XML-based File Format Research Articles

A Tool to Graphically Edit CP-Nets

Conditional preference networks (CP-nets) are a mathematical formalism for compactly representing preferences over combinatorial domains. The software package presented allows editing of CP-nets through a graphical interface, loads and saves to an XML-based file format, and detects properties of the currently loaded CP-net.

Cluster rendering on large high-resolution multi-displays using X3DOM and HTML

In this paper, we propose a platform-independent visualization method that uses HTML and X3DOM for large high-resolution displays. HTML is a platform-independent language used for developing web pages, and X3DOM is a Web 3D visualization framework based on X3D; X3D is a royalty-free ISO standard XML-based file format for representing a 3D scene graph. Large high-resolution displays are used in scientific visualization, immersive virtual reality environment, and collaborative designing to efficiently deliver a large amounts of information. We introduce a run-time cluster configuration method using the component technologies of HTML5 and a data distribution strategy for a cluster rendering system based on the X3DOM framework. The comparative performance analysis and visualization results in diverse large high-resolution displays and mobile devices using widespread web browsers are also introduced. Our approach provides a cluster rendering method that can be easily and readily applied for existing large high-resolution systems, involving various platforms, by enabling novel system architecture.

LCDD: A complete detector description package

LCDD has been developed to provide a complete detector description package for physics detector simulations using Geant4. All aspects of the experimental setup, such as the physical geometry, magnetic fields, and sensitive detector readouts, as well as control of the physics simulations, such as physics processes, interaction models and kinematic limits, are defined at runtime. Users are therefore able to concentrate on the design of the detector system without having to master the intricacies of C++ programming or being proficient in setting up their own Geant4 application. We describe both the XML-based file format and the processors which communicate this information to the underlying Geant4 simulation toolkit.

JqcML: an open-source java API for mass spectrometry quality control data in the qcML format.

The awareness that systematic quality control is an essential factor to enable the growth of proteomics into a mature analytical discipline has increased over the past few years. To this aim, a controlled vocabulary and document structure have recently been proposed by Walzer et al. to store and disseminate quality-control metrics for mass-spectrometry-based proteomics experiments, called qcML. To facilitate the adoption of this standardized quality control routine, we introduce jqcML, a Java application programming interface (API) for the qcML data format. First, jqcML provides a complete object model to represent qcML data. Second, jqcML provides the ability to read, write, and work in a uniform manner with qcML data from different sources, including the XML-based qcML file format and the relational database qcDB. Interaction with the XML-based file format is obtained through the Java Architecture for XML Binding (JAXB), while generic database functionality is obtained by the Java Persistence API (JPA). jqcML is released as open-source software under the permissive Apache 2.0 license and can be downloaded from https://bitbucket.org/proteinspector/jqcml .

Voxel2MCNP: a framework for modeling, simulation and evaluation of radiation transport scenarios for Monte Carlo codes

The basic idea of Voxel2MCNP is to provide a framework supporting users in modeling radiation transport scenarios using voxel phantoms and other geometric models, generating corresponding input for the Monte Carlo code MCNPX, and evaluating simulation output. Applications at Karlsruhe Institute of Technology are primarily whole and partial body counter calibration and calculation of dose conversion coefficients. A new generic data model describing data related to radiation transport, including phantom and detector geometries and their properties, sources, tallies and materials, has been developed. It is modular and generally independent of the targeted Monte Carlo code. The data model has been implemented as an XML-based file format to facilitate data exchange, and integrated with Voxel2MCNP to provide a common interface for modeling, visualization, and evaluation of data. Also, extensions to allow compatibility with several file formats, such as ENSDF for nuclear structure properties and radioactive decay data, SimpleGeo for solid geometry modeling, ImageJ for voxel lattices, and MCNPX’s MCTAL for simulation results have been added. The framework is presented and discussed in this paper and example workflows for body counter calibration and calculation of dose conversion coefficients is given to illustrate its application.

