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”

High resolution tiled display walls

Scalable high-resolution tiled display walls are becoming increasingly important to decision makers and researchers because high pixel counts in combination with large screen areas facilitate content rich, simultaneous display of computer-generated visualization information and high-definition video data from multiple sources. This tutorial is designed to cater for new users as well as researchers who are currently operating tiled display walls or 'OptiPortals'. We will discuss the current and future applications of display wall technology and explore opportunities for participants to collaborate and contribute in a growing community. Multiple tutorial streams will cover both hands-on practical development, as well as policy and method design for embedding these technologies into the research process. Attendees will be able to gain an understanding of how to get started with developing similar systems themselves, in addition to becoming familiar with typical applications and large-scale visualisation techniques. Presentations in this tutorial will describe current implementations of tiled display walls that highlight the effective usage of screen real-estate with various visualization datasets, including collaborative applications such as visualcasting, classroom learning and video conferencing. A feature presentation for this tutorial will be given by Jurgen Schulze from Calit2 at the University of California, San Diego. Jurgen is an expert in scientific visualization in virtual environments, human-computer interaction, real-time volume rendering, and graphics algorithms on programmable graphics hardware.

Of ivory towers and boundary spanners

We all live in a yellow submarine… When I go to work in the morning, in the office building that hosts our BPM research group, on the way up to our level I come by this big breakout room that hosts a number of computer scientists, working away at the next generation software algorithms and iPad applications (I assume). I have never actually been in that room, but every now and then the door is left ajar for a while and I can spot couches, lots (I mean, lots!) of monitors, the odd scientist, a number of Lara Croft posters, and the usual room equipment you’d probably expect from computer scientists (and, no, it’s not like that evil Dennis guy from the Jurassic Park movie, buried in chips, coke, and flickering code screens… It’s also not like the command room from the Nebuchadnezzar, Neo’s hovercraft in the Matrix movies, although I still strongly believe these green lines of code make a good screensaver).

Reduction rules for YAWL workflows with cancellation regions and OR-joins

As the need for concepts such as cancellation and OR-joins occurs naturally in business scenarios, comprehensive support in a workflow language is desirable. However, there is a clear trade-off between the expressive power of a language (i.e., introducing complex constructs such as cancellation and OR-joins) and ease of verification. When a workflow contains a large number of tasks and involves complex control flow dependencies, verification can take too much time or it may even be impossible. There are a number of different approaches to deal with this complexity. Reducing the size of the workflow, while preserving its essential properties with respect to a particular analysis problem, is one such approach. In this paper, we present a set of reduction rules for workflows with cancellation regions and OR-joins and demonstrate how they can be used to improve the efficiency of verification. Our results are presented in the context of the YAWL workflow language.

Free software as a democratic principle

Software forms an important part of the interface between citizens and their government. An increasing amount of government functions are being performed, controlled, or delivered electronically. This software, like all language, is never value-neutral, but must, to some extent, reflect the values of the coder and proprietor. The move that many governments are making towards e-governance, and the increasing reliance that is being placed upon software in government, necessitates a rethinking of the relationships of power and control that are embodied in software.

A deductive system for proving workflow models from operational procedures

Many modern business environments employ software to automate the delivery of workflows; whereas, workflow design and generation remains a laborious technical task for domain specialists. Several differ- ent approaches have been proposed for deriving workflow models. Some approaches rely on process data mining approaches, whereas others have proposed derivations of workflow models from operational struc- tures, domain specific knowledge or workflow model compositions from knowledge-bases. Many approaches draw on principles from automatic planning, but conceptual in context and lack mathematical justification. In this paper we present a mathematical framework for deducing tasks in workflow models from plans in mechanistic or strongly controlled work environments, with a focus around automatic plan generations. In addition, we prove an associative composition operator that permits crisp hierarchical task compositions for workflow models through a set of mathematical deduction rules. The result is a logical framework that can be used to prove tasks in workflow hierarchies from operational information about work processes and machine configurations in controlled or mechanistic work environments.

Reduced-Size microstrip patch antenna for Bluetooth applications

A novel reduced-size microstrip rectangular patch antenna for Bluetooth operation is presented in this paper. The proposed antenna operates in the 2400 to 2484 MHz ISM Band. Although an air substrate is introduced, antenna occupies a small volume of 33.3×6.6×0.8 mm3. The gain and the impedance bandwidth of the antenna are predicted using a commercial Finite Element Method software package. The predicted results show good agreement with measured data.

Clustering composite SaaS components in cloud computing using a grouping genetic algorithm

Recently, Software as a Service (SaaS) in Cloud computing, has become more and more significant among software users and providers. To offer a SaaS with flexible functions at a low cost, SaaS providers have focused on the decomposition of the SaaS functionalities, or known as composite SaaS. This approach has introduced new challenges in SaaS resource management in data centres. One of the challenges is managing the resources allocated to the composite SaaS. Due to the dynamic environment of a Cloud data centre, resources that have been initially allocated to SaaS components may be overloaded or wasted. As such, reconfiguration for the components’ placement is triggered to maintain the performance of the composite SaaS. However, existing approaches often ignore the communication or dependencies between SaaS components in their implementation. In a composite SaaS, it is important to include these elements, as they will directly affect the performance of the SaaS. This paper will propose a Grouping Genetic Algorithm (GGA) for multiple composite SaaS application component clustering in Cloud computing that will address this gap. To the best of our knowledge, this is the first attempt to handle multiple composite SaaS reconfiguration placement in a dynamic Cloud environment. The experimental results demonstrate the feasibility and the scalability of the GGA.

A parallel cooperative co-evolutionary genetic algorithm for the composite SaaS placement problem in Cloud computing

A composite SaaS (Software as a Service) is a software that is comprised of several software components and data components. The composite SaaS placement problem is to determine where each of the components should be deployed in a cloud computing environment such that the performance of the composite SaaS is optimal. From the computational point of view, the composite SaaS placement problem is a large-scale combinatorial optimization problem. Thus, an Iterative Cooperative Co-evolutionary Genetic Algorithm (ICCGA) was proposed. The ICCGA can find reasonable quality of solutions. However, its computation time is noticeably slow. Aiming at improving the computation time, we propose an unsynchronized Parallel Cooperative Co-evolutionary Genetic Algorithm (PCCGA) in this paper. Experimental results have shown that the PCCGA not only has quicker computation time, but also generates better quality of solutions than the ICCGA.

An analytical tool that quantifies cellular morphology changes from three-dimensional fluorescence images

