An Augmented Wiki for Interactive Scientific Visualization and Evolutionary Collaboration

Scientific journals are the de facto medium for communicating details of the research process and its significant results. Here, concise expository text is responsible for communication while imagery is relegated to a subservient role, intended to illustrate the essential points set forth within a scientific paper. Within this context, readers must contend with static imagery and charts scattered about the text. Images are typically small in size, of excessive information density, and often poorly positioned within a page layout, thus minimizing the linkage between them and the narrative. Moreover, many illustrations are snapshots from complex visualizations over multiple spatial and temporal dimensions that, by their nature, are incomplete representations of the systems studied. In contrast, visualization systems create interactive, dynamic imagery displayable on any conforming output device from laptop to video wall, providing a level of visual description and detail not found in print media. But these systems are not designed to accommodate, annotate, and format the large body of descriptive text required for a complete document.

It is possible to create a hypermedia instantiation of a scientific document by assembling text, graphics, and embed interactive visualization software such as Java applets employing traditional HTML-based technologies. But these documents suffer from problems of synchronization brought about by each component’s autonomy. For example, when an HTML document is loaded, text and imagery match; but after an interactive visualization that dynamically changes the graphical representation, the image may no longer illustrates the static text; once again minimizing the linkage between narrative and illustration. In addition, when such a webpage is accessed by means of a standard browser, it cannot be annotated, augmented, or enhanced.

Wiki website technology supports the addition and editing of hypertext. As such, a wiki sustains collaborative authoring of dynamic hypertext documents that evolve over time. In so doing, a wiki can be used to extend the scientific publishing and communication paradigm by opening up a closed scientific paper to augmentation by the scientific community as new data becomes available or new insights are realized. Essential to this wiki system should be a component that supports an interactive visualization that synchronizes with text descriptions, and makes a direct connection to source experimental data, metadata, their representations and transformations.

We have created such a system for use in the molecular sciences. It is an augmented Wiki that supports interactive scientific visualization and asynchronous collaboration. The system was assembled from available open source Wiki technology and visualization software that relies on XHTML, Java, Javascript, and XML. This presentation will demonstrate the system and describe how it may be employed to address the issues we have raised above. In particular, we will explain how narratives may be created that contain text that synchronizes with interactive visualizations. We will also show how these documents may be augmented and evolve over time. This system will be discussed within the context of contemporary hypermedia technology, collaborative systems, and scientific publishing.