Saturday, December 30, 2006

Hacking InChI support into Cb

Ten months ago I wrote about Hacking InChI support into Since then, the software has seen a major update, which I recently followed. This means, that Chemical blogspace is now aggregating the compounds you blog about. That is, if you use the proper markup. At this moment, it only supports InChI and SMILES, as I have no means to deduce the molecular structure from a CAS registry number, and I have not integrated OPSIN yet.

Just to give the proper markup to trigger aggregation from your blog:

  • for SMILES: <span xmlns:chem="" class="chem:smiles">CCO</span>
  • for InChI: <span xmlns:chem="" class="chem:inchi">InChI=1/CH4/h1H4</span>

Here's the screenshot:

Note the PubChem and Google links created with a GreaseMonkey script I wrote.

Some future plans (other ideas are very much appreciated):
  • OPSIN support for <span class="chem:compound">benzene</span>
  • 2D diagrams on Cb
  • Some details on the compound, maybe URLs?
  • once the corpus is large enough, provide to PubChem
  • extract more chemistry from blogs

Friday, December 29, 2006

Popular Posts - Powered by Chemical blogspace

The software that runs the Chemical blogspace website is mostly developed by Euan, now working at Nature; it is the software, though generally a slightly older version. Because it is the same software, it has the almost same functionality.

And, I just figured out how to get the 'Popular Posts' widget working, as you can see on the left of this window (well, not in planet aggregators...), and in the below screenshot:

You can add this to your personal blog by adding this bit of code:

<script src="" type="text/javascript"></script>

where you, obviously, have to change the base_url given as parameter in the URL.

Stew, cheers for your excellent (opensource) software!

New Blogs #1

I can only agree ChemBark with his The Rise of the Chemical Blogosphere. Cb now has 72 blogs, of which the half is active on a weekly (at least) basis, with a growing number of blog items published per day. What ChemBark does not describe, is the huge amount of chemical literature being discussed by these 72 blogs; at the time of writing 300 articles are cited.

In the past days I have added four news blogs:

Friday, December 22, 2006

Updated Chemical Blogspace Layout and Software

As posted in my other blog, I can announce the updated Chemical blogspace website: "Last night I upgraded the software behind Chemical blogspace, to the version online on Google Code, though I needed the help from Eaun to get paper titles correctly picked up for ACS journals. The number of working blogs is a bit down and now at 68, with an average number of 30 active blogs posting more than 100 blog items each day (see Zeitgeist)."

See this item for all the links and the screenshot.