Background
Quantitative models of biochemical and cellular systems are used to answer a variety of questions in the biological sciences. The number of published quantitative models is growing steadily thanks to increasing interest in the use of models as well as the development of improved software systems and the availability of better, cheaper computer hardware. To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. Ideally, the models stored in these repositories should be extensively tested and encoded in community-supported and standardised formats. In addition, the models and their components should be cross-referenced with other resources in order to allow their unambiguous identification.

/pdf/biomodels-database-an-enhanced-curated-and-annotated-2ipsovu23z.pdf

Biomodels database: an enhanced curated and annotated resource for published quantitative kinetic models

We present a model that allows to directly integrate X3D nodes into HTML5 DOM content. This model tries to fulfill the promise of the HTML5 specification, which references X3D for declarative 3D scenes but does not define a specific integration mode. The goal of this model is to ease the integration of X3D in modern web applications by directly mapping and synchronizing live DOM elements to a X3D scene model. This is a very similar approach to the current SVG integration model for 2D graphics.Furthermore, we propose a framework that includes a new X3D Profile for the DOM integration. This profile should make implementation simple, but in addition we show that the current X3D runtime model still scales well. A detailed discussion includes DOM integration issues like events, namespaces and scripting. We finally propose an implementation framework that should work with multiple browser frontends (e.g. Firefox and WebKit) and different X3D runtime backends.We hope to connect the technologies and the X3D/ W3C communities with this proposal and outline a model, how an integration without plugins could work. Moreover, we hope to inspire further work, which could lead to a native X3D implementation in browsers similar to the SVG implementations today.

/pdf/x3dom-a-dom-based-html5-x3d-integration-model-33o3c7cse7.pdf

X3DOM: a DOM-based HTML5/X3D integration model

The design of real-life complex systems calls for advanced software engineering models, methods, and tools in order to meet critical requirements such as reliability, dependability, safety, or resilience that will avoid putting the company, the mission, or even human life at stake. When such systems encompass a substantial interactive component, the same level of confidence is required towards the human-computer interface. Conventional empirical or semiformal techniques, although very fruitful, do not provide sufficient insight on the reliability of the human-system cooperation, and offer no easy way to, for example, quantitatively and qualitatively compare two design options with respect to that reliability. The aim of this article is to present a user interface description language (called ICOs) for the engineering and development of usable and reliable user interfaces. The CASE tool supporting the ICOs notation (called Petshop) is a Petri nets-based-tool for the design, specification, prototyping, and validation of interactive software. In that environment models (built with the formal description technique ICOs) of the interactive application can be interactively modified and executed. This is used to support prototyping phases (when the models and the interactive application evolve significantly to meet late user requirements, for instance) as well as the operation phase (after the system is deployed). The use of ICOs and PetShop is presented on several large-scale systems such as a multimodal ground segment application for satellite control, an air traffic control interactive application, and an application for new generation of interactive cockpits in large civil aircraft such as Airbus A380 or Boeing 787. The article emphasizes the demonstration of the expressive power of the notation and how it can support the description of various aspects of user interfaces, namely interaction techniques (both WIMP and post-WIMP), interactive components (such as widgets), and the behavioral part of interactive applications such as the dialog and the functional core. It also demonstrates that PetShop provides dedicated support for prototyping activities of behavioral aspects at the various levels of the architecture of interactive systems. While the focus is on past work done on various large-scale applications, the article also highlights why and how ICOs and Petshop are able to address challenges raised by next-generation user interfaces.

ICOs: A model-based user interface description technique dedicated to interactive systems addressing usability, reliability and scalability

This article presents an XML-based interchange format for event-driven process chains (EPC) that is called EPC markup language (EPML). EPML builds on EPC syntax related work and is tailored to be a serialization format for EPC modelling tools. Design principles inspired by other standardization efforts and XML design guidelines have governed the specification of EPML. After giving an overview of EPML concepts we present examples to illustrate its features including flat and hierarchical EPCs, business views, graphical information, and syntactical correctness.

EPC markup language (EPML): an XML-based interchange format for event-driven process chains (EPC)

http://alunevans.info/publications/computers_and_graphics_3d_web_survey_final_preprint.pdf

3D graphics on the web: A survey

This article introduces the scalable vector graphics (SVG) standard by highlighting two main SVG themes: graphics capabilities and dynamism. SVG can satisfy needs for distributed, lightweight, graphics-centered applications. Its integration with other XML technologies make it an ideal fit for ever-expanding XML workflows.

A. Quint

Papers

Scalable vector graphics