New Blogs #12

Wednesday, November 25, 2009

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!

Would you be annoyed to see some Google Ads?

Tuesday, November 10, 2009

Would you object to seeing Google Adsense ads on the Cb website? The money it would bring up would be donated to a charity involved in promoting Open Science. Please let us know, either as comment on this blog item or by email.

Looking forward to hearing from you!

New Blogs #11

Friday, July 31, 2009

Not that the last two weeks has seen a boost on blog submissions to Chemical blogspace; just that I was not really finished with New Blogs #10.

• The Realm of Organic Synthesis (entry in Cb)
• Carbon Chemistry (entry in Cb)
• OChemOnline (entry in Cb)
• polymer processing (entry in Cb)
• Metallome (entry in Cb)
• BKBlog (entry in Cb)
• Sam's notes (entry in Cb)
• Zusammen (entry in Cb)
• Kashthealien's Blog (entry in Cb)
• Chemjobber (entry in Cb)
• Henry Rzepa (entry in Cb)
• ChemCafé (entry in Cb)
• Phosphorus carbide (entry in Cb)
• Molecular Modeling Basics (entry in Cb)
• /chemical/structure Blog (entry in Cb)
• Indiana University Cheminformatics News (entry in Cb)
• Accelrys | Blog (entry in Cb)

Happy reading!

New Blogs #10

Thursday, July 23, 2009

Many new blogs have appeared in Chemical blogspace since New Blogs #9. I should really make these overviews more often (I left out the new blogs which have not blogged in 2009 yet):

• Graphene Literature Reviews (entry in Cb)
• RajcaLab Weblog (entry in Cb)
• Making Graphite Work (entry in Cb)
• infiniflux! (entry in Cb)
• PMGB (entry in Cb)
• The road less travelled (entry in Cb)
• PaulingBlog (entry in Cb)
• InkSpot. Science. On Demand (entry in Cb)
• kilomentor (entry in Cb)
• Chemistry in silico (entry in Cb)
• So much to do, so little time (entry in Cb)
• Der Molekülblog (entry in Cb)
• Selenocisteïna (entry in Cb)
• ChEMBL (entry in Cb)
• A Chemistry Question, Daily (entry in Cb)
• Macromolecular Modeling Blog (entry in Cb)
• Practical Fragments (entry in Cb)
• Bridgehead Carbons (entry in Cb)

Cb is back in business

Sunday, December 28, 2008

Two weeks ago, I looked into why Cb was failing once more, as Cb was giving MySQL warnings, and the after that I cleaned up the list of active blogs. Several people reported that, for example, the Blue Obelisk RSS feed was down. Today, I found the cause of the lack of updates: the tags table had grown too much in size, and the Postgenomic.com software's SQL queries are not really optimised... So, our host (Dreamhost) renamed the table to fix the massive load on the MySQL server, causing the MySQL warnings, but also the lack of updates. I emptied the tags table, as the tags are not really crucial anyway, making the website show up nicely again, and hopefully making the update script not fail any more, either...

More SQL trouble #2

Friday, December 12, 2008

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

More SQL trouble..

Saturday, August 30, 2008

I'm not happy to report this, but we got another bit of SQL trouble... we had this a few weeks back too, but it solved itself then... not sure about now :(



I hope to get this solved shortly...

New Blogs #9

Friday, April 25, 2008

Has it already been 6 months since New Blogs #8?!? Time flies... 22 new blogs since then:

• Water in Biology (entry in Cb)
• NEBIOQ-UP (entry in Cb)
• Benoît Jacob (entry in Cb)
• MacinChemBlog (entry in Cb)
• NMR Analysis, Processing and Prediction (entry in Cb)
• Drug Discovery with Quantum Pharmaceuticals (entry in Cb)
• Homebrew and Chemistry (entry in Cb)
• Periodic Tabloid (entry in Cb)
• Tim Vandermeersch's chemical blog (entry in Cb)
• CSEARCH NMR-Database (entry in Cb)
• 1CellPK (entry in Cb)
• SimBioSys Blog (entry in Cb)
• Swain Library News (entry in Cb)
• some kind of blog (entry in Cb)
• A Chemical Sabbatical (entry in Cb)
• Lightnir's blog (entry in Cb)
• C&ENtral Science (entry in Cb)
• Daneel Ariantho's laboratory » Chemistry (entry in Cb)
• practical transmutations (entry in Cb)
• The Eccentric Chemist (entry in Cb)
• Chempedia.net: The Daily Molecule (entry in Cb)
• Philosophy to Chemistry to Elucidation (entry in Cb)

.

