GraXML - Modular Geometric Modeler

Many entities managed by HEP Software Frameworks represent spatial (3-dimensional) real objects. Effective definition, manipulation and visualization of such objects is an indispensable functionality. GraXML is a modular Geometric Modeling toolkit capable of processing geometric data of various kinds (detector geometry, event geometry) from different sources and delivering them in ways suitable for further use. Geometric data are first modeled in one of the Generic Models. Those Models are then used to populate powerful Geometric Model based on the Java3D technology. While Java3D has been originally created just to provide visualization of 3D objects, its light weight and high functionality allow an effective reuse as a general geometric component. This is possible also thanks to a large overlap between graphical and general geometric functionality and modular design of Java3D itself. Its graphical functionalities also allow a natural visualization of all manipulated elements. All these techniques have been developed primarily (or only) for the Java environment. It is, however, possible to interface them transparently to Frameworks built in other languages, like for example C++. The GraXML toolkit has been tested with data from several sources, as for example ATLAS and ALICE detector description and ATLAS event data. Prototypes for other sources, like Geometry Description Markup Language (GDML) exist too and interface to any other source is easy to add.Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003. PSN THJT00

Organizing the Internet

This paper examines XML and its relationships with SGML (Standardized General Markup Language) and HTML (HyperText Markup Language). It examines the importance of metatags and the XML Document Type Definition (DTD) and proposed alternatives. It looks at the differences between the two types of XML data: “valid” and “well-formed” documents

Pattern Reification as the Basis for Description-Driven Systems

One of the main factors driving object-oriented software development for information systems is the requirement for systems to be tolerant to change. To address this issue in designing systems, this paper proposes a pattern-based, object-oriented, description-driven system (DDS) architecture as an extension to the standard UML four-layer meta-model. A DDS architecture is proposed in which aspects of both static and dynamic systems behavior can be captured via descriptive models and meta-models. The proposed architecture embodies four main elements - firstly, the adoption of a multi-layered meta-modeling architecture and reflective meta-level architecture, secondly the identification of four data modeling relationships that can be made explicit such that they can be modified dynamically, thirdly the identification of five design patterns which have emerged from practice and have proved essential in providing reusable building blocks for data management, and fourthly the encoding of the structural properties of the five design patterns by means of one fundamental pattern, the Graph pattern. A practical example of this philosophy, the CRISTAL project, is used to demonstrate the use of description-driven data objects to handle system evolution.Comment: 20 pages, 10 figure

SBML models and MathSBML

MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation

Interchange of electronic design through VHDL and EIS

The need for both robust and unambiguous electronic designs is a direct requirement of the astonishing growth in design and manufacturing capability during recent years. In order to manage the plethora of designs, and have the design data both interchangeable and interoperable, the Very High Speed Integrated Circuits (VHSIC) program is developing two major standards for the electronic design community. The VHSIC Hardware Description Language (VHDL) is designed to be the lingua franca for transmission of design data between designers and their environments. The Engineering Information System (EIS) is designed to ease the integration of data betweeen diverse design automation systems. This paper describes the rationale for the necessity for these two standards and how they provide a synergistic expressive capability across the macrocosm of design environments

A pollen identification expert system ; an application of expert system techniques to biological identification : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Computer Science Massey University

The application of expert systems techniques to biological identification has been investigated and a system developed which assists a user to identify and count air-borne pollen grains. The present system uses a modified taxonomic data matrix as the structure for the knowledge base. This allows domain experts to easily assess and modify the knowledge using a familiar data structure. The data structure can be easily converted to rules or a simple frame-based structure if required for other applications. A method of ranking the importance of characters for identifying each taxon has been developed which assists the system to quickly narrow an identification by rejecting or accepting candidate taxa. This method is very similar to that used by domain experts

GenomeViz: visualizing microbial genomes

BACKGROUND: An increasing number of microbial genomes are being sequenced and deposited in public databases. In addition, several closely related strains are also being sequenced in order to understand the genetic basis of diversity and mechanisms that lead to the acquisition of new genetic traits. These exercises have necessitated the requirement for visualizing microbial genomes and performing genome comparisons on a finer scale. We have developed GenomeViz to enable rapid visualization and subsequent comparisons of several microbial genomes in an interactive environment. RESULTS: Here we describe a program that allows visualization of both qualitative and quantitative information from complete and partially sequenced microbial genomes. Using GenomeViz, data deriving from studies on genomic islands, gene/protein classifications, GC content, GC skew, whole genome alignments, microarrays and proteomics may be plotted. Several genomes can be visualized interactively at the same time from a comparative genomic perspective and publication quality circular genome plots can be created. CONCLUSIONS: GenomeViz should allow researchers to perform visualization and comparative analysis of up to eight different microbial genomes simultaneously

MultiView : a methodology for supporting multiple view schemata in object-oriented databases

It has been widely recognized that object-oriented database (OODB) technology needs to be extended to provide a mechanism similar to views in relational database systems. We define an object-oriented view to be an arbitrarily complex virtual schema graph with possibly restructured generalization and decomposition hierarchies - rather than just one virtual class as has been proposed in the literature. In this paper, we propose a methodology, called MultiView, for supporting multiple such view schemata. MultiView breaks the schema design task into the following independent and well-defined subtasks: (1) the customization of type descriptions and object sets of existing classes by deriving virtual classes, (2) the integration of all derived classes into one consistent global schema graph, and (3) the definition of arbitrarily complex view schemata on this augmented global schema. For the first task of MultiView, we define a set of object algebra operators that can be used by the view definer for class customization. For the second task of MultiView, we propose an algorithm that automatically integrates these newly derived virtual classes into the global schema. We solve the third task of MultiView by first letting the view definer explicitly select the desired view classes from the global schema using a view definition language and then by automatically generating a view class hierarchy for these selected classes. In addition, we present algorithms that verify the closure property of a view and, if found to be incomplete, transform it into a closed, yet minimal, view. In this paper, we introduce the fundamental concept of view independence and show MultiView to be view independent. We also outline implementation techniques for realizing MultiView with existing OODB technology