Unlike many data types, molecular structure representations are not normally unique. Each numbering system you choose for the atoms and bonds of a molecule gives rise to completely accurate, but degenerate molecular representations. This is one of the fundamental peculiarities of chemical information - and the focus of much research activity over the last sixty or so years.

Quick - name your favorite tool for thinking and talking about chemistry. Many of them have become so refined and integral to the practice of chemistry that they no longer seem like mere tools. The atomic model, the periodic table, octet theory, and electronegativity all fall into this category. So do chemical structure diagrams. Two-dimensional chemical structure diagrams are a language with both grammar and aesthetics.

A recent article discussed the renaissance of the command line. Particularly on the Web, command line interfaces have become so advanced, that most of us don’t even realize we’re using them. Consider the Google search box, which is nothing more than one of the most powerful command line interfaces ever developed. A service called YubNub takes this idea one step further. YubNub is a meta command line interface for the Web.

It’s refreshing to see Nature Methods publicly acknowledge the importance of software availability in the sciences. On the other hand, the editorial still leaves wriggle room for an author determined to keep his or her source code private.

Like most scientists, I have a collection of hardcopy journal articles. After they sit on my desk for awhile, I sort them into folders. Each folder has a label such as “dihydroxylation”, “olefin metathesis”, or “InChI”. This system is nothing more than a small ontology. It does the job of building a top-level index of my papers, but it’s not nearly as effective as it could be. There are many problems with ontology.

Whether you’re in academics or industry, a big part of being a scientist is getting your work noticed by other scientists. In years past, scientists relied on subscription-only services such as Chemical Abstracts Service and Science Citation Index. But these services are starting to show their limitations, particularly with respect to being able to sell their products at an affordable price.

Rino is a toolkit for working with the IUPAC International Chemical Identifier (InChI) in Ruby. Because it’s based on the IUPAC/NIST InChI toolkit, Rino can be configured using a variety of useful options. This article summarizes those options and provides an illustrative example.

Startup School brings together hackers interested in building new companies. I’ll be headed to this year’s event, which takes place at Stanford University on March 24th. The speaker linup includes Paul Graham (Viaweb/Yahoo Store), Mitchell Kapor (Lotus), and Paul Bucheit (Gmail). If you’ll be in the neighborhood and would be interested in talking software, science, or startups, I’d like to hear from you.

The command line is alive and well. It’s simply become so sophisticated that most of us don’t realize we’re using it. Whether we’re entering a URL into a browser address bar, taking advantage of autocomplete to look up a co-worker’s name in an address book, or using Google to search the Web, the command line is hard at work. Most people wouldn’t want it any other way. To an end user, a command line is nothing more than a box to enter text.

If you had to design the perfect line notation for the Web, what would it look like? This is hardly an academic exercise given the central role played by line notations in information systems. For a variety of reasons, existing line notations may not be the right match for the Web. This article explores this question and outlines the main qualities needed by a Web-friendly line notation.

Recently, a question was raised on the Yahoo cheminf group list regarding the conversion of IUPAC names into molecular formulas. This can be done quickly with Ruby CDK, as this article will show. Prerequisites This tutorial requires Ruby CDK, which in turn requires Ruby Java Bridge (RJB). A recent Depth-First article described the minimal system configuration required to run RJB on Linux. Another article showed how to install RJB on Windows.