Showing papers in "Journal of Visual Languages and Computing in 2008"

A survey of methods for image annotation

Abstract: In order to evaluate automated image annotation and object recognition algorithms, ground truth in the form of a set of images correctly annotated with text describing each image is required. In this paper, three image annotation approaches are reviewed: free text annotation, keyword annotation and annotation based on ontologies. The practical aspects of image annotation are then considered. We discuss the creation of keyword vocabularies for use in automated image annotation evaluation. As direct manual annotation of images requires much time and effort, we also review various methods to make the creation of ground truth more efficient. An overview of annotated image datasets for computer vision research is provided.

Interactive access to large image collections using similarity-based visualization

Abstract: Image collections are getting larger and larger. To access those collections, systems for managing, searching, and browsing are necessary. Visualization plays an essential role in such systems. Existing visualization systems do not analyze all the problems occurring when dealing with large visual collections. In this paper, we make these problems explicit. From there, we establish three general requirements: overview, visibility, and structure preservation. Solutions for each requirement are proposed, as well as functions balancing the different requirements. We present an optimal visualization scheme, supporting users in interacting with large image collections. Experimental results with a collection of 10,000 Corel images, using simulated user actions, show that the proposed scheme significantly improves performance for a given task compared to the 2D grid-based visualizations commonly used in content-based image retrieval.

Qualitative spatial reasoning about relative point position

Abstract: Qualitative spatial reasoning (QSR) abstracts metrical details of the physical world. The two main directions in QSR are topological reasoning about regions and reasoning about orientations of point configurations. Orientations can refer to a global reference system, e.g. cardinal directions or instead only to relative orientation, e.g. egocentric views. Reasoning about relative orientations poses additional difficulties compared to reasoning about orientations in an absolute reference frame. Qualitative knowledge about relative orientation can be naturally expressed in the form of ternary point calculi. Designing such calculi requires compromising between desired mathematical properties and the power to describe and model concrete ''real-world'' problems. Research has shown that using basic notions such as granularity leads to imprecise reasoning and as a consequence to underdetermined knowledge which is difficult to handle efficiently. Concrete problems need a combination of qualitative knowledge of orientation and qualitative knowledge of distance. We present a calculus based on ternary relations where we introduce a qualitative distance measurement based on two of the three points. Its main advantage is that it utilizes finer distinctions than previously published calculi. Furthermore, it permits differentiations which are useful in realistic application scenarios such as robot navigation that cannot be directly dealt with in coarser calculi.

Euler diagram generation

Abstract: Euler diagrams form the basis of many diagrammatic notations used to represent set theoretic relationships in a wide range of contexts including: file system information, statistical data representation, object-oriented modeling, logical specification and reasoning systems, and database search queries. An abstract Euler diagram is a formal abstract description of the information that is to be displayed as a concrete (or drawn) Euler diagram. If the abstract diagram can be visualized, whilst satisfying certain desirable visual properties (called well-formedness conditions), then we say the diagram is drawable. We solve the drawability problem for a given set of well-formedness conditions, identifying the properties which classify a diagram as drawable or undrawable. Furthermore, we present a high level algorithm which enables the generation of a concrete diagram from an abstract diagram, whenever it is drawable.

A global process to access documents' contents from a geographical point of view

Abstract: Local cultural heritage document repositories are characterized by contents strongly attached to a territory (i.e. geographical references). The user must be able to consider such repositories according to a focus, which takes into account his/her geographical interests, and which allows one to access the relevant document's contents from a geographical point of view. This paper presents the Virtual Itineraries in the Pyrenees (PIV) project. Spatial and temporal core models are proposed to give a formal representation of geographical information. The models take into account the characteristics of heterogeneous human modes of expression: written language and captures of drawings, maps, pictures, etc. Semantic processes have been built to automatically manage the spatial and temporal information from non-structured data. A ''back office'' prototype, which adds these processes to classic information extraction (IE) approaches, while associating a geographical information retrieval (GIR) service is proposed. This service searches for any links between formal representations of geographic information in document collections, and similar representations in a user's information query. Finally, the paper presents the design work, giving the details of the principles of result visualization and navigation, while proposing a ''front office'' first implementation of the system.