QwViz: Visualisation of quantum walks on graphs

qwViz is a software package for interactive visualisation of the time-evolution of quantum walks on arbitrarily complex graphs. The package is written in C and uses OpenGL to generate graphics in real-time. The qwViz package can be used to directly simulate discrete-time quantum walks on undirected graphs when provided with the adjacency matrix of the graph. For more detailed studies, qwViz can also be used to visualise externally generated quantum walk data written in an XML-based file format (QWML). Various aspects of the visualisation can be customised and manipulated in real-time, allowing quantum walk dynamics to be probed at various length and time scales. Program summaryProgram title:qwVizCatalogue identifier: AEJN_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJN_v1_0.htmlProgram obtainable from: CPC Program Library, Queenʼs University, Belfast, N. IrelandLicensing provisions: GNU General Public Licence version 3No. of lines in distributed program, including test data, etc.: 42 881No. of bytes in distributed program, including test data, etc.: 97 152Distribution format: tar.gzProgramming language: CComputer: 32-bit and 64-bit workstationOperating system: Linux, Mac OS X 10.5 (and later)RAM: Depends on size of graph, typically less than 50 MBClassification: 4.15, 14External routines: OpenGL, GLUT, Graphviz [1]Nature of problem: Simulation and visualisation of quantum walks on arbitrarily complex undirected graphs.Solution method: The program uses OpenGL to produce 3D visualisations of time-dependent probability distributions arising from quantum walks on graphs. Graph layouts are automatically generated using Graphviz libraries.Restrictions: Graph layouts are two-dimensional, with the third spatial dimension being used to represent the probability of finding the quantum walker at a certain location.Unusual features: The software can be used in active or dual-stereo modes for 3D visualisation of quantum walks. Images and image sequences for movies can be exported in TIFF and TGA formats.Additional comments: Examples of various input files and an XML schema are provided. Source codes written in C and Fortran are also supplied for generating QWML files from external quantum walk simulations.Running time: Computing quantum walk data and graph layout for a 500-step quantum walk on a fifth-generation Sierpinski gasket (366 vertices) took less than 2 seconds on a 2.53 GHz Intel Core 2 Duo processor with 4 GB of RAM and 3 MB L2 shared cache under Mac OS X 10.6.6. The same simulation for a hyper-branched fractal with 1331 vertices took less than 25 seconds. GNU C compiler with optimisation option -O2 was used for these tests. Once data has been computed, the interactive visualisation can be manipulated in real-time.

Plate tectonic reconstructions with continuously closing plates

We present a new algorithm for modeling a self-consistent set of global plate polygons. Each plate polygon is composed of a finite list of plate margins, all with different Euler poles. We introduce a "continuously closed plate" (CCP), such that, as each margin moves independently, the plate polygon remains closed geometrically as a function of time. This method solves emerging needs in computational geodynamics to combine kinematic with dynamic models. Because they have polygons that are too widely spaced in time and have inconsistent motions between margins and plates, traditional global plate tectonic reconstructions have become inadequate for geodynamics. The CCP algorithm has been incorporated into the GPlates open-source paleogeographic system. The algorithm is a set of procedures and data structures that operate on collections of reconstructed geometric data to form closed plate polygons; the main data structures used for each plate polygon are based on a nested hierarchy of topological elements. Reconstructions with CCPs can be created, edited, visualized, and exported with GPlates. The native storage of the dynamic reconstructions is the GPlates Markup Language, GPML, which uses an XML-based file format called GML. We demonstrate the utility of the CCP method by creating a global reconstruction with continuously closing plates from 140 Ma to the present using data from existing, traditional reconstructions.

LibSBGN: current status and future plans

AbstractLibSBGN is a community project started in 2009: it aims at facilitating the development of SBGN-compliant tools, and improving interoperability between these tools.These goals will be achieved by defining a standardized electronic implementation of the Systems Biology Graphical Notation: an XML-based file format (SBGN-ML), complemented by a software library (LibSBGN).The project is organized around a number of online tools, which allow the community to discuss problems, share ideas, and formalize solutions.Current versions of SBGN-ML and LibSBGN have already been adopted by three different SBGN-compliant tools. The first official release of SBGN-ML is imminent.For more information:http://libsbgn.sourceforge.net

Using Chado to Store Genome Annotation Data

Chado is a relational database schema that can be used to manage a wide variety of biological information, including genome annotation, genetic, phenotypic, and expression data. Its flexibility comes from its use of "ontologies," which are controlled vocabularies that describe data types and the relationships among them. By changing its ontologies, Chado can be customized to suit many different needs. Another aspect that gives Chado its flexibility is its use of a modular design, which means that users can choose to use only those features of Chado that are suitable for their needs. XORT is the main software tool used to move data in and out of Chado databases. XORT uses an XML-based file format for data import and export; this format is called ChadoXML, The protocols described in this chapter show how to use XORT and related software to import genome annotation data into Chado databases, and how to export data stored in Chado databases into different file formats for report and data mining purposes.