Facilitating insight into a simulation model using visualization and dynamic model previews

This paper shows how model simplification, by replacing iterative steps with unitary predictive equations, can enable dynamic interaction with a complex simulation process. Model previews extend the techniques of dynamic querying and query previews into the context of ad hoc simulation model exploration. A case study is presented within the domain of counter-current chromatography. The relatively novel method of insight evaluation was applied, given the exploratory nature of the task. The evaluation data show that the trade-off in accuracy is far outweighed by benefits of dynamic interaction. The number of insights gained using the enhanced interactive version of the computer model was more than six times higher than the number of insights gained using the basic version of the model. There was also a trend for dynamic interaction to facilitate insights of greater domain importance

User-centered visual analysis using a hybrid reasoning architecture for intensive care units

One problem pertaining to Intensive Care Unit information systems is that, in some cases, a very dense display of data can result. To ensure the overview and readability of the increasing volumes of data, some special features are required (e.g., data prioritization, clustering, and selection mechanisms) with the application of analytical methods (e.g., temporal data abstraction, principal component analysis, and detection of events). This paper addresses the problem of improving the integration of the visual and analytical methods applied to medical monitoring systems. We present a knowledge- and machine learning-based approach to support the knowledge discovery process with appropriate analytical and visual methods. Its potential benefit to the development of user interfaces for intelligent monitors that can assist with the detection and explanation of new, potentially threatening medical events. The proposed hybrid reasoning architecture provides an interactive graphical user interface to adjust the parameters of the analytical methods based on the users' task at hand. The action sequences performed on the graphical user interface by the user are consolidated in a dynamic knowledge base with specific hybrid reasoning that integrates symbolic and connectionist approaches. These sequences of expert knowledge acquisition can be very efficient for making easier knowledge emergence during a similar experience and positively impact the monitoring of critical situations. The provided graphical user interface incorporating a user-centered visual analysis is exploited to facilitate the natural and effective representation of clinical information for patient care

trackr: A Framework for Enhancing Discoverability and Reproducibility of Data Visualizations and Other Artifacts in R

Research is an incremental, iterative process, with new results relying and building upon previous ones. Scientists need to find, retrieve, understand, and verify results in order to confidently extend them, even when the results are their own. We present the trackr framework for organizing, automatically annotating, discovering, and retrieving results. We identify sources of automatically extractable metadata for computational results, and we define an extensible system for organizing, annotating, and searching for results based on these and other metadata. We present an open-source implementation of these concepts for plots, computational artifacts, and woven dynamic reports generated in the R statistical computing language

Inviwo -- A Visualization System with Usage Abstraction Levels

The complexity of today's visualization applications demands specific visualization systems tailored for the development of these applications. Frequently, such systems utilize levels of abstraction to improve the application development process, for instance by providing a data flow network editor. Unfortunately, these abstractions result in several issues, which need to be circumvented through an abstraction-centered system design. Often, a high level of abstraction hides low level details, which makes it difficult to directly access the underlying computing platform, which would be important to achieve an optimal performance. Therefore, we propose a layer structure developed for modern and sustainable visualization systems allowing developers to interact with all contained abstraction levels. We refer to this interaction capabilities as usage abstraction levels, since we target application developers with various levels of experience. We formulate the requirements for such a system, derive the desired architecture, and present how the concepts have been exemplary realized within the Inviwo visualization system. Furthermore, we address several specific challenges that arise during the realization of such a layered architecture, such as communication between different computing platforms, performance centered encapsulation, as well as layer-independent development by supporting cross layer documentation and debugging capabilities

Interpretation at the controller's edge: designing graphical user interfaces for the digital publication of the excavations at Gabii (Italy)

This paper discusses the authors’ approach to designing an interface for the Gabii Project’s digital volumes that attempts to fuse elements of traditional synthetic publications and site reports with rich digital datasets. Archaeology, and classical archaeology in particular, has long engaged with questions of the formation and lived experience of towns and cities. Such studies might draw on evidence of local topography, the arrangement of the built environment, and the placement of architectural details, monuments and inscriptions (e.g. Johnson and Millett 2012). Fundamental to the continued development of these studies is the growing body of evidence emerging from new excavations. Digital techniques for recording evidence “on the ground,” notably SFM (structure from motion aka close range photogrammetry) for the creation of detailed 3D models and for scene-level modeling in 3D have advanced rapidly in recent years. These parallel developments have opened the door for approaches to the study of the creation and experience of urban space driven by a combination of scene-level reconstruction models (van Roode et al. 2012, Paliou et al. 2011, Paliou 2013) explicitly combined with detailed SFM or scanning based 3D models representing stratigraphic evidence. It is essential to understand the subtle but crucial impact of the design of the user interface on the interpretation of these models. In this paper we focus on the impact of design choices for the user interface, and make connections between design choices and the broader discourse in archaeological theory surrounding the practice of the creation and consumption of archaeological knowledge. As a case in point we take the prototype interface being developed within the Gabii Project for the publication of the Tincu House. In discussing our own evolving practices in engagement with the archaeological record created at Gabii, we highlight some of the challenges of undertaking theoretically-situated user interface design, and their implications for the publication and study of archaeological materials

TGVizTab: An ontology visualisation extension for Protégé

Ontologies are gaining a lot of interest and many are being developed to provide a variety of knowledge services. There is an increasing need for tools to graphically and in-teractively visualise such modelling structures to enhance their clarification, verification and analysis. Protégé 2000 is one of the most popular ontology modelling tools currently available. This paper introduces TGVizTab; a new Protégé plugin based on TouchGraph technology to graphically visualise Protégé?s ontologies

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

Molecular biology knowledge can be systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist a number of maps of molecular interactions containing detailed description of various cell mechanisms. It is difficult to explore these large maps, to comment their content and to maintain them. Though there exist several tools addressing these problems individually, the scientific community still lacks an environment that combines these three capabilities together. NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. NaviCell combines three features: (1) efficient map browsing based on Google Maps engine; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting the community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of their interest in the context of signaling pathways and cross-talks between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive fashion due to an imbedded blogging system. NaviCell provides an easy way to explore large-scale maps of molecular interactions, thanks to the Google Maps and WordPress interfaces, already familiar to many users. Semantic zooming used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization meaningful to the user. In addition, NaviCell provides a framework for community-based map curation.Comment: 20 pages, 5 figures, submitte

A study of search intermediary working notes: implications for IR system design

This paper reports findings from an exploratory study investigating working notes created during encoding and external storage (EES) processes, by human search intermediates using a Boolean information retrieval (JR) system. EES processes have been an important area of research in educational contexts where students create and use notes to facilitate learning. In the context of interactive IR, encoding can be conceptualized as the process of creating working notes to help in the understanding and translating a user's information problem into a search strategy suitable for use with an IR system. External storage is the process of using working notes to facilitate interaction with IR systems. Analysis of 221 sets of working notes created by human search intermediaries revealed extensive use of EES processes and the creation of working notes of textual, numerical and graphical entities. Nearly 70% of recorded working notes were textual/numerical entities, nearly 30% were graphical entities and 0.73% were indiscernible. Segmentation devices were also used in 48% of the working notes. The creation of working notes during EES processes was a fundamental element within the mediated, interactive IR process. Implications for the design of IR interfaces to support users' EES processes and further research is discussed