An agent-based framework for sketched symbol interpretation

Abstract: Recognizing hand-sketched symbols is a definitely complex problem. The input drawings are often intrinsically ambiguous, and require context to be interpreted in a correct way. Many existing sketch recognition systems avoid this problem by recognizing single segments or simple geometric shapes in a stroke. However, for a recognition system to be effective and precise, context must be exploited, and both the simplifications on the sketch features, and the constraints under which recognition may take place, must be reduced to the minimum. In this paper, we present an agent-based framework for sketched symbol interpretation that heavily exploits contextual information for ambiguity resolution. Agents manage the activity of low-level hand-drawn symbol recognizers, that may be heterogeneous for better adapting to the characteristics of each symbol to be recognized, and coordinate themselves in order to exchange contextual information, thus leading to an efficient and precise interpretation of sketches. We also present AgentSketch, a multi-domain sketch recognition system implemented according to the proposed framework. A first experimental evaluation has been performed on the domain of UML Use Case Diagrams to verify the effectiveness of the proposed approach.

A diagrammatic reasoning system for the description logic ALC

Abstract: Diagrammatic reasoning is a tradition of visual logic that allows sentences that are equivalent to first order logic to be written in a visual or structural form: usually for improved usability. A calculus for the diagram can then be defined that allows well-formed formulas to be derived. This calculus is intended in the analog of logical inference. Description logics (DLs) have become a popular knowledge representation and processing language. DLs correspond to decidable fragments of first order logic; their notation is in the style of symbolic, variable-free formulas. Moreover, DLs are equipped with table au theorem provers that are proven to be sound and complete. Although DLs have roots in diagrammatic languages (such as semantic networks), they are elaborated in a purely symbolic manner. This paper discusses how DLs can be equivalently represented in terms of a diagrammatic reasoning system. First, existing diagrammatic reasoning systems, namely spider- and constraint diagrams, as well as existential and conceptual graphs, are investigated to determine if they are compatible with DLs. It turns out that Peirce's existential graphs are better suited for this purpose than the alternatives we examine. The paper then redevelops the DL ALC, which is the smallest propositional DL, by means of labeled trees, and provides a diagrammatic representation for these trees in the style of Peircean graphs. We provide a calculus based on C.S. Peirce's calculus for existential graphs and prove the soundness and completeness of the calculus. The calculus acts on labeled trees, but can be best understood as a diagrammatic calculus whose rules modify the Peircean-style representation of ALC.

Interactive visual analysis of geographic data on mobile devices based on dynamic queries

Abstract: The capabilities of current mobile devices, especially PDAs, are making it possible to design and develop mobile applications that employ visual techniques for using geographic data in the field. These applications can be extremely useful in areas as diverse as tourism, business, natural resources management and homeland security. In this paper, we present a system aimed at supporting users in the exploratory analysis of geographic data on PDAs through a highly interactive interface based on visual dynamic queries. We propose alternative visualizations to display query results and present an experimental evaluation aimed at comparing their effectiveness on a PDA in a tourist scenario. Our findings provide an experimental confirmation of the unsuitability of the typical visualization, employed by classic dynamic query systems, which displays only those results that fully satisfy a query, in those cases where only sub-optimal results are obtainable. For such cases, the results of our study highlight the usefulness of visualizations that display all results and their degree of satisfaction of the query.

