tag:blogger.com,1999:blog-50632527233458763532024-03-14T01:25:36.535-07:00The Chemical blogspace BlogThis blog is used to announce changes in the Chemical Blogspace aggregator.Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.comBlogger50125tag:blogger.com,1999:blog-5063252723345876353.post-14257919547525133752010-07-14T04:03:00.000-07:002010-07-14T04:03:22.776-07:00New blog URLI am reorganizing my blogs, and will now take advantage of the <a href="http://www.google.com/support/blogger/bin/topic.py?hl=en&topic=12459">labels concept</a> of <a href="http://www.blogger.com">Blogger</a>. The new URL is:<br />
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<a href="http://chem-bla-ics.blogspot.com/search/label/chemicalblogspace">http://chem-bla-ics.blogspot.com/search/label/chemicalblogspace</a>Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com0tag:blogger.com,1999:blog-5063252723345876353.post-46338043375452938412010-04-11T10:01:00.001-07:002010-04-11T10:01:39.188-07:00MySQL database playing upA quick note to confirm the problems with the MySQL database. I will look at it shortly, but do not have time today.Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com0tag:blogger.com,1999:blog-5063252723345876353.post-56441872152599446162010-03-17T00:42:00.000-07:002010-03-17T00:42:02.065-07:00Chemical blogspace back onlineThe 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 <a href="http://cb.openmolecules.net">Cb</a> is back online.Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com1tag:blogger.com,1999:blog-5063252723345876353.post-36065915641020957072010-03-14T04:17:00.000-07:002010-03-14T04:17:32.700-07:00Update server of Chemical blogspace offlineSome of you noted and reported that <a href="http://cb.openmolecules.net">Chemical blogspace</a> 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.Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com0tag:blogger.com,1999:blog-5063252723345876353.post-60473182598777915782009-11-25T03:44:00.000-08:002009-11-25T03:44:52.582-08:00New Blogs #12A bit more than four hands full of new blogs in the four months since <a href="http://chemicalblogspace.blogspot.com/2009/07/new-blogs-11.html">New Blogs #11</a>. 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 <a href="http://cb.openmolecules.net">Cb</a> focuses on personal (accountable) opinions and not corporate blog (which is often polluted with to much advertisement). <ul><li><a href="http://calvinus.wordpress.com/">Post Tenebras Lux</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=219">entry in Cb</a>)</li><li><a href="http://www.opentox.org/">OpenTox Blog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=220">entry in Cb</a>)</li><li><a href="http://cic-fachgruppe.blogspot.com/">Chemie-Information-Computer</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=221">entry in Cb</a>)</li><li><a href="http://blog.accelrys.com/author/dana/">Dana Honeycutt, Ph.D.</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=222">entry in Cb</a>)</li><li><a href="http://blog.accelrys.com/author/george/">George Fitzgerald, PhD</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=223">entry in Cb</a>)</li><li><a href="http://blog.accelrys.com/author/gerhard/">Gerhard Goldbeck-Wood, PhD</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=224">entry in Cb</a>)</li><li><a href="http://blog.accelrys.com/author/mpetersen/">Max Petersen, Ph.D.</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=225">entry in Cb</a>)</li><li><a href="http://blog.accelrys.com/author/nancy/">Nancy Miller Latimer, M.S.</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=226">entry in Cb</a>)</li><li><a href="http://blog.accelrys.com/author/shikna/">Shikha Varma O’Brien</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=227">entry in Cb</a>)</li><li><a href="http://intermolecular.wordpress.com/">Mat Todd's Organic Chemistry Blog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=228">entry in Cb</a>)</li><li><a href="http://luysii.wordpress.com/">Chemiotics II</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=229">entry in Cb</a>)</li><li><a href="http://semanticscience.wordpress.com/">Semantic Science</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=230">entry in Cb</a>)</li><li><a href="http://allthingsmetathesis.com/">All Things Metathesis</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=231">entry in Cb</a>)</li><li><a href="http://tovganesh.blogspot.com/">Blog of V.Ganesh</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=232">entry in Cb</a>)</li><li><a href="http://www.chemene.com:8080/Web/Blog.aspx">Cheminformatics