[Flash Content Scrubbed] I came across this intriguing presentation, apparently by Jonathan Alvarsson, while doing some research on Mychem. Although the context is not described in detail, the fundamental problems should be familiar to anyone who has built a chemical database. For those who may not know, Mychem is is an open source cheminformatics extension for MySQL based on Open Babel.

I’ll be giving a presentation at this March’s ACS Meeting titled “Chempedia: A social medium for chemical information” (ID 10054). Here’s the abstract I submitted: This talk will be part of a symposium titled “The Future of Scholarly Communication”. Judging from the schedule I received, the session looks to be a good one for anyone interested in the ways scientific communication may change in the years ahead.

Depth-First’s first article appeared on August 12, 2006. It used what was at the time an up-and-coming blogging engine called Typo. I chose Typo because it did most of what I needed and was written in Ruby on Rails, a Web development framework I wanted to learn more about. Bitrot I had no idea that 597 articles later, I’d still be using essentially the same software.

By way of Practical Fragments, I learned about The Warren L. DeLano Memorial Award for Computational Biosciences: I think this is a great idea and have already made a contribution. In whatever capacity you knew Warren or knew of him, I encourage you to contribute to this worthy cause.

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Over the last year or so, I’ve become increasingly convinced that implementing Behavior-Driven Development (BDD) practices can lead to significantly cleaner code and better design. And in the case of dynamic languages like Ruby, a good testing framework can be essential in enabling good maintenance practices. JavaScript, that language that for years was written off as a toy at best and an abomination at worst, is now much better understood.

I’ve always viewed the term ‘cheminformatics’ pretty broadly. To me, cheminfomatics is simply the application of information technology to solve problems in chemistry. Unsolved Problems in Cheminformatics For my money, some of the most important unsolved problems in cheminformatics today have to do with the many issues that come with the transition from a paper-centric scientific workflow to a Web-centric scientific workflow.

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Few non-technical topics lead to more heated debate in the field of scientific databases than terms of data reuse. Chempedia, the free chemical substance registry, aims to be different in every significant way from the services that came before it. One of the ways this can be seen is in the terms of use for its data downloads. There are really two bits of news here. The first is that you can now download the Chempedia Registry at no cost.

Bonnie Swoger, Science and Technology Librarian at SUNY Geneseo asks a very interesting question on the CHMINF-L mailing list: For those not familiar with the term, “ILL” means “Inter Library Loan” - a method for a library to offer materials by borrowing them from other libraries. There are several services, commercial and free, that I could mention.

Like so many others, I was shocked to find out this week that Warren DeLano died. He was both an inspiration to me and a genuinely nice guy.