Practical introduction to development of sage applications

Throughout this workshop session we have looked at various configurations of Sage as well as using the Sage UI to run Sage applications (e.g. the image viewer). More advanced usage of Sage has been demonstrated using a Sage compatible version of Paraview highlighting the potential of parallel rendering. The aim of this tutorial session is to give a practical introduction to developing visual content for a tiled display using the Sage libraries. After completing this tutorial you should have the basic tools required to develop your own custom Sage applications. This tutorial is designed for software developers and intermediate programming knowledge is assumed, along with some introductory OpenGL . You will be required to write small portions of C/C++ code to complete this worksheet. However if you do not feel comfortable writing code (or have never written in C or C++), we will be on hand throughout this session so feel free to ask for some help. We have a number of machines in this lab running a VNC client to a virtual machine running Fedora 12. You should all be able to log in with the username “escience”, and password “escience10”. Some of the commands in this worksheet require you to run them as the root user, so note the password as you may need to use it a few times. If you need to access the Internet, then use the username “qpsf01”, password “escience10”

Network protocols and predictive control strategies for distributed real-time control applications

A trend in design and implementation of modern industrial automation systems is to integrate computing, communication and control into a unified framework at different levels of machine/factory operations and information processing. These distributed control systems are referred to as networked control systems (NCSs). They are composed of sensors, actuators, and controllers interconnected over communication networks. As most of communication networks are not designed for NCS applications, the communication requirements of NCSs may be not satisfied. For example, traditional control systems require the data to be accurate, timely and lossless. However, because of random transmission delays and packet losses, the control performance of a control system may be badly deteriorated, and the control system rendered unstable. The main challenge of NCS design is to both maintain and improve stable control performance of an NCS. To achieve this, communication and control methodologies have to be designed. In recent decades, Ethernet and 802.11 networks have been introduced in control networks and have even replaced traditional fieldbus productions in some real-time control applications, because of their high bandwidth and good interoperability. As Ethernet and 802.11 networks are not designed for distributed control applications, two aspects of NCS research need to be addressed to make these communication networks suitable for control systems in industrial environments. From the perspective of networking, communication protocols need to be designed to satisfy communication requirements for NCSs such as real-time communication and high-precision clock consistency requirements. From the perspective of control, methods to compensate for network-induced delays and packet losses are important for NCS design. To make Ethernet-based and 802.11 networks suitable for distributed control applications, this thesis develops a high-precision relative clock synchronisation protocol and an analytical model for analysing the real-time performance of 802.11 networks, and designs a new predictive compensation method. Firstly, a hybrid NCS simulation environment based on the NS-2 simulator is designed and implemented. Secondly, a high-precision relative clock synchronization protocol is designed and implemented. Thirdly, transmission delays in 802.11 networks for soft-real-time control applications are modeled by use of a Markov chain model in which real-time Quality-of- Service parameters are analysed under a periodic traffic pattern. By using a Markov chain model, we can accurately model the tradeoff between real-time performance and throughput performance. Furthermore, a cross-layer optimisation scheme, featuring application-layer flow rate adaptation, is designed to achieve the tradeoff between certain real-time and throughput performance characteristics in a typical NCS scenario with wireless local area network. Fourthly, as a co-design approach for both a network and a controller, a new predictive compensation method for variable delay and packet loss in NCSs is designed, where simultaneous end-to-end delays and packet losses during packet transmissions from sensors to actuators is tackled. The effectiveness of the proposed predictive compensation approach is demonstrated using our hybrid NCS simulation environment.

