Category Archives: chemistry

Comments on comments and agents and eyeballs

Posted on October 1, 2007 by pm286

One of the difficult features of blogs is how to manage comments. On this blog these are relatively infrequent, wile on – say –ChemBark, TotallySynthetic.com or The Chem Blog some articles generate over 100 replies. I got into the habit … Continue reading →

Posted in chemistry, open issues | 2 Comments

Chemical Speeddrawing

Posted on September 28, 2007 by pm286

There used to be an advert on the London Tube advertising “Speedwriting” (something like “f u cn rd ths u cn gt a gd jb”. What about speed-drawing of chemical structures? Here’s Liquid Carbon: Finally, I’d like to offer a … Continue reading →

Posted in chemistry | 3 Comments

The Obelisk SMILES

Posted on September 28, 2007 by pm286

We are delighted that Craig James has suggested making the molecular format SMILES an Open activity. Egin Willighagen writes: SMILES to become an Open Standard 08:03 28/09/2007, Egon Willighagen, Craig James wants to make SMILES an open standard, and this … Continue reading →

Posted in blueobelisk, chemistry, open issues | 2 Comments

What's in a name? hexanoic acid still smells of goats

Posted on September 25, 2007 by pm286

In a recent post I said – rather crudely – that there was no absolute way of understanding chemical names. I have been (rightly) taken to task for imprecision: ChemSpiderMan Says: September 25th, 2007 at 5:04 am e I’m not … Continue reading →

Posted in chemistry, open issues | 5 Comments

Structures that InChI and SMILES can't represent

Posted on September 24, 2007 by pm286

Even in organic chemistry there are lots of strucures that cannot be represented by InChIs and currently cannot be communicated without structure diagrams. I’ve gone randomly to Beilstein Journal of Organic Chemistry (as it’s Open Access) and found three consecutive … Continue reading →

Posted in chemistry, open issues | 1 Comment

Truth or beauty, continued

Posted on September 24, 2007 by pm286

Continuing our discussion on whether a chemical strucure diagram is copyrightable. Steven Bachrach Says: September 24th, 2007 at 9:27 pm ePeter, I have to take exception to some of your claims. The chemical formula drawing is not the only way … Continue reading →

Posted in chemistry, open issues | 1 Comment

Diazonamide : The Blue CrystalEye Greasemonkey lends a hand

Posted on September 24, 2007 by pm286

There is some doubt about what the structure of diazonamide A is. Because there is no absolute way of assigning names to structures. We only agree what aspirin is because everyone has been assigning the same structure to it for … Continue reading →

Posted in blueobelisk, chemistry, data | 4 Comments

Beauty is truth, truth beauty – and copyrightable?

Posted on September 24, 2007 by pm286

In (Finding chemical structures – InChIs et al., an amusement) I explored the varied approaches to drawing structures and the problems of representing them. I commented that Totally Synthetic’s diagrams were not only the most unambiguous but also the most … Continue reading →

Posted in chemistry, open issues | 2 Comments

Finding chemical structures – InChIs et al., an amusement

Posted on September 23, 2007 by pm286

Totally Synthetic, Chemspider and I have been discussing the value of InChIs in blogs. TS’s blog is, of course Openly available under CC licence, and he is widely revered in the community for the beauty and acuuracy of his structural … Continue reading →

Posted in chemistry, open issues | 5 Comments

Webcast: the power of the eThesis

Posted on September 9, 2007 by pm286

I am very grateful to Caltech, specially Eric van der Velde, for organising and recording my presentation on eTheses at Caltech last month. See The power of the Scientific eThesis, a combined audio, video and screenshow. Caltech have done a … Continue reading →

Posted in chemistry, etd2007, open issues, theses, XML | 3 Comments