Wise's Web Words

Biochemistry, M310 Bioinformatics School of Biomedical and Chemical Sciences University of Western Australia Crawley WA 6009 Australia CRICOS Provider Code 00126G mwise123@cyllene.uwa.edu.au (remove digits before use)

JUMP table

Research

• Bioinformatics June 11, 2003
• Troff (mm) to html converter February 25, 2002
• Agrepy (Version 1.2): Python port of Agrep (string matching with errors) September 11, 2002
• Automated Detection of Suspected Plagiarism July 5, 1996
• The Python Programming Language June 27, 2003
• Alan Perlis' ``Epigrams on Programming'' September 16, 1998

There is Life Outside Work

• Fun News - Small Items You Might Have Missed August 3, 1998

And Serious Stuff

• Immunisation Alliance of Western Australia January 23, 2009
• Devastation in NY - Thought for the Day September 12, 2001
• An End to Holocaust Denial April 13, 2000
• The Simon Wiesenthal Centre January 16, 1997
• The Peace Now Movement August 19, 2002
• The Paradox of Peace and Identiy - Thought for the Day September 13, 2002
• Gun Control in Australia and the UK August 4, 1998

The END

RESEARCH

• Bioinformatics

Bioinformatics is the study of molecular biology as an information science. Specifically, it studies the application of computers to the understanding and, eventually, manipulation of the molecules of life. A number of bioinformatics-related projects are underway. Click on the link above for further information.


• Version 1.2 of Python port of agrep (string matching with limited errors)

agrep is a suite of command-line (i.e. UNIX user level) string matching functions, written by Sun Wu and Udi Manber (described in "Fast Text Searching Allowing Errors", CACM, 35(10), 1992). While the majority of the functionality is already found in Python, the ability to perform string searches accepting a limited number of errors has not been available till now. Such searches are able to deal with spelling errors, or the differences between North American and British English. Alternatively, this form of string matching is able to model the attachment of a primer to a target DNA sequence (i.e. attachment occurs if there are no more than, say, 2 indels).


• troff to html converter

Not precisely research, however during 1998 I wrote, in Python, a troff to html convert because none of the ones I could find do a particularly good job. pymm2html does a reasonable job converting documents formatted using troff (mm macros) to HTML. Rather than attempting to reimplement groff, eqn, tbl, pic and refer, significant functionality has been mimicked (i.e. much of the spirit and many of the idioms, but not to the letter). The current version, 1.01 is a small revision on the early system, principally switching from the deprecated regex/regsub modules to using the re module.


• Automated Detection of Suspected Plagiarism

In spite of considerable effort in course design, plagiarism in student assignment submissions still causes difficulties for course providers; if students' work is not their own, how can anyone be certain they have learnt anything? YAP3 is the third version of a series of systems for detecting suspected plagiarism in computer programs. Recent work has indicated that YAP3 is the most effective currently available and arguably the most easily ported to new programming languages. Recent work has also extended the use of YAP3 to English language texts. Click on the above link for more details.


• The Python Programming Language
  Having been through a number of "language wars" over the years, e.g. the sterile debates on the merits of Lisp versus Prolog in the 1980's, I have been reluctant to be drawn into such debates again. None-the-less, in a world that is discovering scripting languages, specifically Perl (also known as the Swiss Army Chainsaw), Python is a wonderful discovery and has multiplied my productivity several times. Lars Marius Garshol has written a very nice account of his journey from Perl to Python What's wrong with Perl. Recommended reading.

  A recent article discusses the success of pharmaceutical company AstraZeneca in rewriting in Python, and then extending, a computational chemistry integration package originally written in Perl.
  
  

• Alan Perlis' ``Epigrams on Programming''
  Alan Perlis (1922-1990) was a pioneer Computer Scientist and early researcher into Artificial Intelligence. Always a sceptic, he published a list of epigrams about programming in the ACM publication SIGPLAN Notices in 1982. While some of the 130 epigrams have become a little dated, most are as insightful now as when they were first published.

