Monthly Archives: January 2008

CML Blog will restart

There has been a long hiatus on the CML blog but I am now convinced it is the best way to discuss the general topics on CML and to leave cml-discuss for more technical ones. I shall make cross references … Continue reading

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Automatic assignment of charges by JUMBO

Egon has spotted a bug in our code for assignment of charges to atoms: Why chemistry-rich RSS feeds matter… data minging, The example shown by Peter was nicely chosen: something is wrong with that example. It uncovers a bug in … Continue reading

Posted in chemistry, crystaleye | 6 Comments

What if chemistry data had been open?

When people ask me for examples of why Open Data matters, I always refer them to the Openness of bioscience – or at least those parts close to the Central Dogma (DNA-> RNA->Protein->Structure->Function). All those parts are Open. You can … Continue reading

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CrystalEye RSS

Nick Day’s CrystalEye system can e thought of as an open, robotically managed, robotically quality-reviewed, data, overlay, “journal”. It’s not a conventional journal, but it ticks most of the buttons. And it publishes a new set of information each day. … Continue reading

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APE2008 thoughts on domain repositories

I’m sitting waiting for about 1 million files to transfer from one laptop to another – in the Computer Officer hideout where we have really strong coffee. I tend to twitch about such transfers – rather like a hermit crab … Continue reading

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APE2008 more thoughts

Because there was no electricity and wireless at the APE meeting ( APE 2008) I took some notes, but they seem rather dry now and have lost some of the immediacy. So I shall use the meeting to catalyze some … Continue reading

Posted in publishing | 1 Comment

Chemistry Repositories

Richard Van Noorden – writing in the RSC’s Chemistry World – has described the eChemistry repository project, Microsoft ventures into open access chemistry. This is very topical as Jim Downing, Jeremy Frey, Simon Coles and me are off to join … Continue reading

Posted in crystaleye, repositories | Tagged , | 1 Comment

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

Big Science and Long-tail Science

Jim Downing and I were privileged to be the guests of Salvatore Mele at CERN yesterday and to see the Atlas detector of the Large Hadron Collider . This is a “wow” experience – although I “knew” it was big, … Continue reading

Posted in open issues | Tagged , , | 12 Comments


I’m not keeping up with the backlog of things I have brought away from APE 2008 Academic Publishing in Europe “Quality & Publishing” – I find it difficult to comment several days after the event (Please can conferences install wireless … Continue reading

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