several data-display facilities, and a library of experimental datasets and scientific equations. The planetary modeling prototype links uncomputed physical variables to computed variables with computational transformations based on a backchaining procedure. The system - implemented in LISP with an object-oriented knowledge-representation tool - is run on a workstation that provides interface with several models. The prototype is expected to form the basis for a sophisticated modeling tool that can permit active experimentation.

Keller, Richard M.↗