Dynamic Influence Networks for Rule-based Models

We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres

Automatic generation of user interfaces from rigorous domain and use case models

Tese de doutoramento. Engenharia Informática. Faculdade de Engenharia. Universidade do Porto. 201

Using a Dynamic Domain-Specific Modeling Language for the Model-Driven Development of Cross-Platform Mobile Applications

There has been a gradual but steady convergence of dynamic programming languages with modeling languages. One area that can benefit from this convergence is modeldriven development (MDD) especially in the domain of mobile application development. By using a dynamic language to construct a domain-specific modeling language (DSML), it is possible to create models that are executable, exhibit flexible type checking, and provide a smaller cognitive gap between business users, modelers and developers than more traditional model-driven approaches. Dynamic languages have found strong adoption by practitioners of Agile development processes. These processes often rely on developers to rapidly produce working code that meets business needs and to do so in an iterative and incremental way. Such methodologies tend to eschew “throwaway” artifacts and models as being wasteful except as a communication vehicle to produce executable code. These approaches are not readily supported with traditional heavyweight approaches to model-driven development such as the Object Management Group’s Model-Driven Architecture approach. This research asks whether it is possible for a domain-specific modeling language written in a dynamic programming language to define a cross-platform model that can produce native code and do so in a way that developer productivity and code quality are at least as effective as hand-written code produced using native tools. Using a prototype modeling tool, AXIOM (Agile eXecutable and Incremental Objectoriented Modeling), we examine this question through small- and mid-scale experiments and find that the AXIOM approach improved developer productivity by almost 400%, albeit only after some up-front investment. We also find that the generated code can be of equal if not better quality than the equivalent hand-written code. Finally, we find that there are significant challenges in the synthesis of a DSML that can be used to model applications across platforms as diverse as today’s mobile operating systems, which point to intriguing avenues of subsequent research

Prototyping Corporate User Interfaces – Towards A Visual Specification Of Interactive Systems

Corporate software development faces very demanding challenges, especially concerning the user interface of a software system. Collaborative design with stakeholders demands informal modeling methods that everybody can understand and apply. But using traditional, paper-based methods to gather and document requirements, an IT organization often experiences frustrating communication issues between the business and development teams. We present ways of agile high-fidelity prototyping for corporate user interface design. Without harming agile principles and practice, detailed prototypes can be employed for collaborative design, can act as visual specifications and substitute paper-based artifacts

The S2 VLBI Correlator: A Correlator for Space VLBI and Geodetic Signal Processing

We describe the design of a correlator system for ground and space-based VLBI. The correlator contains unique signal processing functions: flexible LO frequency switching for bandwidth synthesis; 1 ms dump intervals, multi-rate digital signal-processing techniques to allow correlation of signals at different sample rates; and a digital filter for very high resolution cross-power spectra. It also includes autocorrelation, tone extraction, pulsar gating, signal-statistics accumulation.Comment: 44 pages, 13 figure

Requirements visualization

Meeting user requirements of a software system has been a major challenge to software developers. Experience in a number of large projects reveals that a very large percentage of errors were made at the earlier stages of their development. Therefore, it is a well-accepted fact that it is crucial to express user requirements completely, correctly and unambiguously as possible. Many approaches have been applied to validate requirements, but most of them seem fit better to software developers than customers. In spite of their benefits, they often fail in the user validation process since they are based on formal notations not always comprehensible by users. So, in order to facilitate the comprehension by users, visualization techniques appear as an interesting alternative. Visualization techniques are a powerful tool to facilitate the analysis and understanding of complex information. In spite of the their successful in numerous computing areas, little research has been reported in the area of requirements visualization. In this work, we describe our current efforts towards the application of visualization techniques to achieve a more effective requirements validation process. This paper is organized as follows. Section 2 explains visualization concepts and its benefits in the requirements validation domain. Section 3 describes the current project and identifies the different tasks involved in its development.Eje: Ingeniería del software. Computación gráfica y visualizaciónRed de Universidades con Carreras en Informática (RedUNCI

REBA: A Refinement-Based Architecture for Knowledge Representation and Reasoning in Robotics

This paper describes an architecture for robots that combines the complementary strengths of probabilistic graphical models and declarative programming to represent and reason with logic-based and probabilistic descriptions of uncertainty and domain knowledge. An action language is extended to support non-boolean fluents and non-deterministic causal laws. This action language is used to describe tightly-coupled transition diagrams at two levels of granularity, with a fine-resolution transition diagram defined as a refinement of a coarse-resolution transition diagram of the domain. The coarse-resolution system description, and a history that includes (prioritized) defaults, are translated into an Answer Set Prolog (ASP) program. For any given goal, inference in the ASP program provides a plan of abstract actions. To implement each such abstract action, the robot automatically zooms to the part of the fine-resolution transition diagram relevant to this action. A probabilistic representation of the uncertainty in sensing and actuation is then included in this zoomed fine-resolution system description, and used to construct a partially observable Markov decision process (POMDP). The policy obtained by solving the POMDP is invoked repeatedly to implement the abstract action as a sequence of concrete actions, with the corresponding observations being recorded in the coarse-resolution history and used for subsequent reasoning. The architecture is evaluated in simulation and on a mobile robot moving objects in an indoor domain, to show that it supports reasoning with violation of defaults, noisy observations and unreliable actions, in complex domains.Comment: 72 pages, 14 figure

Control theoretic models of pointing

This article presents an empirical comparison of four models from manual control theory on their ability to model targeting behaviour by human users using a mouse: McRuer’s Crossover, Costello’s Surge, second-order lag (2OL), and the Bang-bang model. Such dynamic models are generative, estimating not only movement time, but also pointer position, velocity, and acceleration on a moment-to-moment basis. We describe an experimental framework for acquiring pointing actions and automatically fitting the parameters of mathematical models to the empirical data. We present the use of time-series, phase space, and Hooke plot visualisations of the experimental data, to gain insight into human pointing dynamics. We find that the identified control models can generate a range of dynamic behaviours that captures aspects of human pointing behaviour to varying degrees. Conditions with a low index of difficulty (ID) showed poorer fit because their unconstrained nature leads naturally to more behavioural variability. We report on characteristics of human surge behaviour (the initial, ballistic sub-movement) in pointing, as well as differences in a number of controller performance measures, including overshoot, settling time, peak time, and rise time. We describe trade-offs among the models. We conclude that control theory offers a promising complement to Fitts’ law based approaches in HCI, with models providing representations and predictions of human pointing dynamics, which can improve our understanding of pointing and inform design