Category Archives: programming for scientists

Please send us your Vistas

Posted on March 19, 2009 by pm286

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 →

Posted in open notebook science, programming for scientists, semanticWeb, Uncategorized | Leave a comment

Semantic Chemical Computing

Posted on January 30, 2008 by pm286

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

Posted on January 6, 2008 by pm286

[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!

Posted on January 5, 2008 by pm286

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 →

Posted in programming for scientists | Tagged , , | 3 Comments

Update on Open crystallography

Posted on December 22, 2007 by pm286

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

Posted on December 22, 2007 by pm286

  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

Posted on December 20, 2007 by pm286

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 →

Posted in programming for scientists | 1 Comment

Refactoring large modules using Eclipse

Posted on December 20, 2007 by pm286

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 →

Posted in programming for scientists | Tagged | 5 Comments

Bioclipse awarded [prize] at Trophees du Libre

Posted on December 3, 2007 by pm286

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 →

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Why is it so difficult to develop systems?

Posted on November 25, 2007 by pm286

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 →

Posted in programming for scientists, repositories | 1 Comment