Category Archives: programming for scientists

Bioclipse and the Information Revolution

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)

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

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Graphics

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

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Algorithm puzzles

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

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

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The War on Error

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

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(Chemical) Images in blogs

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

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Mystery Molecule and Jack Dunitz on Fluorine

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

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

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