Category Archives: chemistry

Open Notebook NMR - Henry's improved protocol

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 | Leave a comment

Open Notebook NMR: Anticipated errors

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

Adding semantic markup with InChI

If we could require all authors to provide machine-readable chemical structures in their chemistry articles the quality of chemistry would increase dramatically and immediately. We could create Open databases immediately, that were machine-searchable (just like crystalEye). No-one doubts that, but … Continue reading

Posted in chemistry, open issues | Leave a comment

OPSIN/OSCAR: you + us = we; please help

I'm exploring how you and we may be able to work to improve OSCAR and OPSIN. Even if you aren't interested in chemical names, you may find the general principles useful. One of the drawbacks of full Open Source and … Continue reading

Posted in chemistry, open issues, oscar, programming for scientists, XML | Leave a comment

My outrage against "Open Access Publisher" continues

[Peter Suber, I'd be grateful if you could comment on what it is legal to index without publishers' permission. And what it is reasonable to expect from someone who labels themselves an Open Access publisher.] In my post Outrage: Repurposing … Continue reading

Posted in chemistry, open issues | 5 Comments

FROG - not just Free, but Open (PRODRG take note)

I am delighted to announce and praise FROG, a free service for creating 3D molecular structures from connection tables. This is yet another module in the list of Open chemistry offerings that will ultimately give the tools to the chemistry … Continue reading

Posted in chemistry, open issues | 1 Comment

Chemspider and "Open Chemistry Web"

Recently the Chemspider company has announced an "Open Chemistry Web" which in my opinion misuses the word "Open". Before I start I'll review my relationships and attitude to Chemspider and Chemspiderman to try to clear the air. Chemspider.com and its … Continue reading

Posted in chemistry, open issues | 9 Comments

Can chemical structures be right or wrong?

Chemspiderman has commented... ChemSpider Blog » Blog Archive » Dictionary Lookups and Optical Structure Recognition Versus Structure Drawing. Which is Less Error Prone? Says: October 2nd, 2007 at 5:48 am e[…] Luqidcarbon has put up a recent blog posting about … Continue reading

Posted in chemistry, open issues | 2 Comments

The chemical blogosphere cares

Wow! I posted a request yesterday (sic) for supporting material for our proposal to JISC for a person to support the blogosphere as a major resource for increasing the quality of published chemistry. I have had valuable contributions from 4 … Continue reading

Posted in blueobelisk, chemistry, open issues | Leave a comment

I submit a Nature article to Nature Precedings

I have been invited by the editors of Nature to submit a review/commentary article, currently on the theme of "Open Chemistry". This is currently under the title "Horizons" though the actual format may change before publication. I wrote the article … Continue reading

Posted in chemistry, open issues | 2 Comments