Computational Modelling Group

Database

Research on databases and data storage, including linking metadata to flat files and other datastores, management of large datasets, distribution, access and security.

For queries about this topic, contact Richard Boardman.

View the calendar of events relating to this topic.

Projects

Application of RNA-Seq for gene fusion identification in blood cancers

William Tapper (Investigator), Marcin Knut

Gene fusions are often the cause of different blood cancers. As such, accurate identification of them provides information on the underlying cause of a cancer, ensuring appropriate choice of treatment. However, due to shortcomings of the currently applied methods for gene fusion identification, some of them escape undetected. We are employing RNA-Seq, a cutting-edge method for sequencing RNA, the messenger of genetic information, to investigate gene fusions.

Bioinformatic identification and physiological analysis of ethanol-related genes in C. elegans

Richard Edwards, Vincent O'Connor, Lindy Holden-Dye (Investigators), Ben Ient

Investigating the broad molecular, cellular and systems level impacts of acute and chronic ethanol in the nematode, Caenorhabditis elegans, as a model.

BioSimGrid

Jonathan Essex, Hans Fangohr (Investigators), Richard Boardman, Syma Khalid, Steven Johnston

The aim of the BioSimGrid project is to make the results of large-scale computer simulations of biomolecules more accessible to the biological community. Such simulations of the motions of proteins are a key component in understanding how the structure of a protein is related to its dynamic function.

DIPLOS - Dispersion of Localised Releases in a Street Network

Trevor Thomas, Ian Castro (Investigators)

The security threat level from international terrorism, introduced by the UK Security Service, has been classified as either "severe" or "critical" for much of its six-year history, and currently remains as "substantial" (source: MI5 website). Part of the risk posed by terrorist threats involves potential releases of air-borne chemical, biological, radiological or nuclear (CBRN) material into highly populated urbanised areas. Smoke from industrial accidents within or in the vicinity of urban areas also pose risks to health and can cause widespread disruption to businesses, public services and residents. The Buncefield depot fire of 2005 resulted in the evacuation of hundreds of homes and closure of more than 200 schools and public buildings for two days; consequences would have been much more severe if prevailing meteorological conditions had promoted mixing or entrainment of the smoke plume into the urban canopy. In both these scenarios it is crucial to be able to model, quickly and reliably, dispersion from localised sources through an urban street network in the short range, where the threat to human health is greatest. However, this is precisely where current operational models are least reliable because our understanding and ability to model short-range dispersion processes is limited. The contribution that DIPLOS will make is:

1. to fill in the gaps in fundamental knowledge and understanding of key dispersion processes,
2. to enable these processes to be parametrized for use in operational models,
3. to implement them into an operational model, evaluate the improvement and apply the model to a case study in central London

Most of the existing research on urban dispersion has focused on air quality aspects, with sources being extensive and distributed in space. Scientifically, this research is novel in focusing on localized releases within urban areas, and on dispersion processes at short range. Through a combination of fundamental studies using wind tunnel experiments and high resolution supercomputer simulations, extensive data analysis and development of theoretical and numerical models, DIPLOS will contribute to addressing this difficult and important problem from both a scientific research and a practical, operational perspective.

Identification of phage DNA, common insertion sites and their effect on genes within S.pneumoniae

Richard Edwards, Amy Dean

This study seeks to find if there are any common insertion sites across different strains of S.pneumoniae and discover genes that undergo frequent mutation due to phages and if these mutations can be linked to virulence of the strains.

Modelling Macro-Nutrient Release & Fate Resulting from Sediment Resuspension in Shelf Seas

Chris Wood

This study involves adapting a previously-published model to take into account the effect resuspension events (both natural and anthropogenic) may have on nutrient dynamics at the sediment-water interface, and hence produce better estimates for the total nutrient budgets for shelf seas.

Network Analysis of Roman Transport Routes in the Imperial Roman Mediterranean

David Potts

This research is designed to explore the nature of the relationships between Portus, Rome, and other selected ports in the Mediterranean and to establish patterns and the changing nature of trading networks derived from the distribution of known Roman artefacts.

Prediction of Psychopathology by MRT data

We aim to predict psychopathological outcomes in adults by functional brain data using multilevel regression and crossvaligdation strategies.

