Monthly Archives: October 2007

Open Notebook NMR – variance is both experimental and theoretical

Posted on October 24, 2007 by pm286

When making claims in foo-metrics and foo-informatics it is essential to have access to the data and the algorithms used. That’s why, for example, Peter Corbett and Sciborg colleagues are so careful in constructing their corpus. In developing our Open … Continue reading →

Posted in Uncategorized | 1 Comment

Well Done OA

Posted on October 24, 2007 by pm286

Peter Suber’s latest post needs no comment: OA mandate at NIH passes the Senate Tonight the Senate passed the Labor-HHS appropriations bill containing the provision to mandate OA at the NIH.  More, the vote was a veto-proof 75-19. Comments Neither … Continue reading →

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Open Notebook NMR – the good and the ugly

Posted on October 24, 2007 by pm286

We’ve started going through the structures in serial order. Here are two in the first 4 I looked at. One shows near perfect agreement, the other is frankly awful. Here’ s the link to NMRShiftDB: nmrshiftdb2470-1 (solvent: chloroform) You can … Continue reading →

Posted in nmr, open issues, open notebook science | 6 Comments

Open Notebook NMR: Commercial re-use of data?

Posted on October 23, 2007 by pm286

Antony Williams of Chemspider has offered to participate in our Open Notebook NMR experiment. Now this offer has been joined by ACDLabs – I am not sure of the formal relation between the companies but they have clear common interests. … Continue reading →

Posted in nmr, open issues, open notebook science | 8 Comments

Open Notebook NMR – interesting outlier(s)

Posted on October 23, 2007 by pm286

Here is an interesting outlier which caught me out, until Christoph explained it. Here are two spectra. They are both from the same source: (There are 3 peaks – note the disagreement) Also 3 peaks. Here is the metadata for … Continue reading →

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Open Notebook NMR – Outliers

Posted on October 23, 2007 by pm286

Egon asks: Egon Willighagen Says: October 23rd, 2007 at 4:00 pm eWhere in which wiki can I find the outliers? That would allows people to indicate problems, and possible annotate existing publications with ratings (”this article has a incorrectly assigned … Continue reading →

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Open Notebook NMR : the act of discovery

Posted on October 23, 2007 by pm286

Things are happening so fast on the Open Notebook NMR project that we need to take stock. Here’s today’s developments: Nick Day is working round the clock to manage the data and create the plots. He has a thesis to … Continue reading →

Posted in data, nmr, open notebook science | 1 Comment

Open Notebook NMR – Henry's improved protocol

Posted on October 22, 2007 by pm286

When we first started this (nearly a month ago). Henry suggested a protocol for calculating the chemical shifts. Nick tooled up for this and had to overcome several technical problems on job submission, etc. (A typical example – the order … Continue reading →

Posted in chemistry, nmr, open notebook science | 3 Comments

Open Notebook NMR: Anticipated errors

Posted on October 22, 2007 by pm286

Nick and I sat down this morning and thought about what possible errors might arise in the “data” or “experimental” axis and also on the “predicted” axis. Some of these may overlap with Antony’s suggestions but they are independent. An … Continue reading →

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Open Notebook NMR – cont

Posted on October 22, 2007 by pm286

We are now close to releasing the first results of the calculations – at present 300+ molecules. We think that really major foul-ups have been superseded (i.e. when all the Gaussian files failed to run because of a missing blank … Continue reading →

Posted in data, nmr, open notebook science | 1 Comment