Footprints</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=233">entry in Cb</a>)</li><li><a href="http://beautifulphotochemistry.wordpress.com/">Beautiful Photochemistry</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=234">entry in Cb</a>)</li><li><a href="http://naturalproductman.wordpress.com/">Naturalproductman's Blog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=235">entry in Cb</a>)</li><li><a href="http://chemicalcrystallinity.blogspot.com/">Chemical Crystallinity</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=236">entry in Cb</a>)</li><li><a href="http://chiraljones.wordpress.com/">Chiral Jones</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=237">entry in Cb</a>)</li><li><a href="http://fug-experimentalerror.blogspot.com/">Experimental Error</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=238">entry in Cb</a>)</li><li><a href="http://madchemistchick.blogspot.com/">Mad Chemist Chick</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=239">entry in Cb</a>)</li><li><a href="http://syntheticnature.wordpress.com/">Syntheticnature</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=240">entry in Cb</a>)</li></ul>Happy reading!Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com3tag:blogger.com,1999:blog-5063252723345876353.post-4788350849135651362009-11-10T08:52:00.000-08:002009-11-10T08:52:08.076-08:00Would you be annoyed to see some Google Ads?Would you object to seeing Google Adsense ads on the <a href="http://cb.openmolecules.net">Cb</a> 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.<br />
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Looking forward to hearing from you!Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com3tag:blogger.com,1999:blog-5063252723345876353.post-10443016257623819532009-07-31T03:08:00.001-07:002009-07-31T03:09:01.532-07:00New Blogs #11Not that the last two weeks has seen a boost on blog submissions to <a href="http://cb.openmolecules.net">Chemical blogspace</a>; just that I was not really finished with <a href="http://chem-bla-ics.blogspot.com/2009/07/new-blogs-10.html">New Blogs #10</a>. <ul><li><a href="http://therealmoforganicsynthesis.blogspot.com/">The Realm of Organic Synthesis</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=201">entry in Cb</a>)</li><li><a href="http://carbontube.blogspot.com/">Carbon Chemistry</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=202">entry in Cb</a>)</li><li><a href="http://ochemonline.wordpress.com/">OChemOnline</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=203">entry in Cb</a>)</li><li><a href="http://polymerprocessing.blogspot.com/">polymer processing</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=204">entry in Cb</a>)</li><li><a href="http://metallome.blogspot.com/">Metallome</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=205">entry in Cb</a>)</li><li><a href="http://notimetolouse.blogspot.com/">BKBlog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=206">entry in Cb</a>)</li><li><a href="http://sea36.blogspot.com/">Sam's notes</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=207">entry in Cb</a>)</li><li><a href="http://zusammen.metamolecular.com/posts">Zusammen</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=208">entry in Cb</a>)</li><li><a href="http://kashthealien.wordpress.com/">Kashthealien's Blog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=209">entry in Cb</a>)</li><li><a href="http://chemjobber.blogspot.com/">Chemjobber</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=210">entry in Cb</a>)</li><li><a href="http://www.ch.ic.ac.uk/rzepa/blog">Henry Rzepa</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=211">entry in Cb</a>)</li><li><a href="http://www.chemcafe.net/">ChemCafé</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=213">entry in Cb</a>)</li><li><a href="http://phoscarb.blogspot.com/">Phosphorus carbide</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=214">entry in Cb</a>)</li><li><a href="http://molecularmodelingbasics.blogspot.com/">Molecular Modeling Basics</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=215">entry in Cb</a>)</li><li><a href="http://cactus.nci.nih.gov/blog">/chemical/structure Blog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=216">entry in Cb</a>)</li><li><a href="http://cheminfonews.blogspot.com/">Indiana University Cheminformatics News</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=217">entry in Cb</a>)</li><li><a href="http://blog.accelrys.com/">Accelrys | Blog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=218">entry in Cb</a>)</li></ul> Happy reading!Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com1tag:blogger.com,1999:blog-5063252723345876353.post-83439193232710613922009-07-23T00:49:00.000-07:002009-07-23T01:17:31.842-07:00New Blogs #10Many new blogs have appeared in <a href="http://cb.openmolecules.net">Chemical blogspace</a> since <a href="http://chemicalblogspace.blogspot.com/2008/04/new-blogs-9.html">New Blogs #9</a>. I should really make these overviews more often (I left out the new blogs which have not blogged in 2009 yet):<ul><li><a href="http://graphenelitreviews.blogspot.com/">Graphene Literature Reviews</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=175">entry in Cb</a>)</li><li><a href="http://rajcalab.wordpress.com/">RajcaLab Weblog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=177">entry in Cb</a>)</li><li><a href="http://graphiteworks.wordpress.com/">Making Graphite Work</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=178">entry in Cb</a>)</li><li><a href="http://infiniflux.blogspot.com/">infiniflux!</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=179">entry in Cb</a>)</li><li><a href="http://pmgb.wordpress.com/">PMGB</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=180">entry in Cb</a>)</li><li><a href="http://altchemcareers.wordpress.com/">The road less travelled</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=182">entry in Cb</a>)</li><li><a href="http://paulingblog.wordpress.com/">PaulingBlog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=183">entry in Cb</a>)</li><li><a href="http://www.inkspotscience.com/blog">InkSpot. Science. On Demand</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=185">entry in Cb</a>)</li><li><a href="http://kilomentor.chemicalblogs.com/55_kilomentor">kilomentor</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=189">entry in Cb</a>)</li><li><a href="http://cheminsilico.blogspot.com/">Chemistry in silico</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=190">entry in Cb</a>)</li><li><a href="http://blog.rguha.net/">So much to do, so little time</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=192">entry in Cb</a>)</li><li><a href="http://www.robthejob.de/">Der Molekülblog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=193">entry in Cb</a>)</li><li><a href="http://www.selenocisteina.info/">Selenocisteïna</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=194">entry in Cb</a>)</li><li><a href="http://chembl.blogspot.com/">ChEMBL</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=195">entry in Cb</a>)</li><li><a href="http://dailychem.blogspot.com/">A Chemistry Question, Daily</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=196">entry in Cb</a>)</li><li><a href="http://rosettadesigngroup.com/blog">Macromolecular Modeling Blog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=197">entry in Cb</a>)</li><li><a href="http://practicalfragments.blogspot.com/">Practical Fragments</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=198">entry in Cb</a>)</li><li><a href="http://bridgeheadcarbons.blogspot.com/">Bridgehead Carbons</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=200">entry in Cb</a>)</li></ul>Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com0tag:blogger.com,1999:blog-5063252723345876353.post-17269657391787672372008-12-28T09:09:00.000-08:002008-12-28T09:15:14.336-08:00Cb is back in businessTwo weeks ago, I looked into why <a href="http://cb.openmolecules.net/">Cb</a> was failing once more, as <a href="http://chemicalblogspace.blogspot.com/2008/12/more-sql-trouble-2.html">Cb was giving MySQL warnings</a>, and the after that I cleaned up the list of active blogs. Several people reported that, for example, the <a href="http://cb.openmolecules.net/atom.php?category=Blue%20Obelisk&type=latest_posts">Blue Obelisk RSS</a> 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 (<a href="http://www.dreamhost.com/">Dreamhost</a>) 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...Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com1tag:blogger.com,1999:blog-5063252723345876353.post-58078715677209352682008-12-12T04:52:00.000-08:002008-12-12T04:59:30.992-08:00More SQL trouble #2<a href="http://chemicalblogspace.blogspot.com/2008/08/more-sql-trouble.html">Like in August</a>, 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 <a href="http://chemicalblogspace.blogspot.com/2008/04/new-blogs-9.html">series New Blogs</a>, as there have been quite a few new blogs. But hey, it's been 8 months since the last in the series...