Monthly Archives: November 2007

SPECTRa tools released

Posted on November 30, 2007 by pm286

The SPECTRa tools allow chemists (perhaps group or departmental analytical spectroscopy groups) to submit their data (spectra, crystal structures, compchem) to a repository. From Jim Downing SPECTRa released Now that a number of niggling bugs have been ironed out, we’ve … Continue reading →

Posted in crystaleye, nmr, open issues | Leave a comment

CML/MathML and OpenStreetmap in Bremen

Posted on November 30, 2007 by pm286

I haven’t posted much because I’m in Bremen (DE) working with Michael Kohlhase on the integration of CML and MathML into scientific publications. We’re hoping to come up with some guidelines shortly. Last tie I was here I got lost … Continue reading →

Posted in Uncategorized | Leave a comment

Chemspider and Pubchem – open data

Posted on November 30, 2007 by pm286

I was very pleased to see: ChemSpider Blog » Blog Archive » The Entire ChemSpider Database is On Its Way to PubChem! which describes how the Chemspider database is being offered to Pubchem as “open data”. Chemspiderman has made a … Continue reading →

Posted in data, open issues | 2 Comments

Data-driven science

Posted on November 26, 2007 by pm286

I’ll be writing more about this later. Catalysed by an email from Douglas Kell at Manchester – we share the same problem – that data-driven science is a second-class activity. He picked up paper from http://www.sis.pitt.edu/~repwkshop/papers.html on data-driven science and … 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

NMR Challenge: what can a machine deduce from a thesis?

Posted on November 24, 2007 by pm286

One of the ways of extracting chemical structures from the literature is to use the NMR to constrain the possibilities. So, to give you an amusement for the weekend, here are some problems. I have a thesis (which I’m not … Continue reading →

Posted in fun, nmr, open issues | 6 Comments

How OSCAR interprets text and data

Posted on November 24, 2007 by pm286

I recently posted ( Open NMR and OSCAR toolchains ) about how OSCAR can extract data from chemical articles, and in particular chemical theses. Wolfgang Robien points out November 24th, 2007 at 11:03 am e I think, no, I am … Continue reading →

Posted in nmr, oscar | Leave a comment

Open means Libre

Posted on November 23, 2007 by pm286

In recent posts (e.g. Open Data – preservation) I have continued to raise the problem that “Open” should not just mean free of charge nbut also free to use. (Peter Suber calls these price and permission barriers).   So I am … Continue reading →

Posted in data, open issues | Leave a comment

Cameron's Open proposal

Posted on November 23, 2007 by pm286

In the last two days Cameron Neylon has posted an idea for Open Science and got a lot of interest, see: e-science for open science – an EPSRC research network proposal and Follow on to network proposal. The idea is … Continue reading →

Posted in "virtual communities", data, open issues, open notebook science | 3 Comments

Open NMR and OSCAR toolchains

Posted on November 22, 2007 by pm286

I am currently refactoring Nick Day’s code that has supported “NMREye” – the collection of Open experiments and Data that he has generated as part of his thesis and have been trailed on this blog ( View post). One intention … Continue reading →

Posted in data, nmr, open issues, oscar | 2 Comments