Proposing a speech to gesture translation architecture for Spanish deaf people

Abstract: This article describes an architecture for translating speech into Spanish Sign Language (SSL). The architecture proposed is made up of four modules: speech recognizer, semantic analysis, gesture sequence generation and gesture playing. For the speech recognizer and the semantic analysis modules, we use software developed by IBM and CSLR (Center for Spoken Language Research at University of Colorado), respectively. Gesture sequence generation and gesture animation are the modules on which we have focused our main effort. Gesture sequence generation uses semantic concepts (obtained from the semantic analysis) associating them with several SSL gestures. This association is carried out based on a number of generation rules. For gesture animation, we have developed an animated agent (virtual representation of a human person) and a strategy for reducing the effort in gesture animation. This strategy consists of making the system automatically generate all agent positions necessary for the gesture animation. In this process, the system uses a few main agent positions (two or three per second) and some interpolation strategies, both issues previously generated by the service developer (the person who adapts the architecture proposed in this paper to a specific domain). Related to this module, we propose a distance between agent positions and a measure of gesture complexity. This measure can be used to analyze the gesture perception versus its complexity. With the architecture proposed, we are not trying to build a domain independent translator but a system able to translate speech utterances into gesture sequences in a restricted domain: railway, flights or weather information.

Evaluating and generalizing constraint diagrams

Abstract: The constraint diagram language was designed to be used in conjunction with the unified modelling language (UML), primarily for placing formal constraints on software models. In particular, constraint diagrams play a similar role to the textual object constraint language (OCL) in that they can be used for specifying system invariants and operation contracts in the context of a UML model. Unlike the OCL, however, constraint diagrams can be used independently of the UML. In this paper, we illustrate a range of intuitive and counter-intuitive features of constraint diagrams and highlight some (potential) expressiveness limitations. The counter-intuitive features are related to how the individual pieces of syntax interact. A generalized version of the constraint diagram language that overcomes the illustrated counter-intuitive features and limitations is proposed. In order to discourage specification readers and writers from overlooking certain semantic information, the generalized notation allows this information to be expressed more explicitly than in the non-generalized case. The design of the generalized notation takes into account five language design principles which are discussed in the paper. We provide a formalization of the syntax and semantics for generalized constraint diagrams. Moreover, we establish a lower bound on the expressiveness of the generalized notation and show that they are at least as expressive as constraint diagrams.

User Hints for map labeling

Abstract: Cartography is one of the oldest forms of visualization. It has applications not only in geography but in many other science fields. A significant visual problem in cartography is the map-labeling problem, which consists of assigning positions for the labels of graphical features of a map so that these elements can be uniquely identified. Although much research has been done on map labeling, practical labeling processes still demand intensive manual work to produce high-quality solutions. One reasons for this is that the optimization problems associated with map labeling are NP-hard. More importantly, existing automatic labeling methods do not incorporate all kinds of domain knowledge that may be of interest for a cartographer. In the present paper, we describe an interactive framework for assisting cartographers in the map-labeling problem. We treat labeling processes as an optimization task, and support human interaction combined with fully automatic methods in a general framework that we call User Hints. An interactive map-labeling system based on the User Hints framework is presented, and an evaluation of such system with real experts in cartography is described. This evaluation shows that our interactive map-labeling framework is promising.

Visualization of cryptographic protocols with GRACE

Abstract: In this paper we present GRACE (graphical representation and animation for cryptography education), a Java-based educational tool that can be used to help in teaching and understanding of cryptographic protocols. The tool adopts an active learning model that engages the learner by asking him to describe, in an exemplification of a real-world scenario, cryptographic protocols using simple primitives whose effects are visualized by means of animated sequences. To this end, the GRACE interface offers the learner the choice of several cryptographic and non-cryptographic related operations with their respective visualizations. By executing a series of these operations in the proper order, a teacher is able to provide a visual introductory description of several protocols. Moreover, since some of the cryptographic operations are not just simulated but concretely implemented, it can be used by students to see which elaborations are performed by each operation of a cryptographic protocol, and their effects on the represented scenario. GRACE comes equipped with the implementation of several cryptographic primitives and cryptosystems. Additional primitives and cryptosystems can easily be plugged in the system. Visualizations prepared with GRACE can be edited, navigated and saved in a file for playback. We also present the results of an experimental lesson taught in the Security on Communication Networks undergraduate course at the University of Salerno during the fall 2004 semester using GRACE. A copy of GRACE and some demo lessons featuring the visualization of some cryptographic protocols are available at http://www.dia.unisa.it/research/grace.

