Topology Verification for Isosurface Extraction

The broad goals of verifiable visualization rely on correct algorithmic implementations. We extend a framework for verification of isosurfacing implementations to check topological properties. Specifically, we use stratified Morse theory and digital topology to design algorithms which verify topological invariants. Our extended framework reveals unexpected behavior and coding mistakes in popular publicly available isosurface codes.

Tomotherapy dose distribution verification using MAGIC-f polymer gel dosimetry

Purpose: This paper presents the application of MAGIC-f gel in a three-dimensional dose distribution measurement and its ability to accurately measure the dose distribution from a tomotherapy unit. Methods: A prostate intensity-modulated radiation therapy (IMRT) irradiation was simulated in the gel phantom and the treatment was delivered by a TomoTherapy equipment. Dose distribution was evaluated by the R2 distribution measured in magnetic resonance imaging. Results: A high similarity was found by overlapping of isodoses of the dose distribution measured with the gel and expected by the treatment planning system (TPS). Another analysis was done by comparing the relative absorbed dose profiles in the measured and in the expected dose distributions extracted along indicated lines of the volume and the results were also in agreement. The gamma index analysis was also applied to the data and a high pass rate was achieved (88.4% for analysis using 3%/3 mm and of 96.5% using 4%/4 mm). The real three-dimensional analysis compared the dose-volume histograms measured for the planning volumes and expected by the treatment planning, being the results also in good agreement by the overlapping of the curves. Conclusions: These results show that MAGIC-f gel is a promise for tridimensional dose distribution measurements. (C) 2012 American Association of Physicists in Medicine. [http://dx.doi.org/10.1118/1.4704496]

URANS calculations for smooth circular cylinder flow in a wide range of Reynolds Numbers: solution verification and validation

The flow around circular smooth fixed cylinder in a large range of Reynolds numbers is considered in this paper. In order to investigate this canonical case, we perform CFD calculations and apply verification & validation (V&V) procedures to draw conclusions regarding numerical error and, afterwards, assess the modeling errors and capabilities of this (U)RANS method to solve the problem. Eight Reynolds numbers between Re = 10 and Re 5 x 10(5) will be presented with, at least, four geometrically similar grids and five discretization in time for each case (when unsteady), together with strict control of iterative and round-off errors, allowing a consistent verification analysis with uncertainty estimation. Two-dimensional RANS, steady or unsteady, laminar or turbulent calculations are performed. The original 1994 k - omega SST turbulence model by Menter is used to model turbulence. The validation procedure is performed by comparing the numerical results with an extensive set of experimental results compiled from the literature. [DOI: 10.1115/1.4007571]

A rigorous approach to facilitate and guarantee the correctness of the genetic testing management in human genome information systems

Abstract Background Recent medical and biological technology advances have stimulated the development of new testing systems that have been providing huge, varied amounts of molecular and clinical data. Growing data volumes pose significant challenges for information processing systems in research centers. Additionally, the routines of genomics laboratory are typically characterized by high parallelism in testing and constant procedure changes. Results This paper describes a formal approach to address this challenge through the implementation of a genetic testing management system applied to human genome laboratory. We introduced the Human Genome Research Center Information System (CEGH) in Brazil, a system that is able to support constant changes in human genome testing and can provide patients updated results based on the most recent and validated genetic knowledge. Our approach uses a common repository for process planning to ensure reusability, specification, instantiation, monitoring, and execution of processes, which are defined using a relational database and rigorous control flow specifications based on process algebra (ACP). The main difference between our approach and related works is that we were able to join two important aspects: 1) process scalability achieved through relational database implementation, and 2) correctness of processes using process algebra. Furthermore, the software allows end users to define genetic testing without requiring any knowledge about business process notation or process algebra. Conclusions This paper presents the CEGH information system that is a Laboratory Information Management System (LIMS) based on a formal framework to support genetic testing management for Mendelian disorder studies. We have proved the feasibility and showed usability benefits of a rigorous approach that is able to specify, validate, and perform genetic testing using easy end user interfaces.