Information and communication technology for E-regions

Information and communication technologies (ICTs) are essential components of the knowledge economy, and have an immense complementary role in innovation, education, knowledge creation, and relations with government, civil society, and business within city regions. The ability to create, distribute, and exploit knowledge has become a major source of competitive advantage, wealth creation, and improvements in the new regional policies. Growing impact of ICTs on the economy and society, rapid application of recent scientific advances in new products and processes, shifting to more knowledge-intensive industry and services, and rising skill requirements have become crucial concepts for urban and regional competitiveness. Therefore, harnessing ICTs for knowledge-based urban development (KBUD) has a significant impact on urban and regional growth (Yigitcanlar, 2005). In this sense, e-region is a novel concept utilizing ICTs for regional development. Since the Helsinki European Council announced Turkey as a candidate for European Union (EU) membership in 1999, the candidacy has accelerated the speed of regional policy enhancements and adoption of the European regional policy standards. These enhancements and adoption include the generation of a new regional spatial division, NUTS-II statistical regions; a new legislation on the establishment of regional development agencies (RDAs); and new orientations in the field of high education, science, and technology within the framework of the EU’s Lisbon Strategy and the Bologna Process. The European standards posed an ambitious new agenda in the development and application of contemporary regional policy in Turkey (Bilen, 2005). In this sense, novel regional policies in Turkey necessarily endeavor to include information society objectives through efficient use of new technologies such as ICTs. Such a development seeks to be based on tangible assets of the region (Friedmann, 2006) as well as the best practices deriving from grounding initiatives on urban and local levels. These assets provide the foundation of an e-region that harnesses regional development in an information society context. With successful implementations, the Marmara region’s local governments in Turkey are setting the benchmark for the country in the implementation of spatial information systems and e-governance, and moving toward an e-region. Therefore, this article aims to shed light on organizational and regional realities of recent practices of ICT applications and their supply instruments based on evidence from selected local government organizations in the Marmara region. This article also exemplifies challenges and opportunities of the region in moving toward an e-region and provides a concise review of different ICT applications and strategies in a broader urban and regional context. The article is organized in three parts. The following section scrutinizes the e-region framework and the role of ICTs in regional development. Then, Marmara’s opportunities and challenges in moving toward an e-region are discussed in the context of ICT applications and their supply instruments based on public-sector projects, policies, and initiatives. Subsequently, the last section discusses conclusions and prospective research.

Information accountability for online healthcare social networks

Online social networking has become one of the most popular Internet applications in the modern era. They have given the Internet users, access to information that other Internet based applications are unable to. Although many of the popular online social networking web sites are focused towards entertainment purposes, sharing information can benefit the healthcare industry in terms of both efficiency and effectiveness. But the capability to share personal information; the factor which has made online social networks so popular, is itself a major obstacle when considering information security and privacy aspects. Healthcare can benefit from online social networking if they are implemented such that sensitive patient information can be safeguarded from ill exposure. But in an industry such as healthcare where the availability of information is crucial for better decision making, information must be made available to the appropriate parties when they require it. Hence the traditional mechanisms for information security and privacy protection may not be suitable for healthcare. In this paper we propose a solution to privacy enhancement in online healthcare social networks through the use of an information accountability mechanism.

Automated proof for formal indistinguishability and its applications

Bana et al. proposed the relation formal indistinguishability (FIR), i.e. an equivalence between two terms built from an abstract algebra. Later Ene et al. extended it to cover active adversaries and random oracles. This notion enables a framework to verify computational indistinguishability while still offering the simplicity and formality of symbolic methods. We are in the process of making an automated tool for checking FIR between two terms. First, we extend the work by Ene et al. further, by covering ordered sorts and simplifying the way to cope with random oracles. Second, we investigate the possibility of combining algebras together, since it makes the tool scalable and able to cover a wide class of cryptographic schemes. Specially, we show that the combined algebra is still computationally sound, as long as each algebra is sound. Third, we design some proving strategies and implement the tool. Basically, the strategies allow us to find a sequence of intermediate terms, which are formally indistinguishable, between two given terms. FIR between the two given terms is then guaranteed by the transitivity of FIR. Finally, we show applications of the work, e.g. on key exchanges and encryption schemes. In the future, the tool should be extended easily to cover many schemes. This work continues previous research of ours on use of compilers to aid in automated proofs for key exchange.