An extension of UML for the modeling of WIMP user interfaces

Abstract: The Unified Modeling Language (UML) [OMG, Unified Modeling Language Specification, Version 2.0, Technical Report, Object Management Group , 2005] provides system architects working on analysis and design (A&D) with one consistent language for specifying, visualizing, constructing, and documenting the artifacts of software systems, as well as for the business modeling. The user interface (UI), as a significant part of most applications, should be modeled using UML, and automatic CASE tools may help to generate UIs from UML designs. In this paper, we describe how to use and specialize UML diagrams in order to describe the UIs of a software system based on WIMP (Windows, Icons, Menus and Pointers). Use case diagrams are used for extracting the main UIs. Use cases are described by means of user-interaction diagrams, a special kind of activity diagrams in which states represent data output actions and transitions represent data input events. Input and output interactions in the user-interaction diagrams help the designer to extract the UI components used in each UI. We obtain a new and specialized version of the use case diagram for the UI modeling (called UI diagram) and a class diagram for UI components-called UI-class diagram. The user-interaction, UI and UI-class diagrams, can be seen as the UML-based UI models of the system. Finally, UI prototypes can be generated from UI-class diagrams with CASE tool support. As case study of our technique, we will describe an Internet book shopping system.

Towards a specification of the ToonTalk language

Abstract: ToonTalk is a child-oriented programming language whose environment is an animated virtual world, with objects that children can pick up and use as in a game, such as birds, trucks, and robots, providing direct child-oriented metaphors for programming constructs. Actions performed by a programmer's avatar with these objects are both code and coding. ToonTalk is a powerful system, not just a ''toy'' system: it is based upon concurrent constraint programming languages, and programs written in languages such as Flat Guarded Horn Clauses and Flat Concurrent Prolog can be straight-forwardly constructed in ToonTalk. However, there is not a specification of ToonTalk, for ready implementation in other environments. We propose that the ToonTalk language lies not in the animations displayed by the current environment, but on the actions performed by the programmer with virtual world objects; we present a description and analysis of the methods the ToonTalk language provides to programmers for expressing programs.

Design planning by end-user web developers

Abstract: We report an exploratory research project that investigates the impacts of different forms of design planning on end users asked to develop a simple interactive web application. End users created their projects (a Ride Board application) using the CLICK end-user web development tool [J. Rode, User-centered design of end-user web development tool, Ph.D. Dissertation, Department of Computer Science, Virginia Tech, Blacksburg, VA, USA, 2005]. Some participants were asked to create a conceptual map to plan their projects and others to write user interaction scenarios; a third group was asked to do whatever they found useful. We describe the planning that each group underwent, how they approached the web development task, and their reactions to the experience afterwards. The overall pattern of results suggests that while the participants who planned using scenarios felt they better understood the web development task, it was the group who created concept maps that explored and incorporated more of the novel programming features of the CLICK tool. We also discuss the role of gender in the CLICK development task, noting that women were less likely to explore the tool's novel features and perceived themselves as less successful in the task. We conclude with a discussion of design implications and future work.

Defining the abstract syntax of visual languages with advanced graph grammars-A case study based on behavior trees

Abstract: Diagrammatic visual languages can increase the ability of engineers to model and understand complex systems. However, to effectively use visual models, the syntax and semantics of these languages should be defined precisely. Since most diagrammatic visual models that are currently used to specify systems can be described as (directed) typed graphs, graph grammars have been identified as a suitable formalism to describe the abstract syntax of visual modeling languages. In this article, we investigate how advanced graph-transformation techniques, such as conditional, structure-generic and type-generic graph-transformation rules, can help to improve and simplify the specification of the abstract syntax of a visual modeling language. To demonstrate the practicability of an approach that unifies these advanced graph-transformation techniques, we define the abstract syntax of behavior trees (BTs), a graphical specification language for functional requirements. Additionally, we provide a translational semantics of BTs by formalizing a translation scheme to the input language of the SAL model checking tool for each of the graph-transformation rules.