<br /><br />However, there was a considerable loss of active blogs today (11)... At the moment I do not know what happened yet, but <a href="http://www.chemblogs.org/">www.chemblogs.org</a> is down... Did the service stop? Or is it just a temporary problem? I hope this is not the end of the <a href="http://chemicalblogspace.blogspot.com/2007/07/rise-of-chemical-blogspace.html">Rise of Chemical blogspace</a>Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com0tag:blogger.com,1999:blog-5063252723345876353.post-61645549580193027702008-08-30T02:16:00.000-07:002008-08-30T02:20:08.421-07:00More 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 :(<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://2.bp.blogspot.com/_5vhaOf2_53I/SLkQnw_3M8I/AAAAAAAAAQE/VLHA7BE5E9A/s1600-h/sqlTrouble.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;" src="http://2.bp.blogspot.com/_5vhaOf2_53I/SLkQnw_3M8I/AAAAAAAAAQE/VLHA7BE5E9A/s400/sqlTrouble.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5240237916775986114" /></a><br /><br />I hope to get this solved shortly...Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com3tag:blogger.com,1999:blog-5063252723345876353.post-90100643639099799362008-04-25T23:32:00.000-07:002008-04-25T23:51:54.478-07:00New Blogs #9Has it already been 6 months since <a href="http://chemicalblogspace.blogspot.com/2007/10/new-blogs-8.html">New Blogs #8</a>?!? Time flies... 22 new blogs since then:<ul><li><a href="http://waterinbiology.blogspot.com/">Water in Biology</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=153">entry in Cb</a>)</li><li><a href="http://nebioq-up.blogspot.com/">NEBIOQ-UP</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=154">entry in Cb</a>)</li><li><a href="http://bjacob.livejournal.com/">Benoît Jacob</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=155">entry in Cb</a>)</li><li><a href="http://homepage.mac.com/swain/Macinchem/default.htm">MacinChemBlog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=156">entry in Cb</a>)</li><li><a href="http://nmr-analysis.blogspot.com/">NMR Analysis, Processing and Prediction</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=157">entry in Cb</a>)</li><li><a href="http://drugdiscoverywizzards.blogspot.com/">Drug Discovery with Quantum Pharmaceuticals</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=158">entry in Cb</a>)</li><li><a href="http://homebrewandchemistry.blogspot.com/">Homebrew and Chemistry</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=159">entry in Cb</a>)</li><li><a href="http://periodictabloid.chemheritage.org/">Periodic Tabloid</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=160">entry in Cb</a>)</li><li><a href="http://timvdm.blogspot.com/">Tim Vandermeersch's chemical blog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=161">entry in Cb</a>)</li><li><a href="http://csearch-nmr-data.blogspot.com/">CSEARCH NMR-Database</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=162">entry in Cb</a>)</li><li><a href="http://1cellpk.blogspot.com/">1CellPK</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=163">entry in Cb</a>)</li><li><a href="http://www.simbiosys.ca/blog">SimBioSys Blog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=164">entry in Cb</a>)</li><li><a href="http://www.stanford.edu/group/swain/cgi-bin/blog">Swain Library News</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=165">entry in Cb</a>)</li><li><a href="http://flo.nigsch.com/">some kind of blog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=166">entry in Cb</a>)</li><li><a href="http://chemicalsabbatical.blogspot.com/">A Chemical Sabbatical</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=167">entry in Cb</a>)</li><li><a href="http://lightnir.blogspot.com/search/label/myChemistry">Lightnir's blog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=168">entry in Cb</a>)</li><li><a href="http://cenblog.org/">C&ENtral Science</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=169">entry in Cb</a>)</li><li><a href="http://daneelariantho.wordpress.com/">Daneel Ariantho's laboratory » Chemistry</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=170">entry in Cb</a>)</li><li><a href="http://selenized.wordpress.com/">practical transmutations</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=171">entry in Cb</a>)</li><li><a href="http://theeccentricchemist.blogspot.com/">The Eccentric Chemist</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=172">entry in Cb</a>)</li><li><a href="http://chempedia.net/dailymolecule/feed.xml">Chempedia.net: The Daily Molecule</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=173">entry in Cb</a>)</li><li><a href="http://acdlabs.typepad.com/elucidation/">Philosophy to Chemistry to Elucidation</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=174">entry in Cb</a>)</li></ul>.Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com1tag:blogger.com,1999:blog-5063252723345876353.post-84502062653369528682008-01-15T23:02:00.000-08:002008-01-15T23:11:10.259-08:00HELP! MySQL optimizations needed<a href="http://cb.openmolecules.net/">Chemical blogspace</a> 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. <a href="http://www.ghastlyfop.com/blog/">Euan</a>, the original author of the software, has <a href="http://www.ghastlyfop.com/blog/2008/01/lamp-performance-for-dummies.html">already been looking into the problem</a> he himself is encountering too, for <a href="http://postgenomic.com/">postgenomic.com</a> it is. But, I do not have time right now to fix those slow SQL queries :(<br /><br />Therefore:<ul><b>HELP!</b></ul>The <a href="http://blueobelisk.svn.sourceforge.net/viewvc/blueobelisk/cb/trunk/">source is available</a> and email me for a dump of the database.Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com2tag:blogger.com,1999:blog-5063252723345876353.post-19003180406637957612007-11-26T03:02:00.000-08:002007-11-26T03:08:01.796-08:0060 day old blog posts still important?Last week some of you noted that the <a href="http://cb.openmolecules.net/">Chemical blogspace</a> 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 <a href="http://blueobelisk.svn.sourceforge.net/viewvc/blueobelisk/cb/trunk/update_posts.pl?view=log">update_posts.pl</a> 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.<br /><br />So, now I made a more radical change, and deleted old posts older than 60 days. That's ancient history, not?Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com9tag:blogger.com,1999:blog-5063252723345876353.post-34256249714803519752007-11-07T05:06:00.000-08:002007-11-07T05:11:59.259-08:00Blog Awards with two Cb candidatesThere is a <a href="http://2007.weblogawards.org/polls/best-science-blog-1.php">weblog 2007 award voting thingy</a>, where two blogs participate in the <i>Best Science Blog</i> section which are aggregated on <a href="http://cb.openmolecules.net/">Chemical blogspace</a>:<ul><li><a href="http://pipeline.corante.com/">In the Pipeline</a></li><li><a href="http://www.sciencebase.com/science-blog/">Sciencebase</a></li></ul>The can use some help:<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://4.bp.blogspot.com/_5vhaOf2_53I/RzG5BpYypwI/AAAAAAAAAJk/YlxebtEYbBQ/s1600-h/bestBlog.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;" src="http://4.bp.blogspot.com/_5vhaOf2_53I/RzG5BpYypwI/AAAAAAAAAJk/YlxebtEYbBQ/s400/bestBlog.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5130084888492549890" /></a><br />You have to hurry, the deadline is the 8th.Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com0tag:blogger.com,1999:blog-5063252723345876353.post-54719098037417270122007-10-21T22:46:00.000-07:002007-10-21T23:04:55.020-07:00New Blogs #8It has been a bit quite with new blogs items during the summer, but 15 new blogs have been added since <a href="http://chemicalblogspace.blogspot.com/2007/06/these-are-new-blogs-that-entered.html">New Blogs #7</a>. These are the new blogs that entered Chemical blogspace in the last month:<ul><li><a href="http://www.drugsandpoisons.com/">Drugs and Poisons</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=137">entry in Cb</a>)</li><li><a href="http://liberalchemistry.blogspot.com/">Liberal Arts Chemistry</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=138">entry in Cb</a>)</li><li><a href="http://5by5b.blogspot.com/">Brandon's Super-Dynamic Blog of Things, and Stuff</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=139">entry in Cb</a>)</li><li><a href="http://chemviz.blogspot.com/">ConcreteChemViz</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=140">entry in Cb</a>)</li><li><a href="http://hackberry.chem.trinity.edu/blog">Computational Organic Chemistry</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=141">entry in Cb</a>)</li><li><a href="http://boscoh.com/">Trapped in the USA</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=142">entry in Cb</a>)</li><li><a href="http://wwmm.ch.cam.ac.uk/blogs/adams">Staudinger's Semantic Molecules</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=143">entry in Cb</a>)</li><li><a href="http://chemradio.com/">ChemRadio</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=144">entry in Cb</a>)</li><li><a href="http://progz-jchem.blogspot.com/">Dutch summer of code - jchempaint</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=145">entry in Cb</a>)</li><li><a