Typogenetics

Originally proposed in Hofstadter's ``Gödel, Escher, Bach'', typogenetics is a formal system intended to capture the essence of what was known about biological genetics at the time (1979).

The system was the topic for my research project undertaken as part of the honours programme within the School of Computer Science and Software Engineering (CSSE), Monash University, during 1999.

Documents

Documents available for download are the:

With the exception of the final thesis, these documents are only available in postscript format. To view them, you can use ghostview under Linux/Unix or GSView under Windows. Alternatively, you can send the documents directly to a postscript-printer. If you don't know how to do this, use one of the viewers mentioned above and print from there. The final thesis is also available as Acrobat's PDF format. To view files of this form you need to use either Acroread or xpdf. For on-screen viewing, the PDF version is preferable but if hardcopy is desired the postscript version of the document is superior.

Research Proposal

This document, written during the early stages of the project, documents the proposed research including the topic (typogenetics) and aims of the project.

The research proposal is available in postscript format.

Interim Presentation

This slide presentation was presented to peers and academics within the department a few months into the project. The presentation includes actual slides (framed) as well as interleaved notes to prompt my talk.

The interim slide presentation is available in postscript format.

Typogenetics Rules

This document was produced during the implementation of software to simulate typogenetics. It specifies unambiguous rules for the typogenetics system. While this was superseded by a chapter in my final thesis, it is useful as a standalone document if the rest of the thesis is of no interest.

This document is available in postscript format.

Literature Review

This document contains a review of literature to-date pertaining to typogenetics itself and related areas of interest for this research project.

This document is available in postscript format.

Final Thesis

This is the final thesis presented for my research project. It ties together the research undertaken and presents findings as well as an overview of the software developed to simulate typogenetics (some of which is listed in the Appendices).

The final thesis is available in both postscript and PDF format.

Software

A considerable amount of software was written during the course of this project, mostly in python. Some of the modules are listed in the appendices of the thesis. If there is any interest, more source code will be made available here.

A spinoff piece of software developed during this project was the PQueue extension module.

PQueue

During the course of this research project, the PQueue extension module for python was implemented. This module implements efficient priority-queues using fibonnaci heaps. While for many purpose this is not as efficient as the more-common binomial heaps, it is very efficient in some aspects that make it very useful for traversal of very large graph structures.

More information about the module is in the README file (read before downloading), while the actual module is available here. The module also has a Freshmeat entry and is made available under the terms of the LGPL. Binaries are not available, but if anyone wishes to provide a binary (especially for Windows) I'd be happy to put it up.