Map-Based Navigation in a Graphical MOO

Traditional MUDs and MOOs lack support for global wareness and simple navigation. These problems can be addressed by the introduction of a map-based navigation tool. In this paper we report on the design and evaluation of such a tool for MOOsburg, a graphical 2D MOO based on the town of Blacksburg, Virginia. The tool supports exploration and place-based tasks in the MOO. It also allows navigation of a large-scale map and encourages users to develop survey knowledge of the town. An evaluation revealed some initial usability problems with our prototype and suggested new design ideas that may better support users. Using these results, the lessons learned about map-based navigation are presented

How people describe their place: Approaches to interpreting and formalizing place descriptions

This cumulative thesis deals with human place descriptions and their interpretation. In particular, it poses four different research questions: What are dominant types of place descriptions? What different types of hierarchical structures do they use? What is the role of spatial relationships in defining the actual location? Can violations in form of flat structures or gaps in levels be related to the applied classification scheme

Interactive metagenomic visualization in a Web browser

<p>Abstract</p> <p>Background</p> <p>A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables.</p> <p>Results</p> <p>Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools.</p> <p>Conclusions</p> <p>Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: <url>http://krona.sourceforge.net</url>.</p

Adaptive content mapping for internet navigation

The Internet as the biggest human library ever assembled keeps on growing. Although all kinds of information carriers (e.g. audio/video/hybrid file formats) are available, text based documents dominate. It is estimated that about 80% of all information worldwide stored electronically exists in (or can be converted into) text form. More and more, all kinds of documents are generated by means of a text processing system and are therefore available electronically. Nowadays, many printed journals are also published online and may even discontinue to appear in print form tomorrow. This development has many convincing advantages: the documents are both available faster (cf. prepress services) and cheaper, they can be searched more easily, the physical storage only needs a fraction of the space previously necessary and the medium will not age. For most people, fast and easy access is the most interesting feature of the new age; computer-aided search for specific documents or Web pages becomes the basic tool for information-oriented work. But this tool has problems. The current keyword based search machines available on the Internet are not really appropriate for such a task; either there are (way) too many documents matching the specified keywords are presented or none at all. The problem lies in the fact that it is often very difficult to choose appropriate terms describing the desired topic in the first place. This contribution discusses the current state-of-the-art techniques in content-based searching (along with common visualization/browsing approaches) and proposes a particular adaptive solution for intuitive Internet document navigation, which not only enables the user to provide full texts instead of manually selected keywords (if available), but also allows him/her to explore the whole database

Conceptual Model-Based Systems Biology: Mapping Knowledge and Discovering Gaps in the mRNA Transcription Cycle

We propose a Conceptual Model-based Systems Biology framework for qualitative modeling, executing, and eliciting knowledge gaps in molecular biology systems. The framework is an adaptation of Object-Process Methodology (OPM), a graphical and textual executable modeling language. OPM enables concurrent representation of the system's structure—the objects that comprise the system, and behavior—how processes transform objects over time. Applying a top-down approach of recursively zooming into processes, we model a case in point—the mRNA transcription cycle. Starting with this high level cell function, we model increasingly detailed processes along with participating objects. Our modeling approach is capable of modeling molecular processes such as complex formation, localization and trafficking, molecular binding, enzymatic stimulation, and environmental intervention. At the lowest level, similar to the Gene Ontology, all biological processes boil down to three basic molecular functions: catalysis, binding/dissociation, and transporting. During modeling and execution of the mRNA transcription model, we discovered knowledge gaps, which we present and classify into various types. We also show how model execution enhances a coherent model construction. Identification and pinpointing knowledge gaps is an important feature of the framework, as it suggests where research should focus and whether conjectures about uncertain mechanisms fit into the already verified model

What Google Maps can do for biomedical data dissemination: examples and a design study

