Bioinformatics PhD Studentship (near London): Text mining, data mining and database development in Bioinformatics

SUPERVISORS

Dr Jacob Koehler, Biomathematics and Bioinformatics Division, Rothamsted Research, Harpenden, UK
Dr Kim Hammond-Kosack, Plant-Pathogen Interaction Division, Rothamsted Research, Harpenden, UK

Sophia Ananiadou, University Supervisor, School of Computer Science, University of Manchester, National Centre for Text Mining


PROJECT DESCRIPTION:
The successful candidate will do research on developing text- and data mining methods using ONDEX http://ondex.sf.net which is written in Java. The methods to be developed are generic and generally applicable. However, they will be tested and applied to support the curation and analysis of data in the Pathogen-Host Interaction database: http://www.phi-base.org. Other important aspects of the project include the extension of the database, the development of data curation interfaces and the development of data analysis methods.

REQUIREMENTS

We anticipate that the successful candidate will have a good degree in computer science or bioinformatics. the focus of the project will be on developing the software and analysis methods, which will require well-developed programming skills.

LOCALE:
You will be based at Rothamsted Research (in Harpenden near London) where you will be part of a growing and vibrant bioinformatics research group http://www.rothamsted.bbsrc.ac.uk/bab/index.php?folder=bioinformatics and in close contact with the expanding molecular genetics group identifying fungal genes required to cause disease on cereal plants, http://www.rothamsted.bbsrc.ac.uk/ppi/wptop.html. You will be a registered at the University of Manchester, where you will work in close collaboration with the National Centre of Text Mining (NaCTeM) http://www.nactem.ac.uk.

TRAINING:
This project will offer training in two key areas – data mining and database development. You will also get the opportunity to experience research training in both a research institute and university setting. Furthermore, you will develop excellent software development skills using a range of methods (algorithm development, requirement analysis, Unit testing etc), programming languages (Java, PHP, SQL, shell scripting etc) and tools (Eclipse, software versioning systems and release management, UML). You will also learn to work on high performance computers, including a medium sized computer cluster. As a result, you will develop a high level of expertise in all aspects of software development.

FUNDING AND ELIGIBILITY:
The studentship will cover tuition fees as well as provide an initial annual maintenance stipend of £12,600. It is anticipated that the project will commence in October 2007. The studentship is restricted to UK nationals and European students who have been resident in the UK for three years. Full eligibility criteria can be found on the BBSRC web site.

HOW TO APPLY:
Please send your CV (tabular format, include grades or expected grades), cover letter and the names of 3 references to:
Jacob Koehler, Principal Investigator, Bioinformatics, BAB
Rothamsted Research
Harpenden, Hertfordshire, AL5 2JQ
Jacob.koehler[at]bbsrc.ac.uk
Phone: +44-(0)1582763133-2851
Fax: +44 (0)1582 763010