Author Archives: pm286

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 We think that really major foul-ups have been superseded (i.e. when all the Gaussian files failed to run because of a missing blank … Continue reading →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

Peter Suber – a model for us all

Posted on October 21, 2007 by pm286

I have just read Richard Poynder’s interview with Peter Suber: The Basement Interviews: Peter Suber, Open and Shut? October 19, 2007. It’s 80 pages and Richard records that it took 3 hours on Skype and landline. It’s almost the equivalent … Continue reading →

Posted in open issues | Leave a comment

Reconciling points of View

Posted on October 21, 2007 by pm286

Over the last few weeks there has been strong and active discussion about issues relating to Openness and some of these have been commented on (or even initiated) here. Some people feel that I have may been simplistic or overly … Continue reading →

Posted in "virtual communities", open issues | 1 Comment

Urgent action need to support the NIH bill

Posted on October 21, 2007 by pm286

Peter Suber has written at length (Urgent action need to support the NIH bill) The provision to mandate OA at the NIH is in trouble.  Late Friday, just before the filing deadline, a Senator acting on behalf of the publishing … Continue reading →

Posted in open issues | Leave a comment

A graph

Posted on October 21, 2007 by pm286

In the tradition of Rich Apodaca’s “Name that graph” (example), here is a graph without axes. You will be seeing more of these later.

Posted in data, puzzles | 4 Comments

Why Green Open Access does not support text- and data-mining

Posted on October 16, 2007 by pm286

Stevan Harnad, Peter Suber and I have been discussing whether Green Open Access (author self-archiving in an Institutional Repository) is sufficient to allow indexing and mining. Stevan comments: Individual re-use capabilities: If a document’s full-text is freely accessible online (OA), … Continue reading →

Posted in Uncategorized | 2 Comments

Industry suffers from Closed Data

Posted on October 16, 2007 by pm286

I received the following unsolicited mail two days ago from a scientist in a major chemical company [I have anonymised everything so you will have to take my word]. I work [in industry] and am very interested in improving our … Continue reading →

Posted in data, open issues | 3 Comments