A hardware-based multi-disciplinary design optimization method for aeronautical applications

There are many applications in aeronautics where there exist strong couplings between disciplines. One practical example is within the context of Unmanned Aerial Vehicle(UAV) automation where there exists strong coupling between operation constraints, aerodynamics, vehicle dynamics, mission and path planning. UAV path planning can be done either online or offline. The current state of path planning optimisation online UAVs with high performance computation is not at the same level as its ground-based offline optimizer's counterpart, this is mainly due to the volume, power and weight limitations on the UAV; some small UAVs do not have the computational power needed for some optimisation and path planning task. In this paper, we describe an optimisation method which can be applied to Multi-disciplinary Design Optimisation problems and UAV path planning problems. Hardware-based design optimisation techniques are used. The power and physical limitations of UAV, which may not be a problem in PC-based solutions, can be approached by utilizing a Field Programmable Gate Array (FPGA) as an algorithm accelerator. The inevitable latency produced by the iterative process of an Evolutionary Algorithm (EA) is concealed by exploiting the parallelism component within the dataflow paradigm of the EA on an FPGA architecture. Results compare software PC-based solutions and the hardware-based solutions for benchmark mathematical problems as well as a simple real world engineering problem. Results also indicate the practicality of the method which can be used for more complex single and multi objective coupled problems in aeronautical applications.

Nursing Sans Frontieres: A Three Year Case Study of Multi-State Registration of Support Nursing Practice Using Information Technology

Objective: To highlight the registration issues for nurses who wish to practice nationally, particularly those practicing within the telehealth sector. Design: As part of a national clinical research study, applications were made to every state and territory for mutual recognition of nursing registration and fee waiver for telenursing cross boarder practice for a period of three years. These processes are described using a case study approach. Outcome: The aim of this case study was to achieve registration in every state and territory of Australia without paying multiple fees by using mutual recognition provisions and the cross-border fee waiver policy of the nurse regulatory authorities in order to practice telenursing. Results: Mutual recognition and fee waiver for cross-border practice was granted unconditionally in two states: Victoria (Vic) and Tasmania (Tas), and one territory: the Northern Territory (NT). The remainder of the Australian states and territories would only grant temporary registration for the period of the project or not at all, due to policy restrictions or nurse regulatory authority (NRA) Board decisions. As a consequence of gaining fee waiver the annual cost of registration was a maximum of $145 per annum as opposed to the potential $959 for initial registration and $625 for annual renewal. Conclusions: Having eight individual nurses Acts and NRAs for a population of 265,000 nurses would clearly indicate a case for over regulation in this country. The structure of regulation of nursing in Australia is a barrier to the changing and evolving role of nurses in the 21st century and a significant factor when considering workforce planning.

Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information

Background The majority of peptide bonds in proteins are found to occur in the trans conformation. However, for proline residues, a considerable fraction of Prolyl peptide bonds adopt the cis form. Proline cis/trans isomerization is known to play a critical role in protein folding, splicing, cell signaling and transmembrane active transport. Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function. Results In this paper, we propose a new approach to predict the proline cis/trans isomerization in proteins using support vector machine (SVM). The preliminary results indicated that using Radial Basis Function (RBF) kernels could lead to better prediction performance than that of polynomial and linear kernel functions. We used single sequence information of different local window sizes, amino acid compositions of different local sequences, multiple sequence alignment obtained from PSI-BLAST and the secondary structure information predicted by PSIPRED. We explored these different sequence encoding schemes in order to investigate their effects on the prediction performance. The training and testing of this approach was performed on a newly enlarged dataset of 2424 non-homologous proteins determined by X-Ray diffraction method using 5-fold cross-validation. Selecting the window size 11 provided the best performance for determining the proline cis/trans isomerization based on the single amino acid sequence. It was found that using multiple sequence alignments in the form of PSI-BLAST profiles could significantly improve the prediction performance, the prediction accuracy increased from 62.8% with single sequence to 69.8% and Matthews Correlation Coefficient (MCC) improved from 0.26 with single local sequence to 0.40. Furthermore, if coupled with the predicted secondary structure information by PSIPRED, our method yielded a prediction accuracy of 71.5% and MCC of 0.43, 9% and 0.17 higher than the accuracy achieved based on the singe sequence information, respectively. Conclusion A new method has been developed to predict the proline cis/trans isomerization in proteins based on support vector machine, which used the single amino acid sequence with different local window sizes, the amino acid compositions of local sequence flanking centered proline residues, the position-specific scoring matrices (PSSMs) extracted by PSI-BLAST and the predicted secondary structures generated by PSIPRED. The successful application of SVM approach in this study reinforced that SVM is a powerful tool in predicting proline cis/trans isomerization in proteins and biological sequence analysis.