HELP! MySQL optimizations needed

Tuesday, January 15, 2008

Chemical blogspace has been closed down; that is, they seemed to have locked down access to the database. As you might have noticed, I have taken steps to reduce the problems with the database, but these were mere temporary fix ups. The real problem is the database design and, in particular, the SQL queries. These are too slow. Euan, the original author of the software, has already been looking into the problem he himself is encountering too, for postgenomic.com it is. But, I do not have time right now to fix those slow SQL queries :(

Therefore:

HELP!

The source is available and email me for a dump of the database.

60 day old blog posts still important?

Monday, November 26, 2007

Last week some of you noted that the Chemical blogspace was no longer nicely updated every X hours. The code is not optimized for performance and the number of old posts (about 10k in 6 months!) made the update_posts.pl break down. Or really, the DreamHost service killed the process after taking too long. Fair; it's the online way to keep the systems from not breaking down over one website. I already had split up processing the first 75 blogs and the rest into two separate jobs.

So, now I made a more radical change, and deleted old posts older than 60 days. That's ancient history, not?

Blog Awards with two Cb candidates

Wednesday, November 7, 2007

There is a weblog 2007 award voting thingy, where two blogs participate in the Best Science Blog section which are aggregated on Chemical blogspace:

• In the Pipeline
• Sciencebase

The can use some help:


You have to hurry, the deadline is the 8th.

InChIKey now added to Chemical blogspace

Monday, September 24, 2007

Using the InChI webservices as introduced by Anthony earlier, I added InChIKeys to the Chemical blogspace Molecules section:

BTW, the molecules were picked up because the (1-3)-beta-D-glucan - How moulds can make you wheeze and sneeze and What I'm up against... items linked to the glucose entry in wikipedia.

10.000 chemistry blog posts!

Wednesday, September 19, 2007

Chemical blogspace is about to hit the 10.000 blog post since the start less than a year ago! Cheers to all bloggers!

Clean up of RSS feeds

Saturday, August 25, 2007

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.

cb.openmolecules.net DNS problem?

Friday, August 17, 2007

In an attempt to get rdf.openmolecules.net online, it seems that the DNS system got confused; At least, the cb.openmolecules.net server is not reachable... more on this soon.

Update: OK, the DNS seems to be updated, maybe fixed itself, or some propagation problem. Anyway, now the MySQL server has gone down. So, still no running Cb :(

RDF in Chemical blogspace

Thursday, August 9, 2007

I have been playing with RDF-ing molecular space a bit, and results are getting slowly in shape:



This screenshot shows the HTML created for this RDF file on the fly by the web browser. The current version extracts information from Chemical blogspace and ChEBI (not much yet, though :).

The molecule pages in Chemical blogspace link to this RDF, and that's really what I wanted to show right now:



Why I do this? Among others, give me all boiling points for some compound with one (SPARQL) query, instead of having to browse several web resources manually. Oh, BTW, the HTML view of the RDF document uses chemical RDFa.

Userscripts you forget about...

Tuesday, July 17, 2007

Peter writes about a Greasemonky userscript pop up:

What are the Pg and Cb all over the TOC. When you bring up the page they aren’t there! What’s happened? Well the chemical blogosphere has posted about several articles here and mentioned their DOIs. The Blue Obelisk has developed a Gresemonkey script (which is a Firefox plugin) which reads the TOC and sees if any DOIs have been mentioned in the Chemical Blogosphere. And, in this case, three articles have been.

This is the screenshot he made:

For the obligatory statistics: Cb now discusses 1184 articles. Because I have trouble accessing the Postgenomic website, I cannot give that number :(

The rise of Chemical blogspace

Wednesday, July 4, 2007

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.

RDFa Operator in action on Cb

Wednesday, June 27, 2007

I reported yesterday on my efforts (and Mike's help) to get RDFa for chemistry going. I did not have time to add the new HTML code to Cb, but have done so now:

Read my Chem-bla-ics blog for the details.