Representing short-term observations of moving objects by a simple visual language

Abstract: In a variety of dynamical systems, formations of motion patterns occur. Observing colonies of animals, for instance, for the scientist it is not only of interest which kinds of formations these animals show, but also how they altogether move around. In order to analyse motion patterns for the purpose of making predictions, to describe the behaviour of systems, or to index databases of moving objects, methods are required for dealing with them. This becomes increasingly important since a number of technologies have been devised which allow objects precisely to get traced. However, the indeterminacy of spatial information in real world environments also requires techniques to approximate reasoning, for example, in order to compensate for small and unimportant distinctions which are due to noisy measurements. As a consequence, precise as well as coarse motion patterns have to be dealt with. A set of 16 atomic motion patterns is proposed. On the one hand, a relation algebra is defined on them. On the other hand, these 16 relations form the basis of a visual language using which motion patterns can easily be dealt with in a diagrammatic way. The relations are coarse but crisp and they allow imprecise knowledge about motion patterns to be dealt with, while their diagrammatic realisation also allow precise patterns to get handled. While almost all approaches consider motion patterns along arbitrary time intervals, this paper in particular focuses on short-term motion patterns as we permanently observe them in our everyday life. The bottom line of the current work, however, is yet more general. While it has been widely argued that it makes sense to use both sentential and diagrammatic representations in order to represent different things in the same system adequately (and hence differently), we argue that it makes even sense to represent the same things differently in order to grasp different aspects of one and the same object of interest from different viewpoints. We demonstrate this by providing both a sentential and a diagrammatic representation for the purpose of grasping different aspects of motion patterns. It shows that both representations complement each other.

Filmification of methods: A visual language for graph algorithms

Abstract: A novel approach for using the filmification of methods concept in the graph algorithm representation, specification, and programming is considered. It is based on a ''cyberFilm'' format, where a set of multimedia frames represents algorithmic features. A brief description of the cyberFilm concept and an observation of graph algorithm features are presented. A number of cyberFilms related to Prim's and Dijkstra's algorithms have been developed and used to explain the basic ideas of the approach. Several versions of the algorithm visualization are demonstrated by corresponding examples of cyberFilm frames and icon language representations. In addition, a method for program generation from the cyberFilm specification is provided with explanations of program templates supporting the cyberFilm frames.

Visual specification of measurements and redesigns for domain specific visual languages

Abstract: Ensuring model quality is a key success factor in many computer science areas, and becomes crucial in recent software engineering paradigms like the one proposed by model-driven software development. Tool support for measurements and redesigns becomes essential to help developers improve the quality of their models. However, developing such helper tools for the wide variety of (frequently domain specific) visual notations used by software engineers is a hard and repetitive task that does not take advantage from previous developments, thus being frequently forgotten. In this paper we present our approach for the visual specification of measurements and redesigns for Domain Specific Visual Languages (DSVLs). With this purpose, we introduce a novel DSVL called SLAMMER that contains generalisations of some of the more used types of internal product measurements and redesigns. The goal is to facilitate the task of defining measurements and redesigns for any DSVL, as well as the generation of tools from such specification reducing or eliminating the necessity of coding. We rely on the use of visual patterns for the specification of the relevant elements for each measurement and redesign type. In addition, SLAMMER allows the specification of redesigns either procedurally or by means of graph transformation rules. These redesigns can be triggered when the measurements reach a certain threshold. These concepts have been implemented in the meta-modelling tool AToM^3. In this way, when a DSVL is designed, it is possible to specify measurements and redesigns that will become available in the final modelling environment generated for the language. As an example, we show a case study in the web modelling domain.

