Representing variant calling format as directed acyclic graphs to enable the use of cloud computing for efficient and cost effective genome analysis

Ever since the completion of the Human Genome Project in 2003, the human genome has been represented as a linear sequence of 3.2 billion base pairs and is referred to as the "Reference Genome". Since then it has become easier to sequence genomes of individuals due to rapid advancements in technology, which in turn has created a need to represent the new information using a different representation. Several attempts have been made to represent the genome sequence as a graph albeit for different purposes. Here we take a look at the Variant Calling Format (VCF) file which carries information about variations within genomes and is the primary format of choice for genome analysis tools. This short paper aims to motivate work in representing the VCF file as Directed Acyclic Graphs (DAGs) to run on a cloud in order to exploit the high performance capabilities provided by cloud computing.N/

Trust-aware information retrieval in peer-to-peer environments

Information Retrieval in P2P environments (P2PIR) has become an active field of research due to the observation that P2P architectures have the potential to become as appealing as traditional centralised architectures. P2P networks are formed with voluntary peers that exchange information and accomplish various tasks. Some of them may be malicious peers spreading untrustworthy resources. However, existing P2PIR systems only focus on finding relevant documents, while trustworthiness of documents and document providers has been ignored. Without prior experience and knowledge about the network, users run the risk to review,download and use untrustworthy documents, even if these documents are relevant. The work presented in this dissertation provide the first integrated framework for trust-aware Information Retrieval in P2P environments, which can retrieve not only relevant but also trustworthy documents. The proposed content trust models extend an existing P2P trust management system, PeerTrust, in the context of P2PIR to compute the trust values of documents and document providers for given queries. A method is proposed to estimate global term statistics which are integrated with existing relevance-based approaches for document ranking and peer selection. Different approaches are explored to find optimal parametersettings in the proposed trust-aware P2PIR systems. Moreover, system architectures and data management protocols are designed to implement the proposed trust-aware P2PIR systems in structured P2P networks. The experimental evaluation demonstrates that P2PIR can benefit from trust-aware P2PIR systems significantly. It can importantly reduce the possibility of untrustworthy documents in the top-ranked result list. The proposed estimated global term statistics can provide acceptable and competitive retrieval accuracy within different P2PIR scenarios.EThOS - Electronic Theses Online ServiceORSSchool ScholarshipGBUnited Kingdo

Dynamic virtual machine placement considering CPU and memory resource requirements

In cloud data centers, cloud providers can offer computing infrastructure as a service in the form of virtual machines (VMs). With the help of virtualization technology, cloud data centers can consolidate VMs on physical machines to minimize costs. VM placement is the process of assigning VMs to the appropriate physical machines. An efficient VM placement solution will result in better VM consolidation ratios which ensures better resource utilization and hence more energy savings. The VM placement process consists of both the initial as well as the dynamic placement of VMs. In this paper, we are experimenting with a dynamic VM placement solution that considers different resource types (namely, CPU and memory). The proposed solution makes use of a genetic algorithm for the dynamic reallocation of the VMs based on the actual demand of the individual VMs aiming to minimize under-utilization and over-utilization scenarios in the cloud data center. Empirical evaluation using CloudSim highlights the importance of considering multiple resource types. In addition, it demonstrates that the genetic algorithm outperforms the well-known best-fit decreasing algorithm for dynamic VM placement

Self-optimizing block transfer in web service grids

Nowadays, Web Services (WSs) play an increasingly impor-tant role in Web data management solutions, since they offer a practical solution for accessing and manipulating data sources spanning administrative domains. Neverthe-less, they are notoriously slow and transferring large data volumes across WSs becomes the main bottleneck in such WS-based applications. This paper deals with the problem of minimizing at runtime, in a self-managing way, the data transfer cost of a WS encapsulating a data source. To reduce the transfer cost, the data volume is typically divided into blocks. In this case, response time exhibits a quadratic-like, non-linear behavior with regards to the block size; as such, minimizing the transfer cost entails finding the optimum block size. This situation is encountered in several systems