Final year B.Sc. projects 2003-2004

Tom Naughton, Room 2.104, tom.naughton@may.ie
Title: Distributed computing for DNA analysis
Pre-Requisites: Good programming skills; Level of project difficulty: high
Description: We are developing a heterogeneous distributed computing environment for the analysis of genomic sequences (in particular, those of tuberculosis and HIV) in order to help biologists gain a greater understanding of these diseases. We intend to use all of the 'spare' clock cycles in the Department to effect a virtual supercomputer. It consists of a server capable of accepting an algorithm and a data set, and capable of partitioning the computational load into variable-sized segments. Clients request a segment (in the form of an algorithm plus data) and return the results. The server combines the results from multiple clients. The system could be described as a programmable general-purpose "SETI@Home" system.

The first generation of this system was designed and built by successive years of 4th year students, and we currently have two IRCSET Embark funded postgraduates working on the system (Thomas Keane and Andrew Page). At its peak, the unused computing power of approximately 200 of the Department's machines was harnessed and we were averaging 3 'Pentium years' of computation per week. We have openings for students to take on selected projects in areas such as security, scheduling, design of efficient parallel algorithms, and design of network administration tools. The student would benefit from the support of, and would be expected to contribute to, our active research group. We are also working closely with members of the Department of Biology, NUIM, who intend to use our results for the understanding of disease and the improvement of quality of life. If you have any questions, or would like to meet and talk about the project, please feel free to contact me at tom.naughton@may.ie

Language(s): Java
References: References: A paper giving an overview of our distributed system and a paper describing a scalable server architecture for our system.
Availability: Taken

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Tom Naughton
Title: Emulation of an unconventional model of computation in Java
Pre-Requisites: Good programming skills; Level of project difficulty: high
Description: An emulator is required for a theoretical model of computation inspired by optics. This novel computer uses continuous space instead of the discrete tape cells of a Turing machine or the discrete registers of a digital electronic computer. It also has a Fourier transform as one of its primitive operations. A programming language for the computer has already been developed, and much of the back-end of the emulator has been built. An individual is required to bring the model to life by completing the emulator. It is planned to use the emulator to design and test algorithms for optical computer.

Since the computer manipulates images rather than bits, a certain level of graphics programming will be involved in this project. Advice will be available from Aidan Delaney (who has done the initial work on the emulator) and Damien Woods (one of the eventual users of the emulator). A very capable student could have the distinction of having contributed to the development the world's first debugger for an optical computer! If you have any questions, or would like to meet and talk about the project, please feel free to contact me at tom.naughton@may.ie

Language(s): Java
References: References: a paper describing initial work on the emulator.
Availability: Taken

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Tom Naughton
Title: Three-dimensional holographic video codec
Pre-Requisites: Good programming skills; Level of project difficulty: high
Description: Do you remember R2D2's hologram message of Leia Organa in Episode IV? Ever wonder if technology was going in that direction? Three-dimensional television and video is currently the subject of intensive research. One promising technique for 3D TV uses digital holography. A digital hologram stores multiple different perspectives of the same real-world object. This allows us to reconstruct the 3D object either digitally (in software) or optically. In the last five years, digital imaging technology has advanced to a stage where the capture, transmission, and display of digital holograms is now a realistic possibility.

A digital holograpic 'camera' has already been built and we have a small database of 3D frames and video clips. The next step is to look at networking issues. We have experimented with coding and compression of digital holograms and want to extend this to video. One or two creative, imaginative, and highly-competent students are required to join our group in the development of the first MPEG-style codec (compressor-decompressor) for digital holographic video. It is hoped that by the end of the project, Internet transmission of holographic video could be demonstrated. If you have any questions, or would like to meet and talk about the project, please feel free to contact me at tom.naughton@may.ie

Language(s): Matlab and/or Java
References: References: Recent presentations on single-frame digital hologram compression and Internet transmission of digital holograms. Two final year projects on this topic from last year are available for viewing. Also, an interesting book on 3D TV and Display Technology can be borrowed from the NUIM library.
Availability: Taken

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Tom Naughton
Title: Research literature organising tool
Pre-Requisites: Good programming skills; Level of project difficulty: medium to high
Description: A software tool is required to organise the research literature of a research group. The tool should manage a database of research papers, and have a WWW interface. Research group members should have the facility to add/remove/update entries in the database. Each entry should include a BibTeX description of the paper, an abstract, a list of keywords, a PDF copy of the paper, and comments on the paper from research group members. There should be a comprehensive set of search options, and result formatting options.

Extensive cross-referencing (for example, implementing the functionality "click here to see this author's other papers in the database"). If desired, a student could also investigate the technologies adopted by citeseer and Google to efficiently implement such functionality as "Click here for a list of similar papers." In particular, how this might be best achieved dynamically is an open research problem. If you have any questions, or would like to meet and talk about the project, please feel free to contact me at tom.naughton@may.ie

Language(s): Unspecified (modifying an existing open source tool could be an option)
References: References: None
Availability: Taken
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