New Blogs #12

A bit more than four hands full of new blogs in the four months since New Blogs #11. Importantly, I have disabled the Accelrys blog in favor if the blogs of its individual contributors, Dana, George, Gerhard, Max, Nancy and Shikna. This is not to boost the number of blogs, but merely reflects that Cb focuses on personal (accountable) opinions and not corporate blog (which is often polluted with to much advertisement).

• Post Tenebras Lux (entry in Cb)
• OpenTox Blog (entry in Cb)
• Chemie-Information-Computer (entry in Cb)
• Dana Honeycutt, Ph.D. (entry in Cb)
• George Fitzgerald, PhD (entry in Cb)
• Gerhard Goldbeck-Wood, PhD (entry in Cb)
• Max Petersen, Ph.D. (entry in Cb)
• Nancy Miller Latimer, M.S. (entry in Cb)
• Shikha Varma O’Brien (entry in Cb)
• Mat Todd's Organic Chemistry Blog (entry in Cb)
• Chemiotics II (entry in Cb)
• Semantic Science (entry in Cb)
• All Things Metathesis (entry in Cb)
• Blog of V.Ganesh (entry in Cb)
• Cheminformatics Footprints (entry in Cb)
• Beautiful Photochemistry (entry in Cb)
• Naturalproductman's Blog (entry in Cb)
• Chemical Crystallinity (entry in Cb)
• Chiral Jones (entry in Cb)
• Experimental Error (entry in Cb)
• Mad Chemist Chick (entry in Cb)
• Syntheticnature (entry in Cb)

Happy reading!

More SQL trouble #2

Like in August, there is SQL trouble again. Did not have time to study the problem earlier this week, but on it right now. These SQL warnings are typically caused by broken RSS/Atom input, and often a clean up from the list of active blogs solves the problem. (I'll soon blog the next in the series New Blogs, as there have been quite a few new blogs. But hey, it's been 8 months since the last in the series...

However, there was a considerable loss of active blogs today (11)... At the moment I do not know what happened yet, but www.chemblogs.org is down... Did the service stop? Or is it just a temporary problem? I hope this is not the end of the Rise of Chemical blogspace

Clean up of RSS feeds

The number of registered RSS feeds are slightly below 150 chemistry oriented blogs; a number of them have ceased to exist, or moved to a different host, or simply changed URL. I just spent an hour or so, debugging these changes, as the Cb software does not really report that. But things are now updated again.

The rise of Chemical blogspace

The Chem Blog wrote about WTF is up with the Science blogosphere?, discussing a podcast on the chemical blogosphere, and wondering why it is larger than that of other natural science fields and mathematics. It is surprising indeed, because chemists generally are very conservative when it comes to anything to do with a monitor, mouse and keyboard. The argument put forward in the podcast is that there are a few strong voices amongst our blogs.

I am hoping the Chemical blogspace helps a bit too here. With about 40 unique users a day it is somewhat lower than it has been before the move to the new server, which was around 60 visitors each day, but I am sure this will recover.

The number of chemistry related blogs is rather large indeed, and the Cb counter is at over 136 now. Not every blog is equally active, but both the absolute number of entries and the number of active blogs per week are continuously increasing:


Interestingly, the blog had a very nice plot of the blogosphere interconnectivity. It is good practice to link to many other blogs and resources in ones entries, to keep discussions going, provide further information etc. Like Peter I was hoping that the plot would refer the Chemical blogspace, but it does not. This interconnectivity information is available from the Cb database, and I will try to create such a plot.

Updated CMLRSS feed

After some questions from Jean-Claude, I worked a bit on the CMLRSS feed. It now links to a page with blog items for that specific molecule. When doing that, I also noted that it was not listing the right molecules, so fixed that too; it now again shows the molecules most recently blogged about.

Red/Yellow, FDA alerts and other properties

Yvonne Martin recently wrote about, in her experience, what works and what does not work in chemoinformatics/computational chemistry (DOI:10.1002/qsar.200610102). She based her conclusions on the 17 month usage of services provided via webpages at Abbott. In that period, almost 3 million (unique?) molecules were processed, for which the following properties were requested most, among a few others:

• red/yellow alerts
• FDA mutagenicity alerts
• logP
• Rule-of-Five
• pKa
• total polar surface area
• solubility

Some of these can be calculated easily, and I tend towards adding those to the Molecules section of Chemical blogspace. The red/yellow and FDA mutagenicity alerts require me to define a list of substructures, and suggestions are most welcome.

Martin discusses the limited accuracy of the computational calculation of LogP, pKa and other properties, but concludes that they are nevertheless used in deciding which compounds to synthesize.

Organic Chemists?

Now, these properties are mostly pharma oriented, and, therefore, I would like the organic chemists on our blogspace what properties you would like to see added.

New Blogs #2

Since New Blogs #1, I have added these new blogs:

• The Chemical blogspace Blog (entry in Cb, yes, this blog)
• Chemical Forums: Chemistry Forum, Chemistry Question, Chemistry Help (entry in Cb)
• www.somewhereville.com (entry in Cb)
• the power of goo (entry in Cb)