A transport protocol for real-time applications in wireless networked control systems

A Networked Control System (NCS) is a feedback-driven control system wherein the control loops are closed through a real-time network. Control and feedback signals in an NCS are exchanged among the system’s components in the form of information packets via the network. Nowadays, wireless technologies such as IEEE802.11 are being introduced to modern NCSs as they offer better scalability, larger bandwidth and lower costs. However, this type of network is not designed for NCSs because it introduces a large amount of dropped data, and unpredictable and long transmission latencies due to the characteristics of wireless channels, which are not acceptable for real-time control systems. Real-time control is a class of time-critical application which requires lossless data transmission, small and deterministic delays and jitter. For a real-time control system, network-introduced problems may degrade the system’s performance significantly or even cause system instability. It is therefore important to develop solutions to satisfy real-time requirements in terms of delays, jitter and data losses, and guarantee high levels of performance for time-critical communications in Wireless Networked Control Systems (WNCSs). To improve or even guarantee real-time performance in wireless control systems, this thesis presents several network layout strategies and a new transport layer protocol. Firstly, real-time performances in regard to data transmission delays and reliability of IEEE 802.11b-based UDP/IP NCSs are evaluated through simulations. After analysis of the simulation results, some network layout strategies are presented to achieve relatively small and deterministic network-introduced latencies and reduce data loss rates. These are effective in providing better network performance without performance degradation of other services. After the investigation into the layout strategies, the thesis presents a new transport protocol which is more effcient than UDP and TCP for guaranteeing reliable and time-critical communications in WNCSs. From the networking perspective, introducing appropriate communication schemes, modifying existing network protocols and devising new protocols, have been the most effective and popular ways to improve or even guarantee real-time performance to a certain extent. Most previously proposed schemes and protocols were designed for real-time multimedia communication and they are not suitable for real-time control systems. Therefore, devising a new network protocol that is able to satisfy real-time requirements in WNCSs is the main objective of this research project. The Conditional Retransmission Enabled Transport Protocol (CRETP) is a new network protocol presented in this thesis. Retransmitting unacknowledged data packets is effective in compensating for data losses. However, every data packet in realtime control systems has a deadline and data is assumed invalid or even harmful when its deadline expires. CRETP performs data retransmission only in the case that data is still valid, which guarantees data timeliness and saves memory and network resources. A trade-off between delivery reliability, transmission latency and network resources can be achieved by the conditional retransmission mechanism. Evaluation of protocol performance was conducted through extensive simulations. Comparative studies between CRETP, UDP and TCP were also performed. These results showed that CRETP significantly: 1). improved reliability of communication, 2). guaranteed validity of received data, 3). reduced transmission latency to an acceptable value, and 4). made delays relatively deterministic and predictable. Furthermore, CRETP achieved the best overall performance in comparative studies which makes it the most suitable transport protocol among the three for real-time communications in a WNCS.

