About four years ago I speculated that JavaScript may be capable of filling some important holes in chemistry software.

Last week’s news was dominated by the initial public offering of Facebook. Although it’s unlikely that many investors understood exactly what they were buying, much of the company’s value derives from the massive social graph created within the last few years, and tools for exploiting it commercially.

Balancing chemical equations is one of the first things taught in most introductory chemistry classes. As such, it might seem as if everything there is to know about the topic was published 75 years ago or more by chemists long since gone.

The now-fading discussion of Elsevier and the Research Works Act got me thinking about the American Chemical Society, which runs a very large scientific publication business of its own. I started wondering why the ACS exists in the first place and what its long-term vision might be. In 1938, a U.S. Congressional Charter was granted to the American Chemical Society. Although essentially honorific, this document makes for interesting reading.

Ein Fehler ist aufgetreten. Sieh dir dieses Video auf www.youtube.com an oder aktiviere JavaScript, falls es in deinem Browser deaktiviert sein sollte. Creating this video was fun, and there’s an obvious business model behind the company making it possible. Guess what? I just published it for free to a worldwide audience. Why doesn’t science work this way?

George Whitesides is well known as an innovator and one of chemistry’s most visible representatives. He has the distinction of being credited with the highest Hirsch index for any living chemist. You could say he knows something about scientific publication. Ein Fehler ist aufgetreten. Sieh dir dieses Video auf www.youtube.com an oder aktiviere JavaScript, falls es in deinem Browser deaktiviert sein sollte.

The Research Works Act (‘RWA’, or HR 3699) would reverse the US federal government policy of requiring recipients of National Institutes of Health (NIH) funds to deposit copies of their research papers into PubMed Central. It would also prevent the adoption of similar policies by other federal funding agencies going forward.

Steve Jobs described the textbook business as an $8 billion a year industry “ripe for digital destruction.” The scientific publication business resembles the textbook industry in many ways, including lack of value-creation Jobs was referring to. The Research Works Act (HR 3699) is the scientific publication industry’s surest path to digital destruction.

MDL V2000 molfile format is the closest thing cheminformatics has to a universally-adopted standard. First publicly described in depth in 1991 and developed over the previous 13 years, the molfile format is read and written by nearly all software doing anything significant with organic chemical structures today. Think about this for a moment - the lingua franca of cheminformatics predates Windows 3.0 and the World Wide Web.

Ein Fehler ist aufgetreten. Sieh dir dieses Video auf www.youtube.com an oder aktiviere JavaScript, falls es in deinem Browser deaktiviert sein sollte. IBM recently announced the donation to PubChem of more than 2.4 million chemical structures extracted from the patent literature and biomedical journals.

Ein Fehler ist aufgetreten. Sieh dir dieses Video auf www.youtube.com an oder aktiviere JavaScript, falls es in deinem Browser deaktiviert sein sollte. PyMOL is designed a bit differently from other applications, which can take some getting used to. The tutorial gives a high-level overview of the user interface.