About me
I recently completed a Ph.D. at the Computational Engineering and Design Group (CED) at the University of Southampton where I also received an MEng degree in Software Engineering from the department of Electronics an Computer Science (ECS).
My research interests include the management and organisation of large volumes of data enabling Data Grid functionality to non technical users. I worked on the design and implementation of the BioSimGrid project, assisting with the management of large simulation data sets.
Thesis
Encouraging collaboration through a new data management approach. PDF (5.2mb)
Abstract
The ability to store large volumes of data is increasing faster than processing power. Some existing data management methods often result in data loss, inaccessibility or repetition of simulations. We propose a framework which promotes collaboration and simplifies data management.
In particular we have demonstrated the proposed framework in the scenario of handling large scale data generated from biomolecular simulations in a multiinstitutional global collaboration. The framework has extended the ability of the Python problem solving environment to manage data files and metadata associated with simulations. We provide a transparent and seamless environment for user submitted code to analyse and post-process data stored in the framework. Based on this scenario we have further enhanced and extended the framework to deal with the more generic case of enabling any existing data file to be post processed from any .NET enabled programming language.
Contact details
Email: email@stevenjohnston.co.uk
Publications
- Richard P. Boardman, Steven Johnston, Jonathan W. Essex, Muan Hong Ng, Hans Fangohr, Kaihsu Tai, and Mark S. P. Sansom. BioSimGrid on the desktop. August 2006. In preparation for submission.
[ bib ] - Steven Johnston, Richard P. Boardman, Muan Hong Ng, Jonathan W. Essex, Hans Fangohr, Kaihsu Tai, and Mark S. P. Sansom. BioSimGrid: Infrastructure, performance and applications. August 2006. In preparation for submission.
[ bib ] - Kaihsu Tai, Marc Baaden, Stuart Murdock, Bing Wu, Muan Hong Ng, Steven Johnston, Richard Boardman, Hans Fangohr, Katherine Cox, Jonathan W. Essex, and Mark S. P. Sansom. Three hydrolases and a transferase: comparative analysis of active-site dynamics via the BioSimGrid database. Journal of Molecular Graphics and Modelling, 2006.
[ bib | .pdf ] - Muan Hong Ng, Steven Johnston, Bing Wu, Stuart Murdock, Kaihsu Tai, Hans Fangohr, Simon J. Cox, Jonathan W. Essex, Mark S. P. Sansom, and Paul Jeffreys. BioSimGrid: Grid-enabled biomolecular simulation data storage and analysis. Future Generation Computer Systems, 22:657-664, 2006.
[ bib | .pdf ] - Stuart E. Murdock, Kaihsu Tai, Muan Hong Ng, Steven Johnston, Bing Wu, Hans Fangohr, Charles A. Laughton, Jonathan W. Essex, and Mark S. P. Sansom. Quality assurance for biomolecular simulations. Journal of Chemical Theory and Computation, 2006. Sumbitted.
[ bib | .pdf ] - Christopher J. Woods, Muan Hong Ng, Steven Johnston, Stuart E. Murdock, Bing Wu, Kaihsu Tai, Hans Fangohr, Paul Jeffreys, Simon Cox, Jeremy G. Frey, Mark S. P. Sansom, and Jonathan W. Essex. Grid computing and biomolecular simulation. Philosophical Transactions: Mathematical, Physical and Engineering Sciences, 363(1833), August 2005.
[ bib | .pdf ] - Bing Wu, Kaihsu Tai, Muan Hong Ng, Steven Johnston, Stuart Murdock, Hans Fangohr, Mark S. P. Sansom, Jonathan Essex, Paul Jeffreys, and Simon Cox. Towards a Grid-enabled biomolecular simulation database. In Proceedings of UK e-Science All Hands Meeting 2005, pages 577Ð-580, 2005.
[ bib | .pdf ] - Steven Johnston. Storage resource broker (SRB), large scientific data and Python. Europython 2005, 2005.
[ bib ] - Bing Wu, Matthew Dovey, Kaihsu Tai, Muan Hong Ng, Stuart, Murdock, Hans Fangohr, Steven Johnston, Paul Jeffreys, Simon Cox, Jonathan W. Essex, and Mark S.P. Sansom. Security and BioSimGrid: A biomolecular simulation database. Proceedings of Workshop on Grid Security Practice and Experience, July 2004. Published as: University of York, Department of Computer Science Technical Report YCS-2004-380.
[ bib | .pdf ] - Kaihsu Tai, Stuart Murdock, Bing Wu, Muan Hong Ng, Steven Johnston, Hans Fangohr, Simon J. Cox, Paul Jeffreys, Jonathan W. Essex, and Mark S. P. Sansom. BioSimGrid: Towards a worldwide repository for biomolecular simulations. Organic & Biomolecular Chemistry, 2:3219-3221, 2004.
[ bib | .pdf ] - Muan Hong Ng, Steven Johnston, Stuart Murdock, Bing Wu, Kaihsu Tai, Hans Fangohr, Simon Cox, Jonathan W. Essex, Mark Sansom, and Paul Jeffreys. Efficient data storage and analysis for generic biomolecular simulation data. In Proceedings of UK e-Science All Hands Meeting 2004, pages 443-450, 2004.
[ bib | .pdf ] - Bing Wu, Matthew Dovey, Muan Hong Ng, Kaihsu Tai, Stuart Murdock, Hans Fangohr, Steven Johnston, Paul Jeffreys, Simon Cox, Jonathan Essex, and Mark S. P. Sansom. A web / Grid portal implementation of BioSimGrid: A biomolecular simulation database. Journal of Digital Information Management, 2(2):74-78, 2004.
[ bib | .pdf ] - Stuart Murdock, Muan Hong Ng, Steven Johnston, Hans Fangohr, and Jon Essex. Comparing the performance of a database, specific binary files and netCDF for data retrieval, 2004. [Online; accessed 10-December-2005], BioSimGrid Website.
[ bib ] - Z. Jiao, J. Wason, M. Molinari, S. Johnston, and S.J. Cox. Integrating data management into engineering applications. Proceedings of UK e-Science All Hands Meeting, Nottingham, UK, pages 687 - 694, September 2003.
[ bib | .pdf ] - Bing Wu, Kaihsu Tai, Stuart Murdock, Muan Hong Ng, Steven Johnston, Hans Fangohr, Paul Jeffreys, Simon Cox, Jonathan Essex, and Mark S.P. Sansom. BioSimGrid: A distributed database for biomolecular simulations. Proceedings of UK e-Science All Hands Meeting 2003, pages 412-419, 2003.
[ bib | .pdf ] - Yalini Arinaminpathy, Oliver Beckstein, Philip Biggin, Peter Bond, Carmen Domene, Andrew Pang, and Mark Sansom. Large scale biomolecular simulations: Current status and future prospects. Proceedings of UK e-Science All Hands Meeting, 2003.
[ bib | .pdf ]