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.

A scalable and automatic mechanism for resource allocation in self-organizing cloud

Taking advantage of the huge potential of consumers’ untapped computing power, self-organizing cloud is a novel computing paradigm where the consumers are able to contribute/sell their computing resources. Meanwhile, host machines held by the consumers are connected by a peer-to-peer (P2P) overlay network on the Internet. In this new architecture, due to large and varying multitudes of resources and prices, it is inefficient and tedious for consumers to select the proper resource manually. Thus, there is a high demand for a scalable and automatic mechanism to accomplish resource allocation. In view of this challenge, this paper proposes two novel economic strategies based on mechanism design. Concretely, we apply the Modified Vickrey Auction (MVA) mechanism to the case where the resource is sufficient; and the Continuous Double Auction (CDA) mechanism is employed when the resource is insufficient. We also prove that aforementioned mechanisms have dominant strategy incentive compatibility. Finally, extensive experiment results are conducted to verify the performance of the proposed strategies in terms of procurement cost and execution efficiency.

The social network learning cloud: architectural education for the 21 century

In less than a decade, architectural education has, in some ways, significantly evolved. The advent of computation has not so much triggered the change, but Social Networks (SN) have ignited a novel way of learning, interaction and knowledge construction. SN enable learners to engage with friends, tutors, professionals and peers, form the base for learning resources, allow students to make their voices heard, to listen to other views and much more. They offer a more authentic, inter-professional and integrated problem based, Just-in-Time (JIT), Just-in-Place (JIP) learning. Online SN work in close association with offline SN to form a blended social learning realm-the Social Network Learning Cloud (SNLC)-that greatly enables and enhances students' learning in a far more influential way than any other learning means, resources or methods do. This paper presents a SNLC for architectural education that provides opportunities for linking the academic Learning Management Systems (LMS) with private or professional SN such that it enhances the learning experience and deepens the knowledge of the students. The paper proposes ways of utilising SNLC in other learning and teaching areas of the curriculum and concludes with directions of how SNLC then may be employed in professional settings.

Remote monitoring system enabling cloud technology upon smart phones and inertial sensors for human kinematics

Stroke is a common neurological condition which is becoming increasingly common as the population ages. This entails healthcare monitoring systems suitable for home use, with remote access for medical professionals and emergency responders. The mobile phone is becoming the easy access tool for self-evaluation of health, but it is hindered by inherent problems including computational power and storage capacity. This research proposes a novel cloud based architecture of a biomedical system for a wearable motion kinematic analysis system which mitigates the above mentioned deficiencies of mobile devices. The system contains three subsystems: 1. Bio Kin WMS for measuring the acceleration and rotation of movement 2. Bio Kin Mobi for Mobile phone based data gathering and visualization 3. Bio Kin Cloud for data intensive computations and storage. The system is implemented as a web system and an android based mobile application. The web system communicates with the mobile application using an encrypted data structure containing sensor data and identifiable headings. The raw data, according to identifiable headings, is stored in the Amazon Relational Database Service which is automatically backed up daily. The system was deployed and tested in Amazon Web Services.

Multi-cloud application execution and data management

Recently, fields with substantial computing requirementshave turned to cloud computing for economical, scalable, and on-demandprovisioning of required execution environments. However, current cloudofferings focus on providing individual servers while tasks such as applicationdistribution and data preparation are left to cloud users. This article presents anew form of cloud called HPC Hybrid Deakin (H2D) cloud; an experimentalhybrid cloud capable of utilising both local and remote computational servicesfor large embarrassingly parallel applications. As well as supporting execution,H2D also provides a new service, called DataVault, that provides transparentdata management services so all cloud-hosted clusters have required datasetsbefore commencing execution.

Fog computing: a cloud to the ground support for smart things and machine-to-machine networks

Cloud services to smart things face latency and intermittent connectivity issues. Fog devices are positioned between cloud and smart devices. Their high speed Internet connection to the cloud, and physical proximity to users, enable real time applications and location based services, and mobility support. Cisco promoted fog computing concept in the areas of smart grid, connected vehicles and wireless sensor and actuator networks. This survey article expands this concept to the decentralized smart building control, recognizes cloudlets as special case of fog computing, and relates it to the software defined networks (SDN) scenarios. Our literature review identifies a handful number of articles. Cooperative data scheduling and adaptive traffic light problems in SDN based vehicular networks, and demand response management in macro station and micro-grid based smart grids are discussed. Security, privacy and trust issues, control information overhead and network control policies do not seem to be studied so far within the fog computing concept.

