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Supported by AITO.
These pages are currently maintained by Alex Potanin
Automating biological data processing using programming by example and PJama
Elzbieta Pustulka-Hunt
( British, Polish )
Department of Computing Science University of Glasgow G12 8QQ Scotland
tel: 44 141 3398855 x 0915
fax: 44 141 3304913
ela@dcs.gla.ac.uk
Keywords:
databases distribution bioinformatics programming by example
Abstract:
We aim to find out if it is possible to automate web and software interactions in biological research. Presently researchers spend up to 50% of their time in front of the computer carrying out repetitive data retrieval and analysis steps. We have conducted case studies of such research, and are now investigating data structures which could be used to store and recognise patterns of user activity. Suffix trees in the context of persistent Java (PJama) are now being studied, as well as their potential use for DNA and protein searching. Suffix trees will be used to analyse web activity of biological researchers, and data processing activities will be traced and stored in a PJama database. This research explores the support that persistent object systems can offer in bioinformatic research, tries to identify appropriate data structures, explores efficiency issues, and will help in automating repetitive interactions with data.
The participant will apply for the
upcoming ECOOP PhD Workshop.
NO HTML3
JAVA
Last modified on Mon Aug 15 14:59:24 2005