There is Life Outside Work

• In Case You Missed It - News Snippets



[Rowing] is, of course, an extraordinarily apt sport for men in public life, because you can face one way while going the other.

Gough Whitlam

Do not place any part of your body in the mouth of a crocodile

Extract from the Queensland Government's new Workplace Health and Safety guide for the crocodile industry

Both quoted in Australian Financial Review, July 23

It was a day on which the long jump never rose to great heights

ABC (Australian Broadcasting Corporation) Radio's Tim Gable, as reported in Australian Financial Review, July 31, 1996

For other, similar snippets that you may have missed, click on the link above. Nothing earth-shattering; just evidence that people are only human.

And Serious Stuff

• Immunisation Alliance of Western Australia
I am the Deputy Chair of the Immunisation Alliance of Western Australa. IAWA is a coalition of individuals, such as myself, and representatives of local organisations.` Our aim of AIWA is to improve the health of the WA community by disseminating high quality information about vaccine-preventable diseases and the vaccines that are available to treat them. In many ways we are "the lucky country"; the majority of vaccines, particularly childhood vaccines, are free. Indeed, there is a Commonwealth Government payment to parents whose children have been fully immunised ( Maternity Immunisation Allowance). In spite of that, there are age-groups and locations in the state where rates are less than wonderful so we are working to reduce the barriers to vaccination. The downside of not vaccinating can be devastating. (See Mengitis Angels - click on Angel Stories.)


• A Moving Reflection on the Devastation in New York
The day following the devastating attack in New York, the Bishop of Bath and Wells, Rev James Thompson, presented an eloquent and moving Thought for the Day on BBC Radio 4. The text, reprinted with permission, can be found here.


• An End to Holocaust Denial?

My grandparents, uncles and aunts were systematically murdered by the Nazis and their local supporters; I would not have been born had not an unknown American soldier liberating Belsen concentration camp noticed that a particular body (my mother's) was slightly more alive than the others. It's been hard growing up knowing that the world largely stood by, but harder still listening to anti-historical rants of the deniers. One, foremost among them, David Irving, has had his day in court and been told to his face what he is. For the BBC coverage see http://news.bbc.co.uk/hi/english/uk/newsid_709000/709203.stm. Click on Hitler historian loses libel case for a chronology of the case and other links. Unfortunately, David Irving's perversion of history is not without its supporters, e.g. here.


• Simon Wiesenthal Centre and Tolerance Museum

The Simon Wiesenthal Center not only is a memorial to whose who died at the hands of the Nazis, but also is dedicated to fostering a spirit of tolerance. Racism is indivisible; today's black-hatred, is tomorrow's asian-hatred or jew-hatred, or ... A tolerant, civilized society is the only real answer.


• Peace Now Movement

The Peace Now movement in Israel is a small sign that peace and sanity are still a possibility in relations between Israelis and Palestinians.


• The Paradox of Peace and Identiy - Thought for the Day, September 13, 2002

In a very thought provoking Thought for the Day, broadcast on BBC Radio 4 on September 13, 2002 - between the anniversary of the tragedy of September 11, 2001 and the Day of Atonement, the Chief Rabbi of the United Hebrew Congregations commented on the paradox of peace and identity, and why those who seek peace can seem like traitors. The text can be found here.


• Gun Control in Australia and the U.K.



``There are more holes in them and the holes are bigger''

John Sugarman of the Violence Policy Center in Washington, D.C., describing a trauma surgeon's answer to the question of how gunshot victims had changed in the US in the last 10 years.
Australian Financial Review, June 7, 1996

``Wedding backfires COPENHAGEN: Two people were killed when a wedding guest fired a gun into the air, sending bullets ricocheting into the wedding party. The man said it was traditional to fire into the air at Turkish weddings. He forgot he was inside''

The Australian, December 27, 1995

Gun Control Australia in Australia and the Gun Control Network in the UK provide cogent and sane arguments to refute the hysterical nonsense peddled by the gun lobby. There is no "right" to bear arms.