Enforced generative patterns for the specification of the syntax and semantics of visual languages

Abstract: We present the new notion of enforced generative pattern, a structure that declares positive or negative conditions that must be satisfied by a model. Patterns are applied to transformation rules resulting in new rules that modify models according to the pattern specification. In the case of a negative pattern, an application condition is added to the rule. In the case of a positive one, the rule is modified to consider additional context in its left-hand side and to increase its effects. We have defined these patterns in an abstract setting, which enables their instantiation for different structures, like graphs, triple graphs and graph transformation rules. We apply the previous concepts to the specification of the syntax and semantics of visual languages. In particular, we show instantiations for: (i) graphs, with applications at the syntactical level; (ii) triple graphs, for the coordination of syntax and static semantics; and (iii) rules, for the incremental construction of execution rules. We present some examples that illustrate the usefulness of the combination of these three instantiations. In particular, we show the specification of environments for visual languages with token-holder semantics, discrete-event semantics and communication semantics.

Balanced cognitive load significantly improves the effectiveness of algorithm animation as a problem-solving tool

Abstract: The question of whether animations depicting running algorithms are beneficial in helping users has received mixed results. This paper provides evidence that the effectiveness of animations as an aid in performing a task is affected by several factors that have no influence on text-only aids. We make our case by comparing two separate studies designed to measure whether the addition of animations to textual descriptions of a running computation promotes understanding of distributed algorithms. The text-based conditions in both experiments resulted in statistically similar results, while the animation-added conditions resulted in different outcomes. The best visualization condition outperforms all other conditions by a significant margin. The factors that were different between the two experiments fall under the concept of cognitive economy. Therefore, the degree of cognitive economy is important both for empirical studies that involve animation and for practical applications in which people rely on dynamic visualization to solve an algorithmic problem.

Visual Zero: A persistent and interactive object-oriented programming environment

Abstract: In this article, an ongoing research project held in the Computer Science department of the University of Vigo is described. Its main objective is to develop an interactive object-oriented environment, serving as a vehicle for learning object-oriented programming. It currently consists of a virtual machine, an assembler, compilers for two high-level programming languages, and an educational visual programming environment. Its main characteristics are (a) the support of prototype-based object orientation, which is a model of object orientation that actually wraps the class-based model; (b) the support for object persistence, which simplifies all input/output issues to the minimum, and (c) the availability of a new visual programming environment is an invaluable help. We the authors think that the combination of all of these possibilities, will lead to an interesting, useful tool that would be recommended for object-oriented teaching. The whole system has been successfully employed in a number of different courses, allowing students to concentrate on objects and their relationships from the very beginning, and thus helping them to achieve a high degree of knowledge about the object-oriented programming paradigm.

Assessing the usability of a visual tool for the definition of e-learning processes

Abstract: In this paper, we present a usability study aiming at assessing a visual language-based tool for developing adaptive e-learning processes. The tool implements the adaptive self-consistent learning object SET (ASCLO-S) visual language, a special case of flow diagrams, to be used by instructional designers to define classes of learners through stereotypes and to specify the more suited adaptive learning process for each class of learners. The usability study is based on the combined use of two techniques: a questionnaire-based survey and an empirical analysis. The survey has been used to achieve feedbacks from the subjects' point of view. In particular, it has been useful to capture the perceived usability of the subjects. The outcomes show that both the proposed visual notation and the system prototype are suitable for instructional designers with or without experience on the computer usage and on tools for defining e-learning processes. This result is further confirmed by the empirical analysis we carried out by analysing the correlation between the effort to develop adaptive e-learning processes and some measures suitable defined for those processes. Indeed, the empirical analysis revealed that the effort required to model e-learning processes is not influenced by the experience of the instructional designer with the use of e-learning tools, but it only depends on the size of the developed process.

Concept keyboards in the animation of standard algorithms

Abstract: Software visualization and algorithm animation have been tackled almost exclusively from the visual point of view; this means representation and control occur through the visual channel. This approach has its limitations. To achieve better comprehension, we deal with multimodal interfaces that include the extended facilities of interaction together with those of the standard systems for data visualization and algorithm animation. The notion of specific concept keyboards is introduced. As a consequence, modern information and learning systems for algorithm animation are enhanced in such a way that control and interaction take place through appropriate interfaces designed and semi-automatically generated for this special purpose. In this paper, we provide some examples and report on a thorough evaluation to show the relevance of this new approach.