href="http://cenboston.wordpress.com/">ACS Fall National Meeting in Boston</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=146">entry in Cb</a>)</li><li><a href="http://agile2robust.com/tt/">Agile2Robust</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=147">entry in Cb</a>)</li><li><a href="http://blog.chenomx.com/">Chenomx Blog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=148">entry in Cb</a>)</li><li><a href="http://nationalchemistryweek2007.blogspot.com/">National Chemistry Week | October 21-27 | 2007</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=149">entry in Cb</a>)</li><li><a href="http://www.chemspider.com/open-chemistry-web">OPEN CHEMISTRY WEB</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=150">entry in Cb</a>)</li><li><a href="http://chemblogs.com/sial_blog/index.php?blog=2">Sigma-Aldrich's ChemBlogs</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=151">entry in Cb</a>)</li><li><a href="http://u-of-o-nmr-facility.blogspot.com/">University of Ottawa NMR Facility Blog</a> (<a href="http://cb.openmolecules.net/blog_search.php?blog_id=152">entry in Cb</a>)</li></ul><br />Quite a few temporary, thematic blogs this time; that's a new evolution of blogspace.Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com1tag:blogger.com,1999:blog-5063252723345876353.post-73962839266614747612007-09-24T04:02:00.000-07:002007-09-24T04:11:18.465-07:00InChIKey now added to Chemical blogspaceUsing the <a href="http://www.chemspider.com/inchi.asmx">InChI webservices</a> as <a href="http://www.chemspider.com/blog/?p=135">introduced by Anthony earlier</a>, I added InChIKeys to the <a href="http://cb.openmolecules.net/inchis.php">Chemical blogspace Molecules section</a>:<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://3.bp.blogspot.com/_5vhaOf2_53I/RveaarajYAI/AAAAAAAAAIE/FXQQNDoIQH4/s1600-h/inchikeyCb.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;" src="http://3.bp.blogspot.com/_5vhaOf2_53I/RveaarajYAI/AAAAAAAAAIE/FXQQNDoIQH4/s400/inchikeyCb.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5113725685023858690" /></a><br />BTW, the molecules were picked up because the <a href="http://www.drugsandpoisons.com/2007/09/1-3-beta-d-glucan-how-moulds-can-make.html">(1-3)-beta-D-glucan - How moulds can make you wheeze and sneeze</a> and <a href="http://wwmm.ch.cam.ac.uk/blogs/corbett/?p=32">What I'm up against...</a> items linked to the <a href="http://en.wikipedia.org/wiki/Glucose">glucose entry in wikipedia</a>.Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com0tag:blogger.com,1999:blog-5063252723345876353.post-75752171508707960142007-09-20T04:09:00.000-07:002007-09-20T04:16:21.112-07:00IUPAC/InChI joins the Microsoft BioIT AllianceOn the <a href="https://listserv.indiana.edu/cgi-bin/wa-iub.exe?A0=CHMINF-L">CHMINF-L mailing list</a> it was reported that the <i>IUPAC InChI/InChIKey project joins Microsoft BioIT Alliance</i>. Quoting:<ul><i>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></ul><br />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 <a href="http://chem-bla-ics.blogspot.com/2007/09/new-inchi-software-beta-license-issues.html">unlike key clash was found</a> ;)Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com0tag:blogger.com,1999:blog-5063252723345876353.post-65324720959121631022007-09-19T05:00:00.000-07:002007-09-19T05:06:04.130-07:0010.000 chemistry blog posts!<a href="http://cb.openmolecules.net/">Chemical blogspace</a> is about to hit <a href="http://cb.openmolecules.net/posts.php">the 10.000 blog post</a> since the start less than a year ago! Cheers to all bloggers!<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://2.bp.blogspot.com/_5vhaOf2_53I/RvEP_whjG-I/AAAAAAAAAHQ/YBeuDqmYLLg/s1600-h/chemblogspace4.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;" src="http://2.bp.blogspot.com/_5vhaOf2_53I/RvEP_whjG-I/AAAAAAAAAHQ/YBeuDqmYLLg/s320/chemblogspace4.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5111884640074013666" /></a>Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com0tag:blogger.com,1999:blog-5063252723345876353.post-69404542722436120962007-08-25T07:54:00.000-07:002007-08-25T07:56:41.876-07:00Clean up of RSS feedsThe 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.Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com0tag:blogger.com,1999:blog-5063252723345876353.post-6954857991567156862007-08-17T01:20:00.000-07:002007-08-17T08:50:47.267-07:00cb.openmolecules.net DNS problem?In an attempt to get <a href="http://cb.openmolecules.net/rdf/?InChI=1/CH4/h1H4">rdf.openmolecules.net</a> online, it seems that the DNS system got confused; At least, the <a href="http://cb.openmolecules.net">cb.openmolecules.net</a> server is not reachable... more on this soon.