Elements pour adapter les systemes de recherche d'information aux dyslexiques [Elements to adapt information retrieval systems to dyslexic users]

RÉSUMÉ. La prise en compte des troubles de la communication dans l’utilisation des systèmes de recherche d’information tels qu’on peut en trouver sur le Web est généralement réalisée par des interfaces utilisant des modalités n’impliquant pas la lecture et l’écriture. Peu d’applications existent pour aider l’utilisateur en difficulté dans la modalité textuelle. Nous proposons la prise en compte de la conscience phonologique pour assister l’utilisateur en difficulté d’écriture de requêtes (dysorthographie) ou de lecture de documents (dyslexie). En premier lieu un système de réécriture et d’interprétation des requêtes entrées au clavier par l’utilisateur est proposé : en s’appuyant sur les causes de la dysorthographie et sur les exemples à notre disposition, il est apparu qu’un système combinant une approche éditoriale (type correcteur orthographique) et une approche orale (système de transcription automatique) était plus approprié. En second lieu une méthode d’apprentissage automatique utilise des critères spécifiques , tels que la cohésion grapho-phonémique, pour estimer la lisibilité d’une phrase, puis d’un texte. ABSTRACT. Most applications intend to help disabled users in the information retrieval process by proposing non-textual modalities. This paper introduces specific parameters linked to phonological awareness in the textual modality. This will enhance the ability of systems to deal with orthographic issues and with the adaptation of results to the reader when for example the reader is dyslexic. We propose a phonology based sentence level rewriting system that combines spelling correction, speech synthesis and automatic speech recognition. This has been evaluated on a corpus of questions we get from dyslexic children. We propose a specific sentence readability measure that involves phonetic parameters such as grapho-phonemic cohesion. This has been learned on a corpus of reading time of sentences read by dyslexic children.

Content-based video indexing for sports applications using integrated multi-modal approach

To sustain an ongoing rapid growth of video information, there is an emerging demand for a sophisticated content-based video indexing system. However, current video indexing solutions are still immature and lack of any standard. This doctoral consists of a research work based on an integrated multi-modal approach for sports video indexing and retrieval. By combining specific features extractable from multiple audio-visual modalities, generic structure and specific events can be detected and classified. During browsing and retrieval, users will benefit from the integration of high-level semantic and some descriptive mid-level features such as whistle and close-up view of player(s).

Web 2.0 applications in enterprises and education

Web 2.0 technology and concepts are being used increasingly by organisations to enhance knowledge, efficiency, engagement and reputation. Understanding the concepts of Web 2.0, its characteristics, and how the technology and concepts can be adopted, is essential to successfully reap the potential benefits. In fact, there is a debate about using the Web 2.0 idiom to refer to the concept behind it; however, this term is widely used in literature as well as in industry. In this paper, the definition of Web 2.0 technology, its characteristics and the attributes, will be presented. In addition, the adoption of such technology is further explored through the presentation of two separate case examples of Web 2.0 being used: to enhance an enterprise; and to enhance university teaching. The similarities between these implementations are identified and discussed, including how the findings point to generic principles of adoption.

Mobile applications of focused link discovery

Interaction with a mobile device remains difficult due to inherent physical limitations. This dif-ficulty is particularly evident for search, which re-quires typing. We extend the One-Search-Only search paradigm by adding a novel link-browsing scheme built on top of automatic link discovery. A prototype was built for iPhone and tested with 12 subjects. A post-use interview survey suggests that the extended paradigm improves the mobile information seeking experience.

Towards semantic search and inference in electronic medical records : an approach using concept-based information retrieval

For more than a decade research in the field of context aware computing has aimed to find ways to exploit situational information that can be detected by mobile computing and sensor technologies. The goal is to provide people with new and improved applications, enhanced functionality and better use experience (Dey, 2001). Early applications focused on representing or computing on physical parameters, such as showing your location and the location of people or things around you. Such applications might show where the next bus is, which of your friends is in the vicinity and so on. With the advent of social networking software and microblogging sites such as Facebook and Twitter, recommender systems and so on context-aware computing is moving towards mining the social web in order to provide better representations and understanding of context, including social context. In this paper we begin by recapping different theoretical framings of context. We then discuss the problem of context- aware computing from a design perspective.