The Blue Obelisk

I’ve promised to write about the Blue Obelisk and I’ve only got a short time before cycling home but at least I need to point to this before the ACS meeting.
Chemoinformatics and much chemical computation is seriously broken. The formats are 30 years old, the producers compete against each other, there are no validated data resources, programs and no communal agreed knowledge. Each producer sees themselves at the centre of the universe and caters only for their own requirements, leading to a forest of “stovepipes” in the antipattern jargon. There is no sign of positive reaction to the developments on the web. Neighbouring disciplines such as bioinformatics sigh meaningfully and then go ahead and create the Open chemical resources they need. More of this later…
Chemical software used to be free. It wasn’t interoperable, but that is because machines weren’t. Even if you used a singel language (FORTRAN) there was a lot of work to transport it. A fine organisation called QCPE (Quantum Chemical Program Exchange) would sell you a distribution for the cost of the mag tape. That’s all changed. First the computational chemistry codes (quantum mechanical), then the chemoinformatics and moelcular graphics ones were bought up by warring software companies in the 1908s. I was on the custome side, in pharma, and I’ll write more later. But everything became closed. One company threatened to sue customers if they revealed its file format…
This mess persists. But about 10 years ago a number of small initiatives took place to create Open alternatives – a real labour of love because theye were generally not innovating, but playing catchup. They weren’t taken seriously. For the most part they still aren’t. But it’s changing. There is now a critical mass of developers in mainstream chemoinformatics – not enormous, but sufficient to create a usable, useful system. That is growing rapdily. I guess there is over 1 million lines of Java code, and the same in C++. Yes, we have to duplicate codes for platform reasons, but it’s a good things to have a few alternatives.
We discover each other by cyber-methods – mailing lists, IRCs, etc. The best known of the IRCs is freenode cdk. So people become cyberfriends. Before the ACS meeting in san Diego 2 years ago we decided to meet in Horton Plaza – by the Blue Obelisk. Amusingly there are two so we nearly didn’t manage it. But we did, and the name stuck. I wrote a short summary of our communal aims and aspirations and it’s taken off from there. We’re meeting again in San Francisco next week.
The Blue Obelisk now has its own mailing list and many members including me have blogs. You can find it all at:
There is also a planetblueobelisk which aggregates the feeds.
I’ll write more about individual components and people as I feel the opportunity.

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