High-Performance Cloud Computing: A View of Scientific Applications

Scientific computing often requires the availability of a massive number of computers for performing large scale experiments. Traditionally, these needs have been addressed by using high-performance computing solutions and installed facilities such as clusters and super computers, which are difficult to setup, maintain, and operate. Cloud computing provides scientists with a completely new model of utilizing the computing infrastructure. Compute resources, storage resources, as well as applications, can be dynamically provisioned (and integrated within the existing infrastructure) on a pay per use basis. These resources can be released when they are no more needed. Such services are often offered within the context of a Service Level Agreement (SLA), which ensure the desired Quality of Service (QoS). Aneka, an enterprise Cloud computing solution, harnesses the power of compute resources by relying on private and public Clouds and delivers to users the desired QoS. Its flexible and service based infrastructure supports multiple programming paradigms that make Aneka address a variety of different scenarios: from finance applications to computational science. As examples of scientific computing in the Cloud, we present a preliminary case study on using Aneka for the classification of gene expression data and the execution of fMRI brain imaging workflow.Comment: 13 pages, 9 figures, conference pape

Structure Refinement for Vulnerability Estimation Models using Genetic Algorithm Based Model Generators

In this paper, a method for model structure refinement is proposed and applied in estimation of cumulative number of vulnerabilities according to time. Security as a quality characteristic is presented and defined. Vulnerabilities are defined and their importance is assessed. Existing models used for number of vulnerabilities estimation are enumerated, inspecting their structure. The principles of genetic model generators are inspected. Model structure refinement is defined in comparison with model refinement and a method for model structure refinement is proposed. A case study shows how the method is applied and the obtained results.model structure refinement, model generators, gene expression programming, software vulnerabilities, performance criteria, software metrics

BioCloud Search EnGene: Surfing Biological Data on the Cloud

The massive production and spread of biomedical data around the web introduces new challenges related to identify computational approaches for providing quality search and browsing of web resources. This papers presents BioCloud Search EnGene (BSE), a cloud application that facilitates searching and integration of the many layers of biological information offered by public large-scale genomic repositories. Grounding on the concept of dataspace, BSE is built on top of a cloud platform that severely curtails issues associated with scalability and performance. Like popular online gene portals, BSE adopts a gene-centric approach: researchers can find their information of interest by means of a simple “Google-like” query interface that accepts standard gene identification as keywords. We present BSE architecture and functionality and discuss how our strategies contribute to successfully tackle big data problems in querying gene-based web resources. BSE is publically available at: http://biocloud-unica.appspot.com/

From access and integration to mining of secure genomic data sets across the grid

The UK Department of Trade and Industry (DTI) funded BRIDGES project (Biomedical Research Informatics Delivered by Grid Enabled Services) has developed a Grid infrastructure to support cardiovascular research. This includes the provision of a compute Grid and a data Grid infrastructure with security at its heart. In this paper we focus on the BRIDGES data Grid. A primary aim of the BRIDGES data Grid is to help control the complexity in access to and integration of a myriad of genomic data sets through simple Grid based tools. We outline these tools, how they are delivered to the end user scientists. We also describe how these tools are to be extended in the BBSRC funded Grid Enabled Microarray Expression Profile Search (GEMEPS) to support a richer vocabulary of search capabilities to support mining of microarray data sets. As with BRIDGES, fine grain Grid security underpins GEMEPS

Towards a virtual research environment for paediatric endocrinology across Europe

Paediatric endocrinology is a medical specialty dealing with variations of physical growth and sexual development in childhood. Genetic anomalies that can cause disorders of sexual development in children are rare. Given this, sharing and collaboration on the small number of cases that occur is needed by clinical experts in the field. The EU-funded EuroDSD project (www.eurodsd.eu) is one such collaboration involving clinical centres and clinical and genetic experts across Europe. Through the establishment of a virtual research environment (VRE) supporting sharing of data and a variety of clinical and bioinformatics analysis tools, EuroDSD aims to provide a research infrastructure for research into disorders of sex development. Security, ethics and information governance are at the heart of this infrastructure. This paper describes the infrastructure that is being built and the inherent challenges in security, availability and dependability that must be overcome for the enterprise to succeed

Cloudbus Toolkit for Market-Oriented Cloud Computing

This keynote paper: (1) presents the 21st century vision of computing and identifies various IT paradigms promising to deliver computing as a utility; (2) defines the architecture for creating market-oriented Clouds and computing atmosphere by leveraging technologies such as virtual machines; (3) provides thoughts on market-based resource management strategies that encompass both customer-driven service management and computational risk management to sustain SLA-oriented resource allocation; (4) presents the work carried out as part of our new Cloud Computing initiative, called Cloudbus: (i) Aneka, a Platform as a Service software system containing SDK (Software Development Kit) for construction of Cloud applications and deployment on private or public Clouds, in addition to supporting market-oriented resource management; (ii) internetworking of Clouds for dynamic creation of federated computing environments for scaling of elastic applications; (iii) creation of 3rd party Cloud brokering services for building content delivery networks and e-Science applications and their deployment on capabilities of IaaS providers such as Amazon along with Grid mashups; (iv) CloudSim supporting modelling and simulation of Clouds for performance studies; (v) Energy Efficient Resource Allocation Mechanisms and Techniques for creation and management of Green Clouds; and (vi) pathways for future research.Comment: 21 pages, 6 figures, 2 tables, Conference pape

Cytoscape: the network visualization tool for GenomeSpace workflows.

Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013

DIAGNOSIS AND RECOMMENDER SYSTEM FOR SOME NEGLECTED TROPICAL DISEASES

Failure to promptly diagnose and treat of some tropical diseases such as chicken pox, cholera and typhoid fever is affecting the community-based management of such diseases. The high mortality rates caused by these diseases make the quest for effective diagnoses and appropriate treatment an essential task. Thus, precise diagnosis of these diseases coupled with appropriate treatment will result in their control, especially in the tropical regions, which also constitute the developing countries. The system works for this research was based on the client/server architecture, structured as a 3-tier application. The Web browser constituted the first tier, a middleware engine using some dynamic Web content technology active server pages (ASP) constituted the middle-tier and the database was the third tier. The implementation of the system had a front- end web based graphical user interface (GUI) application and back-end relational database management system (RDBMS). The Front–end was implemented with ASP.NET (using vb.net-programming language), while the back-end was designed with Microsoft queried language (MS SQL) server 2005. With this development, a prompt medical diagnosis, effective drug recommendations and promulgation of effective policies could be provided at community settings where there are shortages in material and human resources for managing these neglected tropical diseases