Category Archives: open notebook science

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 →

Posted in chemistry, data, nmr, open notebook science | Leave a comment

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 We think that really major foul-ups have been superseded (i.e. when all the Gaussian files failed to run because of a missing blank … Continue reading →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

Experiment and Calculation in WWMM-NMR. Open Notebook Science

Posted on October 22, 2007 by pm286

Antony guessed the graph – regular readers will recognise the context of previous posts. We are starting an Open Notebook project to determine whether theoretical calculations and experimental observations agree – or rather within what limits. (Earlier this year I … Continue reading →

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

Open-Data-driven science and a brokering system for ONS

Posted on October 14, 2007 by pm286

Cameron Neylon and Jean-Claude Bradley have blogged about a directory of Open Notebook Science (ONS) where projects including this approach can register. Growing a community – Open Notebook Science directories 21:19 14/10/2007, Cameron Neylon, As has been flagged up by … Continue reading →

Posted in blueobelisk, data, open issues, open notebook science | 6 Comments

Open NMR

Posted on October 13, 2007 by pm286

As I have already blogged (WWMM calculation of spectra) we are hoping to provide Jean-Claude Bradley and others an Open service to calculate NMR spectra from structure. This  needs a lot of software components and a lot of glueware. With … Continue reading →

Posted in blueobelisk, nmr, open issues, open notebook science, programming for scientists, theses | 6 Comments

Open Notebook Science

Posted on October 12, 2007 by pm286

To clarify … this is a joint project between Henry and us. Until now the emphasis was here, because it was useful for Nick to run some jobs as part of his eScience PhD. Nick has already done about 500 … Continue reading →

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Posting spectra

Posted on October 11, 2007 by pm286

Jean-Claude Bradley Says: October 11th, 2007 at 1:32 pm e http://www.chemspider.com/spectra.aspx and for example benzaldehyde: http://www.chemspider.com/Chemical-Structure.235.html I think a lot of the errors in the literature are due to poor quality spectra and improper referencing. It is really useful to … Continue reading →

Posted in nmr, open notebook science | 3 Comments

WWMM calculation of spectra (proposed)

Posted on October 11, 2007 by pm286

Jean-Claude Bradley has offered us the spectra that come out of his Open Notebook projects… Jean-Claude Bradley Says: October 11th, 2007 at 1:32 pm ePeter – it is great to see you contributing to open NMR data processing. For a … Continue reading →

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