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I've already gotten the "valid SMILES" issue off my chest, but there's something else that's been bugging me about deep learning papers in chemistry, and that's the use of canonical SMILES for training. Why would you use canonical SMILES? And if you did, wouldn't...
Just back from the recent ICCS in Noordwijkerhout, the Netherlands. I really enjoyed it although, as you can see from the picture, it was hard work at times.Here are my notes on the scientific program, which I have just extracted from Twitter. A big thank-you...
I'm a big fan of genetic algorithms. I used one back in the day for inverse design of molecular wires. They are deceptively simple, so much so that when you see one in action, churning out molecules that seem to magically improve generation on generation, it's...

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In an earlier post, I showed the accesses in the first month for the Blue Obelisk and Open Babel papers from late last year. I should have stopped there. Instead I decided to see how the recent Avogadro paper compared (Update 15/09/12: thanks to Geoff for filling...
I've already mentioned using Open Babel for depicting with SVG. That's a handy way to view a large set of molecules; you can zoom in and out and so forth. Let's look at some more of the features, as I've just been adding them to PNG depiction from SVG. Let's...
The Blue Obelisk group was established at the Spring ACS Meeting in 2005. Following on from the presentation/poster I gave at PMR's Symposium in January, I put together an overview of the activities of the group over the past 5 years with help from Rajarshi...

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In January of last year I was invited to attend the Semantic Physical Science Workshop in Cambridge, England. That was a great meeting where I met like-minded scientists and developers working on adding semantic structure to data in the physical sciences. Peter...
I’ve been doing a little work to update iBabel, I’ve updated all the tools developed by Silicos-it to use the new names and options.The SVG support in Openbabel has undergone significant improvements due to the brilliant efforts of Noel O’Boyle...
I guess reader of my blog already heard about it via other channels (e.g. via Noel's blog post), but our second Blue Obelisk paper is out. In the past five-ish years since Peter instantiated this initiative, it has created a solid set of shoulder on which to...