Mat Todd poses some very good questions in response to a recent post on creating chemistry communities: It should be emphasized that whenever we talk about ‘chemists’, we’re really making generalizations about a heterogeneous group. Same applies to ‘software developers’. Keeping that in mind, here are some ideas for how the culture of professional chemists differs from the culture of professional programmers: Numbers.

Ein Fehler ist aufgetreten. Sieh dir dieses Video auf www.youtube.com an oder aktiviere JavaScript, falls es in deinem Browser deaktiviert sein sollte. For the unfamiliar, StackOverflow is a programming question and answer service. There are dozens, if not hundreds, of these things on the Web - and most of them are lame.

I continue to be amazed by the number of people I’ve come into contact with who read Depth-First regularly. Many express appreciation for what I’m doing followed quickly by various reasons why they themselves can’t possibly do it. Not just once or twice, mind you, but almost every time. This is amusing to put it mildly.

Noel O’Boyle raises an important question about the canonicalization algorithms used in chemical line notations such as SMILES and InChI: This isn’t merely an academic exercise. One of the best uses for InChI that I’ve found is as a private primary key in a molecular database.

Creating useful data-driven applications for chemists is not an easy job. Data heterogeneity represents one of the stumbling blocks. Chemists create and use so many different kinds of data, from spectra in XY format to raw FIDs to PDFs to chemical structures to in vivo biological results, that deciding the structure of a database up-front, as required by relational databases can be difficult at best.

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Bosco recently posted some interesting thoughts on the comments and ratings system for the Public Library of Science (PLoS): Sound familiar? I wrote the following as a comment: There have been a few attempts to create centralized rating/discussion services for the scientific literature. For but one example, consider “The Scientific Debate”, a now defunct service that was originally reviewed here.

The representation of ferrocene is a longstanding problem in cheminformatics. What makes ferrocene a problem is that the deeply entrenched simplification that covalent bonds only ever consist of two atoms sharing a multiple of two electrons simply doesn’t apply. When we try to stick with this model anyway, Bad Things can happen. This is a problem that deserves attention and vigorous debate.

In late March a company called Outsell published an article on InChI by Daniel Pollock that has created a bit of a stir. The article, titled Chemical Bonding InChI by InChI was retracted by Outsell, who write: The reasons for retraction seem to revolve around statements made about SciFinder and speculations made in the article about the Chemical Abstracts Service (CAS) response to InChI.

Chemical Markup Language (CML) is an XML-based language for chemistry developed by Peter Murray-Rust, Henry Rzepa and many other contributors. Designed as a communication medium for chemistry based on open standards, CML aims to provide a uniform, extensible system for representing, storing, and transmitting chemical information. CML enables a range of concepts to be modeled, including molecules, reactions, and chemical metadata.