Natural XML for Data Binding, Processing, and Persistence

The article explains what you need to do to incorporate XML directly into your computational science application. The exploration involves the use of a standard parser to automatically build object trees entirely from application-specific classes. This discussion very much focuses on object-oriented programming languages such as Java and Python, but it can work for non-object-oriented languages as well. The ideas in the article provide a glimpse into the Natural XML research project

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

Semantic Technologies for Manuscript Descriptions — Concepts and Visions

The contribution at hand relates recent developments in the area of the World Wide Web to codicological research. In the last number of years, an informational extension of the internet has been discussed and extensively researched: the Semantic Web. It has already been applied in many areas, including digital information processing of cultural heritage data. The Semantic Web facilitates the organisation and linking of data across websites, according to a given semantic structure. Software can then process this structural and semantic information to extract further knowledge. In the area of codicological research, many institutions are making efforts to improve the online availability of handwritten codices. If these resources could also employ Semantic Web techniques, considerable research potential could be unleashed. However, data acquisition from less structured data sources will be problematic. In particular, data stemming from unstructured sources needs to be made accessible to SemanticWeb tools through information extraction techniques. In the area of museum research, the CIDOC Conceptual Reference Model (CRM) has been widely examined and is being adopted successfully. The CRM translates well to Semantic Web research, and its concentration on contextualization of objects could support approaches in codicological research. Further concepts for the creation and management of bibliographic coherences and structured vocabularies related to the CRM will be considered in this chapter. Finally, a user scenario showing all processing steps in their context will be elaborated on

Early aspects: aspect-oriented requirements engineering and architecture design

This paper reports on the third Early Aspects: Aspect-Oriented Requirements Engineering and Architecture Design Workshop, which has been held in Lancaster, UK, on March 21, 2004. The workshop included a presentation session and working sessions in which the particular topics on early aspects were discussed. The primary goal of the workshop was to focus on challenges to defining methodical software development processes for aspects from early on in the software life cycle and explore the potential of proposed methods and techniques to scale up to industrial applications

Design and Implementation Strategies for IMS Learning Design

SIKS Dissertation Series No. 2008-27The IMS Learning Design (LD) specification, which has been released in February 2003, is a generic and flexible language for describing the learning practice and underlying learning designs using a formal notation which is computer-interpretable. It is based on a pedagogical meta-model (Koper & Manderveld, 2004) and supports the use of a wide range of pedagogies. It supports adaptation of individual learning routes and orchestrates interactions between users in various learning and support roles. A formalized learning design can be applied repeatedly in similar situations with different persons and contexts. Yet because IMS Learning Design is a fairly complex and elaborate specification, it can be difficult to grasp; furthermore, designing and implementing a runtime environment for the specification is far from straightforward. That IMS Learning Design makes use of other specifications and e-learning services adds further to this complexity for both its users and the software developers. For this new specification to succeed, therefore, a reference runtime implementation was needed. To this end, this thesis addresses two research and development issues. First, it investigates research into and development of a reusable reference runtime environment for IMS Learning Design. The resulting runtime, called CopperCore, provides a reference both for users of the specification and for software developers. The latter can reuse the design principles presented in this thesis for their own implementations, or reuse the CopperCore product through the interfaces provided. Second, this thesis addresses the integration of other specifications and e-learning services during runtime. It presents an architecture and implementation (CopperCore Service Integration) which provides an extensible lightweight solution to the problem. Both developments have been tested through real-world use in projects carried out by the IMS Learning Design community. The results have generally been positive, and have led us to conclude that we successfully addressed both the research and development issues. However, the results also indicate that the LD tooling lacks maturity, particularly in the authoring area. Through close integration of CopperCore with a product called the Personal Competence Manager, we demonstrate that a complementary approach to authoring in IMS Learning Design solves some of these issues

The architecture of discovery net : towards grid-based discovery services

Imperial Users onl

COEL: A Web-based Chemistry Simulation Framework

The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage, which is susceptible to loss, lacks searchable structure, and does not support concurrency. Furthermore, simulations are often single-threaded, and user interfaces are non-trivial to use. Therefore there are significant hurdles to conducting efficient and collaborative chemical research. In this paper, we introduce a new enterprise chemistry simulation framework, COEL, which addresses these issues. COEL is the first web-based framework of its kind. A visually pleasing and intuitive user interface, simulations that run on a large computational grid, reliable database storage, and transactional services make COEL ideal for collaborative research and education. COEL's most prominent features include ODE-based simulations of chemical reaction networks and multicompartment reaction networks, with rich options for user interactions with those networks. COEL provides DNA-strand displacement transformations and visualization (and is to our knowledge the first CRN framework to do so), GA optimization of rate constants, expression validation, an application-wide plotting engine, and SBML/Octave/Matlab export. We also present an overview of the underlying software and technologies employed and describe the main architectural decisions driving our development. COEL is available at http://coel-sim.org for selected research teams only. We plan to provide a part of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl