Enhancing cloud computing environments using a cluster as a service

The emergence of cloud computing has caused a significant change in how IT infrastructures are provided to research and business organizations. Instead of paying for expensive hardware and incur excessive maintenance costs, it is now possible to rent the IT infrastructure of other organizations for a minimal fee. While the existence of cloud computing is new. The elements used to create clouds have been around for some time. Cloud computing systems have been made possible through the use of large-scale clusters, service-oriented architecture (SOA), Web services, and virtualization. While the idea of offering resources via Web services is commonplace in cloud computing, little attention has been paid to the clients themselves specifically, human operators. Despite that clouds host a variety of resources which in turn are accessible to a variety of clients, support for human users is minimal.

Stream management within the CloudMiner

Nowadays cloud computing has become a major trend that enterprises and research organizations are pursuing with increasing zest. A potentially important application area for clouds is data analytics. In our previous publication, we introduced a novel cloud infrastructure, the CloudMiner, which facilitates data mining on massive scientific data. By providing a cloud platform which hosts data mining cloud services following the Software as a Service (SaaS) paradigm, CloudMiner offers the capability for realizing cloud-based data mining tasks upon traditional distributed databases and other dataset types. However, little attention has been paid to the issue of data stream management on the cloud so far. We have noticed the fact that some features of the cloud meet very well the requirements of data stream management. Consequently, we developed an innovative software framework, called the StreamMiner, which is introduced in this paper. It serves as an extension to the CloudMiner for facilitating, in particular, real-world data stream management and analysis using cloud services. In addition, we also introduce our tentative implementation of the framework. Finally, we present and discuss the first experimental performance results achieved with the first StreamMiner prototype.

Toward exposing and accessing HPC applications in a SaaS cloud

The cost and time of deploying HPC applications on clouds is a problem. Instead of conducting their research discipline specialists are forced to carry out activities for application deployment, publication and ease of access. In response, a new approach for HPC application deployment and access in clouds is proposed. The major innovations are a new approach to deploying and executing HPC applications on IaaS and PaaS clouds, and exposing HPC applications as services. Through three case studies this paper demonstrates the feasibility and effectiveness of the proposed approach that could lead to the building of a SaaS library of discipline-oriented services evocable through user friendly, discipline specific interfaces. The new approach will reduce the time and money needed to deploy and expose discipline HPC applications.

Function-based approach to mixed haptic effects rendering

Commonly, surface and solid haptic effects are defined in such a way that they hardly can be rendered together. We propose a method for defining mixed haptic effects including surface, solid, and force fields. These haptic effects can be applied to virtual scenes containing various objects, including polygon meshes, point clouds, impostors, and layered textures, voxel models as well as function-based shapes. Accordingly, we propose a way how to identify location of the haptic tool in such virtual scenes as well as consistently and seamlessly determine haptic effects when the haptic tool moves in the scenes with objects having different sizes, locations, and mutual penetrations. To provide for an efficient and flexible rendering of haptic effects, we propose to concurrently use explicit, implicit and parametric functions, and algorithmic procedures.

A VMD plugin for NAMD simulations on Amazon EC2

VMD and NAMD are two major molecular dynamics simulation software packages, which can work together for mining structural information of bio-molecules. Carrying out such molecular dynamics simulations can help researchers to understand the roles and functions of various bio-molecules in life science research. Recently, clouds have provided HPC clusters on demand that allow users to benefit from their flexibility, elasticity, and lower costs. Although cloud computing promises to provide seamless access to HPC clusters through the abstraction of services, which hide the details of the underlying software and hardware infrastructure, users without in depth computing knowledge are still forced to cope with many low level system and programming details. Therefore, we have designed and developed a software plugin of VMD, which can provide an integrated framework for NAMD to be executed on Amazon EC2. The proposed Amazon EC2 Plugin for VMD frees users from performing many tedious computing tasks such as launching, connecting and terminating Amazon EC2 compute instances; configuring a HPC cluster; and installing middleware and software applications before the system is readily available for any scientific investigation. This allows VMD/NAMD users to spend less time getting applications to work on HPC clusters but more time for bio-research.

Sensor-cloud computing : novel applications and research problems

Recent developments in sensor networks and cloud computing saw the emergence of a new platform called sensor-clouds. While the proposition of such a platform is to virtualise the management of physical sensor devices, we are seeing novel applications been created based on a new class of social sensors. Social sensors are effectively a human-device combination that sends torrent of data as a result of social interactions and social events. The data generated appear in different formats such as photographs, videos and short text messages. Unlike other sensor devices, social sensors operate on the control of individuals via their mobile devices such as a phone or a laptop. And unlike other sensors that generate data at a constant rate or format, social sensors generate data that are spurious and varied, often in response to events as individual as a dinner outing, or a news announcement of interests to the public. This collective presence of social data creates opportunities for novel applications never experienced before. This paper discusses such applications as a result of utilising social sensors within a sensor-cloud environment. Consequently, the associated research problems are also presented.

Evanescent

Exhibition of original artworks created in 2013. Evanescent is a new series produced in 2013 which premiered at the Castlemaine State Festival 15-24 March 2013. The series revisits a childhood delight and fascination with the projected image and the natural world. For me then, as it is now, a magnifying glass was a wonder; its simple optics twisted light into abstract comas and sci-fi aberrations; able to compact a whole view into a luminous, paradoxically inverted phantom that could fit literally into the palm of my hand. By curling fingers and thumb around the lens and cupping both hands around the elusive rays, and by peering into the space in which I had trapped them, I fancied that I had entered into the secret workings of the eye. Chrysalis, for example, appears as a scenic projection from a hand-held lens and simultaneously as the litter of the forest floor. It is produced with a makeshift camera-obscura. The nebulous silhouettes of trees, some blurred under the passing clouds of a summer wind resolve here and there into crisp lines curled across the surface of a fallen leaf on which a moth chrysalis adheres. The leaf assumes Brobdingnagian proportions and thickness as the evanescent image shrinks and is foreshortened then dissolves in the enlarged dust and grit. It manifests the unique sight anchored at this fixed point, to reveal what we might see if we were to become vegetable or mineral. Near and far, large and small, superimpose, trigonometrically exact in their adjacency and spatial relations, presenting us with a located point of view.Why? I want to understand more intimately the interior of the natural landscape, rather than any ‘scene’ of human presence, or the context of any cultural landmark. In the steep, bush locations in which I am making these images, my means are necessarily makeshift; my camera and an old manual-aperture lens able to be carried in a backpack with a black T-shirt as a 'dark-tent'. The project is not systematic but intuitive and responsive to prevailing conditions and the effect on the projection caused by sun, shade, weather and situation. I am guided by the response of objects, textures and surfaces to the projected image and how they modulate and map it. This is landscape, but not from a human point of view.

N-dimensional animal energetic niches clarify behavioural options in a variable marine environment

Animals respond to environmental variation by exhibiting a number of different behaviours and/or rates of activity, which result in corresponding variation in energy expenditure. Successful animals generally maximize efficiency or rate of energy gain through foraging. Quantification of all features that modulate energy expenditure can theoretically be modelled as an animal energetic niche or power envelope; with total power being represented by the vertical axis and n-dimensional horizontal axes representing extents of processes that affect energy expenditure. Such an energetic niche could be used to assess the energetic consequences of animals adopting particular behaviours under various environmental conditions. This value of this approach was tested by constructing a simple mechanistic energetics model based on data collected from recording devices deployed on 41 free-living Magellanic penguins (Spheniscus magellanicus), foraging from four different colonies in Argentina and consequently catching four different types of prey. Energy expenditure was calculated as a function of total distance swum underwater (horizontal axis 1) and maximum depth reached (horizontal axis 2). The resultant power envelope was invariant, irrespective of colony location, but penguins from the different colonies tended to use different areas of the envelope. The different colony solutions appeared to represent particular behavioural options for exploiting the available prey and demonstrate how penguins respond to environmental circumstance (prey distribution), the energetic consequences that this has for them, and how this affects the balance of energy acquisition through foraging and expenditure strategy.

Introduction: secularization and its discontents

Sigmund Freud’s 1927 work The Future of Illusion expresses the great psychoanalyst’s most whiggish assessment of the situation of Western, post-enlightenment societies. In it, Freud reanimates the ancient tradition of the materialist-Epicurean criticism of religion, with its skepticism concerning all invisible powers. For Freud, famously, the religious belief in higher, supernatural deities—particularly, the monotheistic God—represents a wish-fulfillment and illusion (Freud 1927: 30, 43). This illusion takes its particular shapes from our earliest childhood experiences of helplessness, and the longing for an all-protecting, omnibenevolent father. With the progress of science, and its benefits in technology, Freud opined that the period of the cultural pre-eminence of religion in the West was over. Civilization and its Discontents, written 3 years later, expresses a similarly sceptical assessment of religion. Whether founded in an oceanic, mystical sentiment of oneness, or the refined language of the theologians, religion remains for Freud ‘patently infantile’ (Freud 1930: 86). Between 1927 and 1930, however, Freud’s assessment of the wider prospects of modern Kultur shifted, if it did not entirely reverse. With the fortunes of fascism rising, and the first clouds of renewed European war forming on the horizon, Freud now argues that the psychological price demanded by the modern world’s manifold civilizational advances is perhaps too high. The sexual and aggressive impulses modern society demands subjects renounce must return in the forms of organized violence, collective and individual neuroses—and in the same form of unconscious guilt Freud had argued elsewhere animated the totems and taboos of the great religions (Freud 1913, 1938). Although Freud did not draw the conclusion, the logic of his wider Kulturpessimismus points to the claim that the psychologically deep-set ‘illusions’ of religion could expect a long and viable future.

Service and cloud computing supporting genomic analysis of the mammalian species

 This research focused on building Software as a Service clouds to support mammalian genomic applications such as personalized medicine. Outcomes of this research included a Software as a Service cloud framework, the Uncinus research cloud and novel genomic analysis software. Results have been published in high ranking peer-reviewed international journals.

A survey of approaches and frameworks to carry out genomic data analysis on the cloud

High Performance Computing (HPC) clouds have started to change the way how research in science, in particular medicine and genomics (bioinformatics) is being carried out. Researchers who have taken advantage of this technology can process larger amounts of data and speed up scientific discovery. However, most HPC clouds are provided at an Infrastructure as a Service (IaaS) level, users are presented with a set of virtual servers which need to be put together to form HPC environments via time consuming resource management and software configuration tasks, which make them practically unusable by discipline, non-computing specialists. In response, there is a new trend to expose cloud applications as services to simplify access and execution on clouds. This paper firstly examines commonly used cloud-based genomic analysis services (Tuxedo Suite, Galaxy and Cloud Bio Linux). As a follow up, we propose two new solutions (HPCaaS and Uncinus), which aim to automate aspects of the service development and deployment process. By comparing and contrasting these five solutions, we identify key mechanisms of service creation, execution and access that are required to support genomic research on the SaaS cloud, in particular by discipline specialists. © 2014 IEEE.

A survey of cloud-based service computing solutions for mammalian genomics

Cloud-based service computing has started to change the way how research in science, in particular biology, medicine, and engineering, is being carried out. Researchers in the area of mammalian genomics have taken advantage of cloud computing technology to cost-effectively process large amounts of data and speed up discovery. Mammalian genomics is limited by the cost and complexity of analysis, which require large amounts of computational resources to analyse huge amount of data and biology specialists to interpret results. On the other hand the application of this technology requires computing knowledge, in particular programming and operations management skills to develop high performance computing (HPC) applications and deploy them on HPC clouds. We carried out a survey of cloud-based service computing solutions, as the most recent and promising instantiations of distributed computing systems, in the context their use in research of mammalian genomic analysis. We describe our most recent research and development effort which focuses on building Software as a Service (SaaS) clouds to simplify the use of HPC clouds for carrying out mammalian genomic analysis.

Taxonomy of contention management in interconnected distributed systems

Interconnected distributed computing systems, such as computing Grids and federated Clouds, have been of special importance in both industry and academia. Resources provided in these environments are usually shared between users from different groups and/or organizations. Therefore these environments are prone to contention between user requests for accessing resources. Particularly, resource contention takes place when a user requests cannot be admitted or cannot sufficiently access resources because they are occupied by other requests. In this paper, we deal with different types of resource contentions occurring in interconnected distributed systems as well as approaches for resolving them. Approaches developed to resolve resource contentions share similarities in many aspects while being different in other aspects. We investigate the features of these approaches, identify and categorize the similarities and differences of them. Additionally, we review various resource management systems of interconnected distributed systems and group them based on the identified specifications.

Exposing HPC and sequential applications as services through the development and deployment of a SaaS cloud

Cloud and service computing has started to change the way research in science, in particular biology and medicine, is being carried out. Researchers that have taken advantage of this technology (making use of public and private cloud compute resources) can process large amounts of data (big data) and speed up discovery. However, this requires researchers to acquire a solid knowledge and skills in the development of sequential and high performance computing (HPC), and cloud development and deployment background. In response a technology exposing HPC applications as services through the development and deployment of a SaaS cloud, and its proof of concept in the form of implementation of a cloud environment, Uncinus, has been developed and implemented to allow researchers easy access to cloud computing resources. The new technology offers and Uncinus supports the development of applications as services and the sharing of compute resources to speed up applications' execution. Users access these cloud resources and services through web interfaces. Using the Uncinus platform, a bio-informatics workflow was executed on a private (HPC) cloud, server and public cloud (Amazon EC2) resources, performance results showing a 3 fold improvement compared to local resources' performance. Biology and medicine specialists with no programming and application deployment on clouds background could run the case study applications with ease.