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.
Getting Real is an approach to designing software that emphasizes minimalism, simplicity, and agility. Many in the business view software development as something akin to an arms race in which the product with the most features wins. Getting Real takes the heretical perspective that less software, fewer features, and embracing constraints can work better for everyone. Over on Zusammen, a review of mylims.org has been posted.
One of the best ways to keep current with new developments in programming is to try new languages. Fortunately, there are so many to choose from that finding an unfamiliar language is less of a problem than finding one that’s interesting enough to make the effort worthwhile. In this new series of articles, we’ll explore many of the most interesting programming languages through the lense of cheminformatics.
As part of a new program to contain costs, the American Chemical Society (ACS) plans to phase out and suspend print publication of all journals within one year.
The last installment in this series discussed the limitations in today’s molecular languages and how FlexMol is designed to overcome them. Although these limitations are clearly present theoretically, what’s the practical effect likely to be? For the last two years, a series of articles highlighting specific examples from the current chemical literature have appeared here.
Over at Zusammen, the first five installments in a sixty-four part series on free chemistry databases and Web services have been posted: PubChem Sigma-Aldrich Reaction Search Heterocycles Web Edition Electronic Encyclopedia of Reagents for Organic Synthesis CrystalEye Keep those suggestions for new sites coming in!
This second paper on the subject of power laws and synthetic organic chemistry (previous paper) is chock full of interesting and potentially useful observations on the principles behind the art, science, and business of synthetic organic chemistry. Whether you’re a chemical supplier looking to optimize return on investment or an assistant professor struggling to do ‘relevant’ research, this article is a must-read.
Here’s a simple question: what’s the best way to draw ferrocene? This question was posed in a recent article on Metallome. It turns out there are some differences of opinion. But this problem isn’t limited to ‘drawing’ ferrocene - it extends to storing, transmitting, and manipulating representations of ferrocene with computers. And it isn’t simply limited to ferrocene and multicentered bonding - it extends to stereochemistry as well.
A recent issue of Wired is running a story about a Chemical Abstracts Service (CAS) study on the distribution of scaffold frequencies in the CAS Registry database. Cheminformatics doesn’t often make it into the popular press (or any other kind of press for that matter), so the Wired article is remarkable for that aspect alone.
