The previous New Blogs was not the regular month ago, but will be on holiday for the next two weeks, and there have been nine new blogs anyway:
After having solved a performance issue (caused by NULL columns), it is time for the fifth New Blogs issue. There are quite a few new blogs online in Chemical blogspace:
The machine that is running the database behind the Chemical blogspace is having trouble keeping alive. This is happening since the (scheduled) power outage of this weekend. Now, since the CUBIC has shut down as organization, my postdoc contract has ended too. As a consequence, I will not have frequent access to the machine, and remote SSH access is having hickups too. So far, a (former) collegue (Miguel) is helping me out, by rebooting every now and then, but I will work on a more permanent solution.
The best solution would be to get some permanent hosting somewhere, but without a university position where the machine could run, that is not cheap. Not too expansive either, but for a hobby... In the short term, I am considering moving the database to frontend machine, which has somewhat higher load, but is more stable too.
To be continued...
Already the fourth in the series (after #1, #2 and #3), and there are ten new blogs, summing up to 96 blogs now:
Lamentations on Chemistry is proposing to meet at the next ACS meeting in Chicago. I think this is an excellent idea, and hope to meet the other bloggers in chemical blogspace in person. Mitch replied that a similar thing was done at the previous ACS meeting.
Interestingly, the program of the meeting contains talks on blogging too:
CHED 25: "Teaching organic chemistry with blogs and wikis" Jean-Claude Bradley
... The evolution in the use of blogs and wikis in the teaching of undergraduate organic chemistry classes will be described, both as convenient tools to deliver course material and as platforms for student assignments. ...
CHED 21: "Blogging the culture of chemistry" Michelle M. Francl
... The Culture of Chemistry blog explores the relationship between chemistry, chemists and everything else. The connections between science content blogs and science culture blogs will be explored using the Culture of Chemistry as a jumping off point. ...
What about Monday or Wednesday afternoon?
I noticed last Wednesday that not all blog items are reaching the webpage... there are found and stored in the database, but then nothings happens... But I have not had time to further explore the cause, but will look at this tomorrow again. Sorry for the inconvenience.
Update: I tracked down the problem to a RDF which was no longer a RDF feed, but now showed HTML content that the page was no longer found.
My Chem-bla-ics blog contains a couple of blog items about CMLRSS, that is RSS feeds enriched with Chemical Markup Language. Some time ago, I wrote a plugin for CMLRSS for Bioclipse, as replacement for the Jmol and JChemPaint plugins shown in the CMLRSS article (DOI:10.1021/ci034244p).
Now, since I was looking at some bug reports to fix for the upcoming Bioclipse 1.0.1 release, I discovered that the plugin did not work well with Atom 1.0 feeds from blogger.com. Because Chemical blogspace uses Atom 1.0 too, I wanted to extend the feed with latest molecules with CML content; that is, to make it a nice CMLRSS feed.
Molecules in Chemical blogspace
I mentioned the InChI extension of Chemical blogspace before, and worked a bit more on it today. For example, I only today discovered that the 'pagination' was not working. And, for some days, I wanted the Molecules page to show all molecules being discussed, not only those that are known in PubChem.
Finally, I fixed the sorting, so that the molecules are now sorted based on the post date of the blog item that cites the molecule. It now looks like this (note the molecule count, and that the second InChI does not have an image):
The CMLRSS feed of Chemical blogspace
The next step was to actually include CML in this feed. The CML is created with OpenBabel from a MDL molfile downloaded from PubChem. BTW, this CML can be accessed from the Molecules page too, as can be seen in the above screenshot.
After some tweaking of the Atom feed of Chemical blogspace, and having Bioclipse work with URLConnections for web servers that do not return a Content-Length: field, this was the result:
Ten months ago I wrote about Hacking InChI support into postgenomic.com. Since then, the PostGenomic.com 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:
The software that runs the Chemical blogspace website is mostly developed by Euan, now working at Nature; it is the PostGenomic.com 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="http://wiki.cubic.uni-koeln.de/cb/widget.php?base_url=http://chem-bla-ics.blogspot.com" type="text/javascript"></script>
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:
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.
