Aisling O'Driscoll

'Big data', Hadoop and cloud computing in genomics

Since the completion of the Human Genome project at the turn of the Century, there has been an unprecedented proliferation of genomic sequence data. A consequence of this is that the medical discoveries of the future will largely depend on our ability to process and analyse large genomic data sets, which continue to expand as the cost of sequencing decreases. Herein, we provide an overview of cloud computing and big data technologies, and discuss how such expertise can be used to deal with biologys big data sets. In particular, big data technologies such as the Apache Hadoop project, which provides distributed and parallelised data processing and analysis of petabyte (PB) scale data sets will be discussed, together with an overview of the current usage of Hadoop within the bioinformatics community.

An Infrastructure Enhanced Geographic Routing Protocol for urban vehicular environments

This paper presents an Infrastructure Enhanced Geographic Routing Protocol (IEGRP) for urban vehicular environments. IEGRP is a hybrid vehicular routing protocol that facilitates V2V or V2I unicast routing by dynamically changing its routing decisions in the presence of full or partial Road-Side Unit (RSU) infrastructure in order to maximise packet delivery rate. To the best of the authors knowledge this is the first hybrid approach where the routing algorithm exploits the presence of infrastructure where available but also utilises efficient multi-hop communications using greedy forwarding, store and forward buffering and predictive link stability techniques. IEGRP is evaluated using realistic vehicular radio propagation and movement conditions and demonstrates much improved delivery rates with partial and full infrastructure compared to related protocols.

Hierarchical clustering as an approach for supporting P2P SIP sessions in ubiquitous environments

Both Peer-To-Peer (P2P) and mobile ad-hoc networks (MANETs) aim to provide seamless connectivity and services in a dynamic and decentralised environment. These two technologies, if unified, may be able to realise MANETs as a viable commercial technology and will enable the development of widespread distributed applications for MANETs. The push towards wireless ubiquitous computing means that service providers will need to adapt to a highly dynamic mobile topology and given that client-server applications can not be supported in such an environment, P2P applications will be essential. Therefore as MANETs are devoid of a stable infrastructure, mechanisms are required to support P2P services such as IP telephony and this paper discusses the integration of such services with hierarchical cluster based techniques.

Draft Genome Sequence of a Streptococcus agalactiae Strain Isolated from a Preterm Neonate Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland

ABSTRACT Herein, we report the draft genome sequence of Streptococcus agalactiae ED-NGS-1000, cultivated from a blood sample taken from a preterm neonate blood sepsis patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.

Hybrid geo-routing in urban vehicular networks

It is expected that future vehicular networks will consist of a combination of ad-hoc network and infrastructure components. Road Side Units (RSUs) will form part of the infrastructure element. However, it is anticipated that a fully deployed RSU infrastructure may not be economically feasible in the short term, therefore, a partial infrastructure in urban environments is more likely, at least initially while vehicular networks are being adopted. It is further likely that low vehicle penetration rates will exist while 802.11p On-Board Unit (OBU) technology is being rolled out, thus routing schemes should exploit infrastructure where available to improve packet delivery. This paper presents a hybrid vehicular routing protocol that facilitates unicast routing by dynamically changing its routing decisions in the presence of RSU infrastructure in order to maximise packet delivery rate. A quantitative evaluation of the proposed Infrastructure Enhanced Geographic Routing Protocol (IEGRP) is provided as a function of varied source to destination distances, vehicular densities, infrastructure availability and application QoS characteristics. It exhibits much improved delivery rates with partial and full infrastructure compared to related protocols.

Draft Genome Sequences of Six Different Staphylococcus epidermidis Clones, Isolated Individually from Preterm Neonates Presenting with Sepsis at Edinburgh's Royal Infirmary

ABSTRACT Herein, we report the draft genome sequences of six individual Staphylococcus epidermidis clones, cultivated from blood taken from different preterm neonatal sepsis patients at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.

Draft Genome Sequence of a Staphylococcus aureus Isolate Taken from the Blood of a Preterm Neonatal Blood Sepsis Patient.

ABSTRACT Herein, we report the draft genome sequence of Staphylococcus aureus ED-NGS-1006, cultivated from a blood sample taken from a neonatal sepsis patient at the Royal Infirmary in Edinburgh, Scotland, United Kingdom.

Draft Genome Sequence of a Pantoea sp. Isolated from a Preterm Neonatal Blood Sepsis Patient

ABSTRACT Herein, we report the draft genome sequence of Pantoea sp. ED-NGS-1003, cultivated from a blood sample taken from a neonatal sepsis patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom.

Draft Genome Sequence of an Enterococcus faecalis Strain Isolated from a Neonatal Blood Sepsis Patient

ABSTRACT Herein, we report the draft genome sequence of Enterococcus faecalis ED-NGS-1009, cultivated from a blood sample taken from a neonatal sepsis patient at the Royal Infirmary in Edinburgh, Scotland, United Kingdom.

Draft Genome Sequence of a Serratia marcescens Strain Isolated from a Preterm Neonatal Blood Sepsis Patient at the Royal Infirmary, Edinburgh, Scotland, United Kingdom

ABSTRACT Herein, we report the draft genome sequence for isolate ED-NGS-1015 of Serratia marcescens, cultivated from a blood sample obtained from a neonatal sepsis patient at the Royal Infirmary in Edinburgh, Scotland, United Kingdom.