Energy efficiency on location based applications in mobile cloud computing: a survey

The constrained battery power of mobile devices poses a serious impact on user experience. As an increasingly prevalent type of applications in mobile cloud environments, location-based applications (LBAs) present some inherent limitations concerning energy. For example, the Global Positioning System based positioning mechanism is well-known for its extremely power-hungry attribute. Due to the severity of the issue, considerable researches have focused on energy-efficient locating sensing mechanism in the last a few years. In this paper, we provide a comprehensive survey of recent work on low-power design of LBAs. An overview of LBAs and different locating sensing technologies used today are introduced. Methods for energy saving with existing locating technologies are investigated. Reductions of location updating queries and simplifications of trajectory data are also mentioned. Moreover, we discuss cloud-based schemes in detail which try to develop new energy-efficient locating technologies by leveraging the cloud capabilities of storage, computation and sharing. Finally, we conclude the survey and discuss the future research directions. © 2013 Springer-Verlag Wien.

FEACS: a flexible and efficient access control scheme for cloud computing

In the past few years, cloud computing has emerged as one of the most influential paradigms in the IT industry. As promising as it is, this paradigm brings forth many new challenges for data security because users have to outsource sensitive data on untrusted cloud servers for sharing. In this paper, to guarantee the confidentiality and security of data sharing in cloud environment, we propose a Flexible and Efficient Access Control Scheme (FEACS) based on Attribute-Based Encryption, which is suitable for fine-grained access control. Compared with existing state-of-the-art schemes, FEACS is more practical by following functions. First of all, considering the factor that the user membership may change frequently in cloud environment, FEACS has the capability of coping with dynamic membership efficiently. Secondly, full logic expression is supported to make the access policy described accurately and efficiently. Besides, we prove in the standard model that FEACS is secure based on the Decisional Bilinear Diffie-Hellman assumption. To evaluate the practicality of FEACS, we provide a detailed theoretical performance analysis and a simulation comparison with existing schemes. Both the theoretical analysis and the experimental results prove that our scheme is efficient and effective for cloud environment.

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.

Selected approaches and frameworks to carry out genomic data provision and analysis on the cloud

While High Performance Computing clouds allow researchers to process large amounts of genomic data, complex resource and software configuration tasks must be carried out beforehand. The current trend exposes applications and data as services, simplifying access to clouds. This paper examines commonly used cloud-based genomic analysis services, introduces the approach of exposing data as services and proposes two new solutions (HPCaaS and Uncinus) which aim to automate service development, deployment process and data provision. By comparing and contrasting these solutions, we identify key mechanisms of service creation, execution and data access required to support non-computing specialists employing clouds.

Denitrification measurements of sediments using cores and chambers

Denitrification is commonly measured using in situ benthic chambers or laboratory incubations of sediment cores. These techniques are similar in principle but differ considerably in cost and practicality. Despite widespread use of both techniques, it is uncertain whether they give comparable results. We compared cores and chambers for measuring fluxes (dissolved oxygen [DO], N 2, NH4+, NO3- and NO 2-) and denitrification efficiency at 2 sites in Port Phillip Bay, Victoria, Australia. Overall, denitrification efficiency was not significantly different between cores and chambers, but fluxes of DO, NO 3- and NO2- differed. Chambers demonstrated higher levels of oxygen consumption and net fluxes of NO 3- and NO2- out of the sediment, suggesting that denitrification and nitrification were closely coupled. In contrast, there was a greater relative importance for uncoupled denitrification in cores as indicated by reduced oxygen consumption and net fluxes of NO 3- into the sediment. We conclude that cores and chambers give different flux results and therefore are not comparable techniques for measuring denitrification. To ascertain the cause of this, we tested the hypothesis that cores failed to adequately incorporate the impacts of macrofauna on fluxes, due to the small size of cores relative to chambers. However, densities of macrofauna were not significantly different in cores and chambers. We then hypothesised that disturbance during core collection, transportation, and handling may account for differences, but cores deployed in situ and in the laboratory gave similar results. We suggest that compression of sediment during insertion of core cylinders into the sediment may account for differences between core and chamber fluxes.

Participating creatively: e-portfolio learning in diabetes education on the cloud

Abstract: The evolution of online teaching in higher education demands a change in the types of pedagogical philosophies and methods used in these courses. This chapter will discuss how a jigsaw model facilitated independent learning and enhanced student learning by working in teams. To accomplish this objective each student needed to communicate with a small group of other students on line and contribute equally for a common goal. A parallel aim was to overcome postgraduate students’ reluctance to utilise technology and communicate within the Cloud, in particular when student groups are big. The authors have found that postgraduate students often experience a sense of learning in isolation. An added benefit was the social dimension experienced within the activity. The chapter will reveal how a jigsaw style integrated learning tool was a successful collaborative learning experience in a classroom setting. The jigsaw activity was designed to enable students to share ‘artefacts’ and knowledge with a small group of students and the lecturer by using the E-Portfolio.  In conclusion, it will be argued that this creative and innovative participatory Cloud learning experience offered more students the opportunity to collaborate within a team in the Cloud. This E-portfolio learning activity introduced the electronic style of information sharing to postgraduate students and additionally the interactive and creative jigsaw learning activity assisted students to navigate the Cloud, use E-portfolio and engage in an environment in which they felt comfortable to communicate in.