New blog URL

I am reorganizing my blogs, and will now take advantage of the labels concept of Blogger. The new URL is:

http://chem-bla-ics.blogspot.com/search/label/chemicalblogspace

MySQL database playing up

A quick note to confirm the problems with the MySQL database. I will look at it shortly, but do not have time today.

Chemical blogspace back online

The new server hosting the indexing scripts seems to have a more strict memory usage, and the code base really needs an overhaul. Practically, this meant that the indexing failed because of running out of memory, causing the system to not index at all anymore. I have done some clean up, and Cb is back online.

Update server of Chemical blogspace offline

Some of you noted and reported that Chemical blogspace has not seen any updates since March 4. I can confirm this problem, which is likely due to server movement on our ISP. My apologies for the inconvenience, and I hope to restore indexing on short notice, but given other priorities, I cannot give an ETA yet.

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!

Would you be annoyed to see some Google Ads?

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

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

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

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

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..

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

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

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?

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

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.

New Blogs #8

It has been a bit quite with new blogs items during the summer, but 15 new blogs have been added since New Blogs #7. These are the new blogs that entered Chemical blogspace in the last month:

• Drugs and Poisons (entry in Cb)
• Liberal Arts Chemistry (entry in Cb)
• Brandon's Super-Dynamic Blog of Things, and Stuff (entry in Cb)
• ConcreteChemViz (entry in Cb)
• Computational Organic Chemistry (entry in Cb)
• Trapped in the USA (entry in Cb)
• Staudinger's Semantic Molecules (entry in Cb)
• ChemRadio (entry in Cb)
• Dutch summer of code - jchempaint (entry in Cb)
• ACS Fall National Meeting in Boston (entry in Cb)
• Agile2Robust (entry in Cb)
• Chenomx Blog (entry in Cb)
• National Chemistry Week | October 21-27 | 2007 (entry in Cb)
• OPEN CHEMISTRY WEB (entry in Cb)
• Sigma-Aldrich's ChemBlogs (entry in Cb)
• University of Ottawa NMR Facility Blog (entry in Cb)

Quite a few temporary, thematic blogs this time; that's a new evolution of blogspace.

InChIKey now added to Chemical blogspace

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.

IUPAC/InChI joins the Microsoft BioIT Alliance

On the CHMINF-L mailing list it was reported that the IUPAC InChI/InChIKey project joins Microsoft BioIT Alliance. Quoting:

The establishment of the BioIT Alliance in April 2006 by Microsoft and leading organizations in the life science industries was very much a reflection of this scenario, and the Alliance has now been extended to include a major Scientific Union, the International Union of Pure and Applied Chemistry (IUPAC). The importance of IUPACs contribution to the enterprise lies primarily in the responsibility of this organization for establishing standards for transmitting chemical information.

I am political quite illiterate, and have no idea why the BioIT Alliance could not use InChI or InChIKey without this mashup. However, I am comforted in the knowledge that the IUPAC InChI/InChIKey project will make sure the Microsoft will not use the InChIKey as drug identifier, which would give very nice (but letal) Millenium-bug like situations when that unlike key clash was found ;)

10.000 chemistry blog posts!

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

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.