BACKGROUND: Biologists often need to assess whether unfamiliar datasets warrant the time investment required for more detailed exploration. Basing such assessments on brief descriptions provided by data publishers is unwieldy for large datasets that contain insights dependent on specific scientific questions. Alternatively, using complex software systems for a preliminary analysis may be deemed as too time consuming in itself, especially for unfamiliar data types and formats. This may lead to wasted analysis time and discarding of potentially useful data. RESULTS: We present an exploration of design opportunities that the Google Maps interface offers to biomedical data visualization. In particular, we focus on synergies between visualization techniques and Google Maps that facilitate the development of biological visualizations which have both low-overhead and sufficient expressivity to support the exploration of data at multiple scales. The methods we explore rely on displaying pre-rendered visualizations of biological data in browsers, with sparse yet powerful interactions, by using the Google Maps API. We structure our discussion around five visualizations: a gene co-regulation visualization, a heatmap viewer, a genome browser, a protein interaction network, and a planar visualization of white matter in the brain. Feedback from collaborative work with domain experts suggests that our Google Maps visualizations offer multiple, scale-dependent perspectives and can be particularly helpful for unfamiliar datasets due to their accessibility. We also find that users, particularly those less experienced with computer use, are attracted by the familiarity of the Google Maps API. Our five implementations introduce design elements that can benefit visualization developers. CONCLUSIONS: We describe a low-overhead approach that lets biologists access readily analyzed views of unfamiliar scientific datasets. We rely on pre-computed visualizations prepared by data experts, accompanied by sparse and intuitive interactions, and distributed via the familiar Google Maps framework. Our contributions are an evaluation demonstrating the validity and opportunities of this approach, a set of design guidelines benefiting those wanting to create such visualizations, and five concrete example visualizations

A Visualization Framework for Designing Process Mining Diagrams

Sündmuslogid sisaldavad väärtuslikku informatsiooni äriprotsesside seisundi kohta. Informatsioonile ligi pääsemiseks peab andmestiku viima arusaadavale kujule. Protsissikaeve tööriistad kasutavad erinevaid diagramme, mis toetavad sündmuslogide visuaalset uurimist. Nende diagrammide kujundamine ei ole lihtne ülesanne, sest tihti ei tea arendaja ega kasutaja, kus huvipakkuv informatsioon võib asuda. Seepärast peavad diagrammid olema paindlikud, kuid samas lihtsad ja intuitiivsed, et nii analüütikud kui ka mitteasjatundjad saaksid tööriista kasutada. Antud töö uurib olemasolevate protsessikaeve diagrammide kujundusi ja kuidas need kujundused on autorite poolt põhjendatud. Töös tutvustatakse ka raamistikku, mis on välja töötatud selleks, et lihtsustada ja täiustada protsessikaeve diagrammide kujundamist. See põhineb andmete visualiseerimise teoorial ja visualiseerimise praktikatel protsessikaeves. Raamistiku tõhusust on katsetatud juhtumuuringus.Event logs hold valuable information about the health of business processes. In order to access this information, raw data must be transformed to a comprehensible format. Process mining tools use various diagrams to support visual exploration of process logs. Designing such diagrams is not an easy task because oftentimes neither the developer nor user know where interesting or intriguing information lays. Therefore, the diagrams require thoughtful designs that on the one hand allow flexible exploration, and on the other hand, are simple and intuitive to use for analysts as well as non-experts. This work takes a look into existing solutions of process mining visualizations and the design decisions the visualizations are based on. A framework is proposed to simplify and improve the design process for process mining diagrams. It is based on data visualization theory as well as visualization practices in process mining. The effectiveness of the framework is tested in a case study

From Keyword Search to Exploration: How Result Visualization Aids Discovery on the Web

A key to the Web's success is the power of search. The elegant way in which search results are returned is usually remarkably effective. However, for exploratory search in which users need to learn, discover, and understand novel or complex topics, there is substantial room for improvement. Human computer interaction researchers and web browser designers have developed novel strategies to improve Web search by enabling users to conveniently visualize, manipulate, and organize their Web search results. This monograph offers fresh ways to think about search-related cognitive processes and describes innovative design approaches to browsers and related tools. For instance, while key word search presents users with results for specific information (e.g., what is the capitol of Peru), other methods may let users see and explore the contexts of their requests for information (related or previous work, conflicting information), or the properties that associate groups of information assets (group legal decisions by lead attorney). We also consider the both traditional and novel ways in which these strategies have been evaluated. From our review of cognitive processes, browser design, and evaluations, we reflect on the future opportunities and new paradigms for exploring and interacting with Web search results