The Persint visualization program for the ATLAS experiment

The Persint program is designed for the three-dimensional representation of objects and for the interfacing and access to a variety of independent applications, in a fully interactive way. Facilities are provided for the spatial navigation and the definition of the visualization properties, in order to interactively set the viewing and viewed points, and to obtain the desired perspective. In parallel, applications may be launched through the use of dedicated interfaces, such as the interactive reconstruction and display of physics events. Recent developments have focalized on the interfacing to the XML ATLAS General Detector Description AGDD, making it a widely used tool for XML developers. The graphics capabilities of this program were exploited in the context of the ATLAS 2002 Muon Testbeam where it was used as an online event display, integrated in the online software framework and participating in the commissioning and debug of the detector system.Comment: 9 pages, 10 figures, proceedings of CHEP200

An Investigation into Animating Plant Structures within Real-time Constraints

This paper is an analysis of current developments in rendering botanical structures for scientic and entertainment purposes with a focus on visualising growth. The choices of practical investigations produce a novel approach for parallel parsing of difficult bracketed L-Systems, based upon the work of Lipp, Wonka and Wimmer (2010). Alongside this is a general overview of the issues involved when looking at growing systems, technical details involving programming for the Graphics Processing Unit (GPU) and other possible solutions for further work that also could achieve the project's goals

Utilizing a 3D game engine to develop a virtual design review system

A design review process is where information is exchanged between the designers and design reviewers to resolve any potential design related issues, and to ensure that the interests and goals of the owner are met. The effective execution of design review will minimize potential errors or conflicts, reduce the time for review, shorten the project life-cycle, allow for earlier occupancy, and ultimately translate into significant total project savings to the owner. However, the current methods of design review are still heavily relying on 2D paper-based format, sequential and lack central and integrated information base for efficient exchange and flow of information. There is thus a need for the use of a new medium that allow for 3D visualization of designs, collaboration among designers and design reviewers, and early and easy access to design review information. This paper documents the innovative utilization of a 3D game engine, the Torque Game Engine as the underlying tool and enabling technology for a design review system, the Virtual Design Review System for architectural designs. Two major elements are incorporated; 1) a 3D game engine as the driving tool for the development and implementation of design review processes, and 2) a virtual environment as the medium for design review, where visualization of design and design review information is based on sound principles of GUI design. The development of the VDRS involves two major phases; firstly, the creation of the assets and the assembly of the virtual environment, and secondly, the modification of existing functions or introducing new functionality through programming of the 3D game engine in order to support design review in a virtual environment. The features that are included in the VDRS are support for database, real-time collaboration across network, viewing and navigation modes, 3D object manipulation, parametric input, GUI, and organization for 3D objects

Requirements for a geometry programming language for CFD applications

A number of typical problems faced by the aerodynamicist in using computational fluid dynamics are presented to illustrate the need for a geometry programming language. The overall requirements for such a language are illustrated by examples from the Boeing Aero Grid and Paneling System (AGPS). Some of the problems in building such a system are also reviewed along with suggestions as to what to look for when evaluating new software problems

Declarative Ajax Web Applications through SQL++ on a Unified Application State

Implementing even a conceptually simple web application requires an inordinate amount of time. FORWARD addresses three problems that reduce developer productivity: (a) Impedance mismatch across the multiple languages used at different tiers of the application architecture. (b) Distributed data access across the multiple data sources of the application (SQL database, user input of the browser page, session data in the application server, etc). (c) Asynchronous, incremental modification of the pages, as performed by Ajax actions. FORWARD belongs to a novel family of web application frameworks that attack impedance mismatch by offering a single unifying language. FORWARD's language is SQL++, a minimally extended SQL. FORWARD's architecture is based on two novel cornerstones: (a) A Unified Application State (UAS), which is a virtual database over the multiple data sources. The UAS is accessed via distributed SQL++ queries, therefore resolving the distributed data access problem. (b) Declarative page specifications, which treat the data displayed by pages as rendered SQL++ page queries. The resulting pages are automatically incrementally modified by FORWARD. User input on the page becomes part of the UAS. We show that SQL++ captures the semi-structured nature of web pages and subsumes the data models of two important data sources of the UAS: SQL databases and JavaScript components. We show that simple markup is sufficient for creating Ajax displays and for modeling user input on the page as UAS data sources. Finally, we discuss the page specification syntax and semantics that are needed in order to avoid race conditions and conflicts between the user input and the automated Ajax page modifications. FORWARD has been used in the development of eight commercial and academic applications. An alpha-release web-based IDE (itself built in FORWARD) enables development in the cloud.Comment: Proceedings of the 14th International Symposium on Database Programming Languages (DBPL 2013), August 30, 2013, Riva del Garda, Trento, Ital

A Concurrency-Agnostic Protocol for Multi-Paradigm Concurrent Debugging Tools

Today's complex software systems combine high-level concurrency models. Each model is used to solve a specific set of problems. Unfortunately, debuggers support only the low-level notions of threads and shared memory, forcing developers to reason about these notions instead of the high-level concurrency models they chose. This paper proposes a concurrency-agnostic debugger protocol that decouples the debugger from the concurrency models employed by the target application. As a result, the underlying language runtime can define custom breakpoints, stepping operations, and execution events for each concurrency model it supports, and a debugger can expose them without having to be specifically adapted. We evaluated the generality of the protocol by applying it to SOMns, a Newspeak implementation, which supports a diversity of concurrency models including communicating sequential processes, communicating event loops, threads and locks, fork/join parallelism, and software transactional memory. We implemented 21 breakpoints and 20 stepping operations for these concurrency models. For none of these, the debugger needed to be changed. Furthermore, we visualize all concurrent interactions independently of a specific concurrency model. To show that tooling for a specific concurrency model is possible, we visualize actor turns and message sends separately.Comment: International Symposium on Dynamic Language

Mapping the Space of Genomic Signatures

We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR), is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM), implicitly compares the occurrences of oligomers of length up to $k$ (herein $k=9$) in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS) to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence homology and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (super)kingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information.Comment: 14 pages, 7 figures. arXiv admin note: substantial text overlap with arXiv:1307.375