I work at the Sanger Institute in Hinxton on sequence improvement using Smith-Waterman based algorithms. Before that, I worked at the Computer Laboratory, and have supervised and directed studies for several colleges over the last ten years. This page has some ideas for Part II projects. I would be happy to supervise any projects based on material covered in the Part II AI, NLP or Bioinformatics courses, or the Part IB Java or Compiler courses. You can contact me by emailing ksw1000.

Bioinformatics and AI

Here is an Open Source Java pairwise aligner which would be a good starting point.

Idea 1: can you optimise the alignment matrix based on characteristics in the input sequence and the reference sequence?

Idea 2: how well does this perform against other pairwise alignments such as HMMER. Here is a full list of software available for free. Can you deduce which method to use just by looking at the input sequence and the reference sequence?

I am also happy to discuss any simulation or compiler based ideas you have. I have included previous projects I have supervised below.

Bus monitoring system

Simulate buses and other traffic around the Cambridge ring road. This was done in Java using threads, but you could use C++ or BCPL.

Natural language processing

Deduce a headline from a body of text. This was done in Prolog a few years ago, but you could use Java or C++.

Deduce the keywords from a body of text to add into a WordNet® database. WordNet® is a large lexical database of English. Nouns, verbs, adjectives and adverbs are grouped into sets of cognitive synonyms (synsets), each expressing a distinct concept. Synsets are interlinked by means of conceptual-semantic and lexical relations. The resulting network of meaningfully related words and concepts can be navigated This would be done in Prolog because of the link into WordNet.

Compilers

Statement re-ordering to make the most of C++ optimisations is one of many ideas here

The courses that I supervise at present are Software Engineering and Design, Java, Compilers, Natural Language Processing, Comparative Programming Languages, Databases and Artificial Intelligence 1

I am also happy to work with Part 2 students looking to do their project in any of these areas.

My Background

Previously, I was a Teaching Associate for the Hardware Group at the Computer Laboratory, University of Cambridge, working on a web-based tutorial for the second year ECAD labs .

This tutorial has interactive programming pages with an explainer to interpret compiler messages and give hints, and a Verilog Google-style searcher to find relevant help pages to provide support in solving compilation errors. You can also ask questions in English which directly query the ontology underlying the web tutorial.

I have been Director of Studies (academic tutor) at Hughes Hall, Homerton, Pembroke College and Newnham College, Cambridge.

Before coming to Cambridge, I worked for Logica The projects I worked on were mostly in the commercial large database development and design. We tried out software engineering and project management techniques that now form part of UK and ISO standards.

In 1990, in the days when video on computers was still a dream, we worked with the Department of Transport to link a video disk player into a mainframe terminal to match a database of roads with the appropriate video stills. This project was shown on Tomorrow's World. I also worked on Human Computer Interaction and Logic Programming projects at Logica's research office in Cambridge, where I wrote one of the first frame buffer drivers to make a bi-headed Sun workstation called Zaphod as part of a project for air traffic controllers.

Publications

Posters

Taylor K, Moore S My Compiler really understands me: An Adaptive Programming Language Tutor 4th International Conference on Adaptive Hypermedia & Adaptive Web-based Systems June 20-23 2006

Workshop Papers

Moore S, Taylor K An Intelligent Interactive Online Tutor for Computer Languages, 25th Annual Conference of the British Computer Society's Special Interest Group on Artificial Intelligence (SGAI) (December 2005)

Papers

Taylor K, Moore S Adding Question Answering to an e-Tutor for Programming Languages, accepted for 26th Annual Conference of the British Computer Society's Special Interest Group on Artificial Intelligence (SGAI) (December 2006)

Here is my curriculum vitae.