Supernova Rates in the Local Universe

Mark Sullivan (Investigator), Christopher Frohmaier

This project will calculate the frequency of exploding stars -- or supernovae -- in the nearby universe. We simulate a 'toy universe' by exploding billions of stars in a computer, and then artificially 'observing' these explosions by replicating a real astronomical sky survey, the Palomar Transient Factory (PTF). The results of this simulation allows us to discover the rate at which supernovae occur in the local universe each year.

ยต-VIS Computed Tomography Centre

Ian Sinclair, Richard Boardman, Dmitry Grinev, Philipp Thurner, Simon Cox, Jeremy Frey, Mark Spearing, Kenji Takeda (Investigators)

A dedicated centre for computed tomography (CT) at Southampton, providing complete support for 3D imaging science, serving Engineering, Biomedical, Environmental and Archaeological Sciences. The centre encompasses five complementary scanning systems supporting resolutions down to 200nm and imaging volumes in excess of one metre: from a matchstick to a tree trunk, from an ant's wing to a gas turbine blade.

People

Andrew Collins
Professor, Medicine (FM)
Simon Cox
Professor, Engineering Sciences (FEE)
Jonathan Essex
Professor, Chemistry (FNES)
Hans Fangohr
Professor, Engineering Sciences (FEE)
Jeremy Frey
Professor, Chemistry (FNES)
Lindy Holden-Dye
Professor, Biological Sciences (FNES)
Ian Sinclair
Professor, Engineering Sciences (FEE)
Mark Spearing
Professor, Engineering Sciences (FEE)
Graeme Day
Reader, Chemistry (FNES)
Nicolas Green
Reader, Electronics and Computer Science (FPAS)
Vincent O'Connor
Reader, Biological Sciences (FNES)
Robert Ewing
Senior Lecturer, Biological Sciences (FNES)
Denis Kramer
Lecturer, Engineering Sciences (FEE)
Paul Skipp
Lecturer, Biological Sciences (FNES)
Trevor Thomas
Lecturer, Engineering Sciences (FEE)
Philipp Thurner
Lecturer, Engineering Sciences (FEE)
Syma Khalid
Principal Research Fellow, Chemistry (FNES)
Mark Sullivan
Principal Research Fellow, Physics & Astronomy (FPAS)
Richard Boardman
Senior Research Fellow, Engineering Sciences (FEE)
Reno Choi
Senior Research Fellow, Geography (FSHS)
Petros Bogiatzis
Research Fellow, Ocean & Earth Science (FNES)
Nicola De Tullio
Research Fellow, Engineering Sciences (FEE)
Dmitry Grinev
Research Fellow, Engineering Sciences (FEE)
Steven Johnston
Research Fellow, Engineering Sciences (FEE)
Leonidas Bourikas
Postgraduate Research Student, Civil Engineering & the Environment (FEE)
Graham Elliott
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Christopher Frohmaier
Postgraduate Research Student, Physics & Astronomy (FPAS)
Tom Hebbron
Postgraduate Research Student, Electronics and Computer Science (FPAS)
Joshua Jeeson Daniel
Postgraduate Research Student, Engineering Sciences (FEE)
Marcin Knut
Postgraduate Research Student, Medicine (FM)
David Potts
Postgraduate Research Student, Humanities (FH)
Chris Wood
Postgraduate Research Student, Ocean & Earth Science (FNES)
Matthew Higgins
Undergraduate Research Student, Biological Sciences (FNES)
Elena Vataga
Technical Staff, iSolutions
Petrina Butler
Administrative Staff, Research and Innovation Services
Ella Marley-Zagar
Enterprise staff, Medicine (FM)
Amy Dean
Alumnus, former UG, Biological Sciences
Richard Edwards
Alumnus, University of New South Wales, Australia
Ben Ient
Alumnus, Biological Sciences (FNES)
Arthur Lugtigheid
Alumnus, Psychology (FSHS)
Kieren Lythgow
Alumnus, Health Protection Agency
Mohsen Mesgarpour
Alumnus, University of Southampton
Kenji Takeda
Alumnus, Engineering Sciences (FEE)
Daniel Pope
External Member, Mauve Internet Ltd.
Mohamed Bakoush
None, None
Ian Castro
None, None
Stephen Green
None, None
William Tapper
None, None