Category Archives: programming for scientists

Bioclipse and the Information Revolution

Posted on May 20, 2007 by pm286

I have been honoured to have been asked to talk at the 07.05.23 Embrace Workshop on Bioclipse 2007 (EWB 07), BMC, Uppsala … meeting next week in Sweden. This post explains why Bioclipse is so important (it goes beyond bio/chem) … Continue reading →

Posted in blueobelisk, open issues, programming for scientists, XML | 2 Comments

Parsing Microformats (revised post)

Posted on May 12, 2007 by pm286

Useful presentation online (in S5) from Ryan King (of Technorati) on parsing microfomats. (I’ve been out of touch with HTML4 and I’m learning things.) We’ll need a day or two of virtual Blue Obelisk discussion to make sure we are … Continue reading →

Posted in programming for scientists, www2007, XML | Leave a comment

Graphics

Posted on November 30, 2006 by pm286

I have worked with computer graphics for many years – this has been catalysed by Noel’s discussion of the Algorithm puzzles Noel OBoyle Says: November 30th, 2006 at 1:59 pm eI would be *very* impressed if you could figure out … Continue reading →

Posted in programming for scientists | 2 Comments

Algorithm puzzles

Posted on November 28, 2006 by pm286

I love algorithms. I’m not good at them, but I think they’re a wonderful expression of human creativity. An algorithm is a formal procedure which – in simple terms – works out the answer to a problem. A good algorithm … Continue reading →

Posted in programming for scientists, puzzles | 8 Comments

Premature Optimization

Posted on November 19, 2006 by pm286

For many years I have believed (and still believe) in the following (quoted in Wikipedia) : Tony Hoare first said, and Donald Knuth famously repeated, “Premature optimization is the root of all evil.” It is important to have sound algorithms … Continue reading →

Posted in programming for scientists | 1 Comment

The War on Error

Posted on November 18, 2006 by pm286

There’s been a lot of  excitement over Pete Lacey’s The S stands for Simple. This Socratic dialogue, which I blogged yesterday has shown the futility of the overengineered madness from the W3C committees. There are other similar postings, summarised in … Continue reading →

Posted in programming for scientists, XML | Leave a comment

(Chemical) Images in blogs

Posted on November 15, 2006 by pm286

I am following up a post where I suggested we could provide a service for drawing molecules in blogs. One problem is how to incorporate them into the post. (I’m still working on this post, so don’t believe it all) … Continue reading →

Posted in chemistry, general, programming for scientists | Leave a comment

Mystery Molecule and Jack Dunitz on Fluorine

Posted on November 13, 2006 by pm286

Jack Dunitz (one of the greatest chemical crystallographers) visited our lab today. I had told people beforehand that I would ask him what the mystery molecule was and prophesied that he would get it immediately. He did. This gives me … Continue reading →

Posted in general, programming for scientists | 13 Comments

Enjoyable version control with the Tortoise

Posted on October 30, 2006 by pm286

Update, merge, test, add, update, commit… that’s what I do when working in a communal software project. Update, merge, test, add, update, commit… So I’ve written some additional tests for JUMBO. Now I have to save them and share them … Continue reading →

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Unit tests or get a life

Posted on October 29, 2006 by pm286

My unit tests have taken over my life this weekend. This post is a brief respite… Unit tests are one of the great successes of modern approaches to programming. If written briefly about them before and Egon has an introduction … Continue reading →

Posted in programming for scientists | 3 Comments