I’ve mentioned Geoff Hutchison and Open Babel here before in the context of the Blue Obelisk awards. Open Babel is an Open Source “universal adapter” (see below). So it’s nice to report his announcement of 5 Years of Open Babel from the mailing list. To quote:
I’d like to take the opportunity to outline a bit of what’s happening with Open Babel right now and what 2007 might bring. Last year, we released version 2.0, representing a full stable release. Since then, we’ve released two updates to fix bugs, thanks in part to many user reports and contributions. There are contributed binary copies for Windows, Mac OS X, and a range of Linux distributions.
So what is Open Babel. Basically it’s one of those universal adapters such as you get in airports.
(Thanks to Wikipedia – it’s so liberating to be able to paste pictures without worrying about copyright). This adapter can take 1 input (US) and transform to 2 different outputs (UK and European). Note that this transforms the mechanical format, not the voltage. (it’s a bit similar to transforming the syntax, but not the semantics). There are smarter adapters – some can manage 4 inputs and 4 outputs. But they feel as if they may fall to bits any time.
Open Babel is a lot more powerful than that! It can manage 70 formats. And also carry out some semantic conversion. It’s not a Swiss army knife – CDK and JOELib are more like that. It does a single job – syntactic and semantic conversion – and it does it through Open voluntary labour.
It is critical to highlight how important Open Babel and other Blue Obelisk activities are to the pharma industry. I’ve highlighted this before. I expect that Open Babel is used by every pharma company in the world. I estimate that in direct costs, staff etc. the pharma industry spends several billion (that’s a US billion = 10^9) USD per year on chemical informatics of some sort. (For example we can guess the amount spent on CAS, Beilstein, and chemoinformatics software). None of this goes on Open Babel.
That’s not quite true. Last year we had support for a summer student from Merck (Nick England) who added some exciting routines to Open Babel. Note directly costed – let’s say ca. 5000 USD. So thank you Merck. And also thanks to MDL for a summer student to write a CML Reader in Java.
But that’s about it. In IT there is a huge industry investment (direct and implied) in things like Apache, Eclipse, etc. But in chemistry nothing. It’s pure free-riding by the pharma industry.
Now there is no moral argument here. We write these systems for a variety of motivations and they are fulfilling (though non-hackers have NO IDEA how much effort actually goes in.) NO IDEA. I have spent the weekend trying to refactor my molecule builder, and the gear wheels are spread out across the floor. Nothing is working. I promised my colleagues it would be ready for tomorrow. We’ll see. This post is a welcome relief.
So, dear pharma industry, if you read this – think about what you owe Geoff and the rest of us. It doesn’t just happen. It isn’t easy. The refactoring is desperate. We know you are shy – people in pharma don’t like to come out into the daylight so if you mail me I’ll keep it confidential. Or you can post an anonymous comment to the blog. I will have no idea who your are. At the very least add a post that says something like “Thank you Geoff from an anonymous person in pharma who has found Open Babel useful”. That sort of message is highly motivational.