Using scenario-based requirements to direct research on web macro tools

Abstract: Web macros automate the interactions of end users with web sites and related information systems. Though web macro recorders and players have grown in sophistication over the past decade, these tools cannot yet meet many tasks that people perform in daily life. Based on observations of browser users, we have compiled ten scenarios describing tasks that users would benefit from automating. Our analysis of these scenarios yields specific requirements that web macro tools should support if those tools are to be applicable to these real-life tasks. Our set of requirements constitutes a benchmark for evaluating tools, which we demonstrate by evaluating the Robofox, CoScripter, and iMacros tools.

Spatial inference and similarity retrieval of an intelligent image database system based on object's spanning representation

Abstract: In this paper, we presented a novel image representation method to capture the information about spatial relationships between objects in a picture. Our method is more powerful than all other previous methods in terms of accuracy, flexibility, and capability of discriminating pictures. In addition, our method also provides different degrees of granularity for reasoning about directional relations in both 8- and 16-direction reference frames. In similarity retrieval, our system provides twelve types of similarity measures to support flexible matching between the query picture and the database pictures. By exercising a database containing 3600 pictures, we successfully demonstrated the effectiveness of our image retrieval system. Experiment result showed that 97.8% precision rate can be achieved while maintaining 62.5% recall rate; and 97.9% recall rate can be achieved while maintaining 51.7% precision rate. On an average, 86.1% precision rate and 81.2% recall rate can be achieved simultaneously if the threshold is set to 0.5 or 0.6. This performance is considered to be very good as an information retrieval system.

Visual software tools for bioinformatics

Abstract: Bioinformatics is the application of techniques from computer science, statistics and mathematics to problems in molecular biology. This interdisciplinary approach is rapidly revolutionizing biology. A survey of software tools for bioinformatics is presented. A special emphasis is placed on the visual aspects of these tools. The most important visualization tasks in bioinformatics are data sequence visualization and visualizing protein structures. The visualization of interactions between molecules in a metabolic pathway or network is an emerging area. Many important visualization techniques have yet to be applied in this application area.

A formalism for visual security protocol modeling

Abstract: Existing visual modeling paradigms do not adequately cover the visual modeling of security protocols: sequences of interactions between principals in a security system. A visual formalism for security protocol modeling should not only be well-defined but also satisfy certain pragmatic criteria: support for compositional, comprehensive, laconic, and lucid models. Candidate techniques from the OMG's Model Driven Architecture, based largely on UML 2.0, lack a formal syntax and semantics. Well-defined visual formalisms outside of UML have shortcomings with respect to one or more of the pragmatic criteria. We present the GSPML visual formalism as a solution that satisfies all of the pragmatic criteria. We show that GSPML is well-defined with structural operational semantics and a hypergraph grammar syntax.

MOVIS: A system for visualizing distributed mobile object environments

Abstract: This paper presents MOVIS-a system for visualizing mobile object frameworks. In such frameworks, the objects can migrate to remote hosts, along with their state and behavior, while the application is running. An innovative graph-based visualization is used to depict the physical and the logical connections in the distributed object network. Scalability is achieved by using a focus+context technique jointly with a user-steered clustering algorithm. In addition, an event synchronization model for mobile objects is presented. The system has been applied to visualizing several mobile object applications.

MAVIS: A multi-level algorithm visualization system within a collaborative distance learning environment

Abstract: This paper presents a new model for an algorithm visualization system. Our model views the visualization system as an integral part of a broader distance learning environment. As such, it supports the heterogeneity of the Internet the visualization is expected to run on and the diversity of the expected users. It does so by defining several ways for handling multi-level visualizations. First, a visualization can run in various abstraction levels of the algorithm, depending on the familiarity of the students with the studied materials. Second, a visualization can use various levels of graphics, depending on the capabilities of the client machines. Third, the messages sent between the machines can be of various levels, depending on the communication loads. Another important aspect of a distance learning environment is collaboration and data sharing. Our model facilitates the collaboration between the students and the instructor and between the students themselves. Finally, this paper presents a system, MAVIS, that realizes the model, and demonstrates its use on several algorithms.