The most common software analysis tools available for measuring fluorescence images are for two-dimensional (2D) data that rely on manual settings for inclusion and exclusion of data points, and computer-aided pattern recognition to support the interpretation and findings of the analysis. It has become increasingly important to be able to measure fluorescence images constructed from three-dimensional (3D) datasets in order to be able to capture the complexity of cellular dynamics and understand the basis of cellular plasticity within biological systems. Sophisticated microscopy instruments have permitted the visualization of 3D fluorescence images through the acquisition of multispectral fluorescence images and powerful analytical software that reconstructs the images from confocal stacks that then provide a 3D representation of the collected 2D images. Advanced design-based stereology methods have progressed from the approximation and assumptions of the original model-based stereology(1) even in complex tissue sections(2). Despite these scientific advances in microscopy, a need remains for an automated analytic method that fully exploits the intrinsic 3D data to allow for the analysis and quantification of the complex changes in cell morphology, protein localization and receptor trafficking. Current techniques available to quantify fluorescence images include Meta-Morph (Molecular Devices, Sunnyvale, CA) and Image J (NIH) which provide manual analysis. Imaris (Andor Technology, Belfast, Northern Ireland) software provides the feature MeasurementPro, which allows the manual creation of measurement points that can be placed in a volume image or drawn on a series of 2D slices to create a 3D object. This method is useful for single-click point measurements to measure a line distance between two objects or to create a polygon that encloses a region of interest, but it is difficult to apply to complex cellular network structures. Filament Tracer (Andor) allows automatic detection of the 3D neuronal filament-like however, this module has been developed to measure defined structures such as neurons, which are comprised of dendrites, axons and spines (tree-like structure). This module has been ingeniously utilized to make morphological measurements to non-neuronal cells(3), however, the output data provide information of an extended cellular network by using a software that depends on a defined cell shape rather than being an amorphous-shaped cellular model. To overcome the issue of analyzing amorphous-shaped cells and making the software more suitable to a biological application, Imaris developed Imaris Cell. This was a scientific project with the Eidgenössische Technische Hochschule, which has been developed to calculate the relationship between cells and organelles. While the software enables the detection of biological constraints, by forcing one nucleus per cell and using cell membranes to segment cells, it cannot be utilized to analyze fluorescence data that are not continuous because ideally it builds cell surface without void spaces. To our knowledge, at present no user-modifiable automated approach that provides morphometric information from 3D fluorescence images has been developed that achieves cellular spatial information of an undefined shape (Figure 1). We have developed an analytical platform using the Imaris core software module and Imaris XT interfaced to MATLAB (Mat Works, Inc.). These tools allow the 3D measurement of cells without a pre-defined shape and with inconsistent fluorescence network components. Furthermore, this method will allow researchers who have extended expertise in biological systems, but not familiarity to computer applications, to perform quantification of morphological changes in cell dynamics.

A penalty-based grouping genetic algorithm for multiple composite SaaS components clustering in Cloud

Software as a Service (SaaS) in Cloud is getting more and more significant among software users and providers recently. A SaaS that is delivered as composite application has many benefits including reduced delivery costs, flexible offers of the SaaS functions and decreased subscription cost for users. However, this approach has introduced a new problem in managing the resources allocated to the composite SaaS. The resource allocation that has been done at the initial stage may be overloaded or wasted due to the dynamic environment of a Cloud. A typical data center resource management usually triggers a placement reconfiguration for the SaaS in order to maintain its performance as well as to minimize the resource used. Existing approaches for this problem often ignore the underlying dependencies between SaaS components. In addition, the reconfiguration also has to comply with SaaS constraints in terms of its resource requirements, placement requirement as well as its SLA. To tackle the problem, this paper proposes a penalty-based Grouping Genetic Algorithm for multiple composite SaaS components clustering in Cloud. The main objective is to minimize the resource used by the SaaS by clustering its component without violating any constraint. Experimental results demonstrate the feasibility and the scalability of the proposed algorithm.

Eat Cook Grow : Mixing Human-Computer Interactions with Human-Food Interactions

Food has been a major agenda in political, socio-cultural, and environmental domains throughout history. The significance of food has been particularly highlighted in recent years with the growing public awareness of the unfolding impacts of climate change, challenging our understanding, practice, and expectations of our relationship with food. Parallel to this development has been the rise of web applications such as blogs, wikis, video and photo sharing sites, and social networking systems that are arguably more open, collaborative, and personalisable. These so-called ‘Web 2.0’ technologies have contributed to a more participatory Internet experience than what had previously been possible. An increasing number of these social applications are now available on mobile technologies where they take advantage of device-specific features such as sensors, location and context awareness, further expanding potential for the culture of participation and creativity. This international volume assembles a diverse collection of book chapters that contribute towards exploring and better understanding the opportunities and challenges provided by tools, interfaces, methods, and practices of social and mobile technology to enable engagement with people and creativity in the domain of food in contemporary society. It brings together an international group of academics and practitioners from a diverse range of disciplines such as computing and engineering, social sciences, digital media and human-computer interaction to critically examine a range of applications of social and mobile technology, such as social networking, mobile interaction, wikis, twitter, blogging, mapping, shared displays and urban screens, and their impact to foster a better understanding and practice of environmentally, socio-culturally, economically, and health-wise sustainable food culture.