Category Archives: programming for scientists

Please send us your Vistas

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

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Semantic Chemical Computing

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

Posted in chemistry, programming for scientists | Tagged , , , | 1 Comment

CMLBlog: Sourceforge resources

[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

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Learning RDF and RDFS - help!

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

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Update on Open crystallography

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

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FoX marches on

  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

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Java: labelled break considered harmful

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

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Refactoring large modules using Eclipse

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

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Bioclipse awarded [prize] at Trophees du Libre

Ola Spjuth reports that Bioclipse - theĀ  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

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Why is it so difficult to develop systems?

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

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