Integration and visualization of systems biology data in context of the genome

Background: High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results: The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions: Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.

Incremental parsing in language-based editors: user needs and how to meet them

Incremental parsing has long been recognized as a technique of great utility in the construction of language-based editors, and correspondingly, the area currently enjoys a mature theory. Unfortunately, many practical considerations have been largely overlooked in previously published algorithms. Many user requirements for an editing system necessarily impact on the design of its incremental parser, but most approaches focus only on one: response time. This paper details an incremental parser based on LR parsing techniques and designed for use in a modeless syntax recognition editor. The nature of this editor places significant demands on the structure and quality of the document representation it uses, and hence, on the parser. The strategy presented here is novel in that both the parser and the representation it constructs are tolerant of the inevitable and frequent syntax errors that arise during editing. This is achieved by a method that differs from conventional error repair techniques, and that is more appropriate for use in an interactive context. Furthermore, the parser aims to minimize disturbance to this representation, not only to ensure other system components can operate incrementally, but also to avoid unfortunate consequences for certain user-oriented services. The algorithm is augmented with a limited form of predictive tree-building, and a technique is presented for the determination of valid symbols for menu-based insertion. Copyright (C) 2001 John Wiley & Sons, Ltd.

An approach for graphical user interface bad smells detection

In the context of an e ort to develop methodologies to support the evaluation of interactive system, this paper investigates an approach to detect graphical user interface bad smells. Our approach consists in detecting user interface bad smells through model-based reverse engineering from source code. Models are used to de ne which widgets are present in the interface, when can particular graphical user interface (GUI) events occur, under which conditions, which system actions are executed, and which GUI state is generated next.

Lightweight user modeling – a case study

In the context of previous publications, we propose a new lightweight UM process, intended to work as a tourism recommender system in a commercial environment. The new process tackles issues like cold start, gray sheep and over specialization through a rich user model and the application of a gradual forgetting function to the collected user action history. Also, significant performance improvements were achieved regarding the previously proposed UM process.

An emotional and context-aware model for adapting RSS news to users and groups

The exhibition of information does not always attend to the preferences and characteristics of the users, nor the context that involves the user. With the aim of overcoming this gap, we propose an emotional context-aware model for adapting information contents to users and groups. The proposed model is based on OCC and Big Five models to handle emotion and personality respectively. The idea is to adapt the representation of the information in order to maximize the positive emotional valences and minimize the negatives. To evaluate the proposed model it was developed a prototype for adapting RSS news to users and group of users.

Integration of forest fire management with SDI: user requirements.

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Bringing Context Awareness to IoT-Based Wireless Sensor Networks

IEEE International Conference on Pervasive Computing and Communications (PerCom). 23 to 26, Mar, 2015, PhD Forum. Saint Louis, U.S.A..

Context-aware personalization environment for mobile computing

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Dimensions of source credibility in the case of user-generated advertisements

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics

User-centered design of the interface prototype of a business intelligence mobile application

Dissertação para obtenção do Grau de Mestre em Engenharia e Gestão Industrial

Avatar modeling: a telepresence study with natural user interface

Dissertação para obtenção do Grau de Mestre em Engenharia Electrotécnica e de Computadores

Dimensions of source credibility in the case of user-generated advertisements

User-generated advertising changed the world of advertising and changed the strategies used by marketers. Many researchers explored the dimensions of source credibility in traditional media and online advertising. However, little previous research explored the dimensions of source credibility in the context of user-generated advertising. This exploratory study aims to investigate the different dimensions of source credibility in the case of user-generated advertising. More precisely, this study will explore the following factors: (1) objectivity, (2) trustworthiness, (3) expertise, (4) familiarity, (5) attractiveness and (6) frequency. The results suggest that some of the dimensions of source credibility (objectivity, trustworthiness, expertise, familiarity and attractiveness) remain the same in the case of user-generated advertising. Additionally, a new dimension is added to the factors that explain source credibility (reputation). Furthermore, the analysis suggests that the dimension “frequency” is not an explanatory factor of credibility in the case of user-generated advertisement. The study also suggests that companies using user-generated advertisement as part of their overall marketing strategy should focus on objectivity, trustworthiness, expertise, attractiveness and reputation when selecting users that will communicate sponsored user-generated advertisements.

Adaptive Privacy Management System Design For Context-Aware Mobile Devices

While mobile technologies can provide great personalized services for mobile users, they also threaten their privacy. Such personalization-privacy paradox are particularly salient for context aware technology based mobile applications where user's behaviors, movement and habits can be associated with a consumer's personal identity. In this thesis, I studied the privacy issues in the mobile context, particularly focus on an adaptive privacy management system design for context-aware mobile devices, and explore the role of personalization and control over user's personal data. This allowed me to make multiple contributions, both theoretical and practical. In the theoretical world, I propose and prototype an adaptive Single-Sign On solution that use user's context information to protect user's private information for smartphone. To validate this solution, I first proved that user's context is a unique user identifier and context awareness technology can increase user's perceived ease of use of the system and service provider's authentication security. I then followed a design science research paradigm and implemented this solution into a mobile application called "Privacy Manager". I evaluated the utility by several focus group interviews, and overall the proposed solution fulfilled the expected function and users expressed their intentions to use this application. To better understand the personalization-privacy paradox, I built on the theoretical foundations of privacy calculus and technology acceptance model to conceptualize the theory of users' mobile privacy management. I also examined the role of personalization and control ability on my model and how these two elements interact with privacy calculus and mobile technology model. In the practical realm, this thesis contributes to the understanding of the tradeoff between the benefit of personalized services and user's privacy concerns it may cause. By pointing out new opportunities to rethink how user's context information can protect private data, it also suggests new elements for privacy related business models.

Embedding Emotional Context in Recommender Systems

Emotions are crucial for user's decision making in recommendation processes. We first introduce ambient recommender systems, which arise from the analysis of new trends on the exploitation of the emotional context in the next generation of recommender systems. We then explain some results of these new trends in real-world applications through the smart prediction assistant (SPA) platform in an intelligent learning guide with more than three million users. While most approaches to recommending have focused on algorithm performance. SPA makes recommendations to users on the basis of emotional information acquired in an incremental way. This article provides a cross-disciplinary perspective to achieve this goal in such recommender systems through a SPA platform. The methodology applied in SPA is the result of a bunch of technology transfer projects for large real-world rccommender systems