Category Archives: programming for scientists

I recently got an invitation to speak (anonymized as I don’t want to fall out) which included: “I would very much appreciate a copy of your presentation in advance of the event in Windows XP format as the venue is … Continue reading →

Several threads come together to confirm we are seeing a change in the external face of scientific computing. Not what goes on inside a program, but what can be seen from the outside. Within simple limits what goes on inside … Continue reading →

[This is the first of a continuing series of posts destined for the revitalised CMLBlog.] The major developers resource for CML is at sourceforge. This is the traditional page which each project has and has several useful features: There has … Continue reading →

I’m getting myself up to speed on RDF (and RDFS) and building molecular repositories as an example. I’m using the Jena Semantic Web Framework (Open Source , Java, HP-inspired) and so far like it. But I have only done a … Continue reading →

There’s now a growing movement to publishing crystallography directly into the Open. Several threads include: The Crystallography Open Database which pioneered the idea of collecting crystallographic data and making them Openly available. Nick Day’s CrystalEye – aggregation of published Open … Continue reading →

Toby White joined us – Jim Downing, Peter Corbett and me – in the pub yesterday to unwind and explore the challenges of tomorrow’s information. Toby has been one of the pillars of supporting CML – there was no … Continue reading →

Readers of my last post may have thought that Eclipse makes refactoring easy. It does – up to a point. I had started to refactor an 800-line module with deeply nested loops – just a matter of extracting the inner … Continue reading →

I have recently had to consider refactoring a piece of Java which had got slightly out of hand – the module was 800 lines long and the if statements so deeply nested that they ran well off the right-hand edge … Continue reading →

Ola Spjuth reports that Bioclipse – the collaborative bi/chem client based on Eclipse – has won another prize. Bioclipse awarded at Trophees du Libre I [Ola] just arrived home from the international contest for free software, Trophees du Libre 2007, … Continue reading →

Dorothea Salo (who runs Caveat Lector blog) is concerned (Permalink) that developers and users (an ugly word) don’t understand each other: (I posted a lengthy polemic to the DSpace-Tech mailing list in response to a gentle question about projected DSpace … Continue reading →