text: We present ScaleTrotter, a conceptual framework for an interactive, multi-scale visualization of biological mesoscale data and, specifically, genome data. ScaleTrotter allows viewers to smoothly transition from the nucleus of a cell to the atomistic composition of the DNA, while bridging several orders of magnitude in scale. The challenges in creating an interactive visualization of genome data are fundamentally different in several ways from those in other domains like astronomy that require a multi-scale representation as well. First, genome data has intertwined scale levels---the DNA is an extremely long, connected molecule that manifests itself at all scale levels. Second, elements of the DNA do not disappear as one zooms out---instead the scale levels at which they are observed group these elements differently. Third, we have detailed information and thus geometry for the entire dataset and for all scale levels, posing a challenge for interactive visual exploration. Finally, the conceptual scale levels for genome data are close in scale space, requiring us to find ways to visually embed a smaller scale into a coarser one. We address these challenges by creating a new multi-scale visualization concept. We use a scale-dependent camera model that controls the visual embedding of the scales into their respective parents, the rendering of a subset of the scale hierarchy, and the location, size, and scope of the view. In traversing the scales, ScaleTrotter is roaming between 2D and 3D visual representations that are depicted in integrated visuals. We discuss, specifically, how this form of multi-scale visualization follows from the specific characteristics of the genome data and describe its implementation. Finally, we discuss the implications of our work to the general illustrative depiction of multi-scale data.
  @cite_39: We explore the concept of abstraction as it is used in visualization, with the ultimate goal of understanding and formally defining it. Researchers so far have used the concept of abstraction largely by intuition without a precise meaning. This lack of specificity left questions on the characteristics of abstraction, its variants, its control, or its ultimate potential for visualization and, in particular, illustrative visualization mostly unanswered. In this paper we thus provide a first formalization of the abstraction concept and discuss how this formalization affects the application of abstraction in a variety of visualization scenarios. Based on this discussion, we derive a number of open questions still waiting to be answered, thus formulating a research agenda for the use of abstraction for the visual representation and exploration of data. This paper, therefore, is intended to provide a contribution to the discussion of the theoretical foundations of our field, rather than attempting to provide a completed and final theory.
  @cite_8: Virtual three-dimensional (3-D) environments have become pervasive tools in a number of professional and recreational tasks. However, interacting with these environments can be challenging for users, especially as these environments increase in complexity and scale. In this paper, we argue that the design of 3-D interaction techniques is an ill-defined problem. This claim is elucidated through the context of data-rich and geometrically complex multiscale virtual 3-D environments, where unexpected factors can encumber intellection and navigation. We develop an abstract model to guide our discussion, which illustrates the cyclic relationship of understanding and navigating; a relationship that supports the iterative refinement of a consistent mental representation of the virtual environment. Finally, we highlight strategies to support the design of interactions in multiscale virtual environments, and propose general categories of research focus.
summary: In general, as one navigates through large-scale 3D scenes, the underlying subject matter is intrinsically complex and requires appropriate interaction to aid intellection @cite_8 . The inspection of individual parts is challenging, in particular if the viewer is too far away to appreciate its visual details. Yet large, detailed datasets or procedural approaches are essential to create believable representations. To generate not only efficient but visualizations, we thus need to remove detail in Viola and Isenberg's @cite_39 visual abstraction sense. This allows us to render at interactive rates as well as to see the intended structures, which would otherwise be hidden due to cluttered views. Consequently, even most single-scale small-scale representations use some type of multi-scale approach and with it introduce abstraction. Generally we can distinguish three fundamental techniques: multi-scale representations by leaving out detail of a single data source, multi-scale techniques that actively represent preserved features at different scales, and multi-scale approaches that can also transit between representations of different scales. We discuss approaches for these three categories next.