<br /><br /><b>Update:</b> 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 :(Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com2tag:blogger.com,1999:blog-5063252723345876353.post-58413274163802634862007-08-09T23:36:00.001-07:002007-08-09T23:50:20.380-07:00RDF in Chemical blogspaceI have been playing with <a href="http://chem-bla-ics.blogspot.com/2007/07/rdf-ing-molecular-space.html">RDF-ing molecular space</a> a bit, and results are getting slowly in shape:<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://3.bp.blogspot.com/_5vhaOf2_53I/RrwINL9A_GI/AAAAAAAAAFo/NKUq_1p3bTE/s1600-h/CbRDF1.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;" src="http://3.bp.blogspot.com/_5vhaOf2_53I/RrwINL9A_GI/AAAAAAAAAFo/NKUq_1p3bTE/s320/CbRDF1.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5096957900916587618" /></a><br /><br />This screenshot shows the HTML created for <a href="http://cb.openmolecules.net/rdf/?InChI=1/C6H8N2O2S/c7-5-1-3-6(4-2-5)11(8,9)10/h1-4H,7H2,(H2,8,9,10)/f/h8H2">this RDF file</a> on the fly by the web browser. The current version extracts information from Chemical blogspace and <a href="http://www.ebi.ac.uk/chebi/">ChEBI</a> (not much yet, though :).<br /><br />The <a href="http://cb.openmolecules.net/inchis.php">molecule pages</a> in Chemical blogspace link to this RDF, and that's really what I wanted to show right now:<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://4.bp.blogspot.com/_5vhaOf2_53I/RrwJKb9A_HI/AAAAAAAAAFw/a-2dJkixMF8/s1600-h/CbRDF.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;" src="http://4.bp.blogspot.com/_5vhaOf2_53I/RrwJKb9A_HI/AAAAAAAAAFw/a-2dJkixMF8/s320/CbRDF.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5096958953183575154" /></a><br /><br />Why I do this? Among others, give me all boiling points for some compound with one (SPARQL) query, instead of having to <a href="http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=459">browse several web resources manually</a>. Oh, BTW, the HTML view of the RDF document uses <a href="http://chem-bla-ics.blogspot.com/2007/06/chemical-rdfa-with-operator-in-firefox.html">chemical RDFa</a>.Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com0tag:blogger.com,1999:blog-5063252723345876353.post-18117321849241267372007-07-17T03:57:00.000-07:002007-07-17T04:16:31.181-07:00Userscripts you forget about...Peter <a href="http://wwmm.ch.cam.ac.uk/blogs/murrayrust/">writes</a> about <a href="http://chemicalblogspace.blogspot.com/2007/03/jacs-toc-featuring-your-review.html">a Greasemonky userscript</a> pop up:<ul><i>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.</i></ul><br />This is the screenshot he made:<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://3.bp.blogspot.com/_5vhaOf2_53I/RpyhZOTMprI/AAAAAAAAAFI/4TEveCRrYPY/s1600-h/grease.PNG"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;" src="http://3.bp.blogspot.com/_5vhaOf2_53I/RpyhZOTMprI/AAAAAAAAAFI/4TEveCRrYPY/s320/grease.PNG" border="0" alt=""id="BLOGGER_PHOTO_ID_5088119133729236658" /></a><br /><br />For the obligatory statistics: Cb now discusses 1184 articles. Because I have trouble accessing the Postgenomic website, I cannot give that number :(Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com0tag:blogger.com,1999:blog-5063252723345876353.post-47798608033247074532007-07-04T00:38:00.000-07:002007-07-04T01:17:15.729-07:00The rise of Chemical blogspace<a href="http://www.thechemblog.com/">The Chem Blog</a> wrote about <a href="http://www.thechemblog.com/?p=591">WTF is up with the Science blogosphere?</a>, discussing a podcast on the chemical blogosphere, and wondering why it is larger than that of other natural science fields and <a href="http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=383">mathematics</a>. 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.<br /><br />I am hoping the <a href="http://cb.openmolecules.net/">Chemical blogspace</a> helps a bit too here. With about 40 unique users a day it is somewhat lower than it has been before <a href="http://chemicalblogspace.blogspot.com/2007/06/cb-moved-to-new-location.html">the move to the new server</a>, which was around 60 visitors each day, but I am sure this will recover.<br /><br />The number of chemistry related blogs is rather large indeed, and the <a href="http://chemicalblogspace.blogspot.com/2007/06/these-are-new-blogs-that-entered.html">Cb counter is at over 136 now</a>. Not every blog is equally active, but both the absolute number of entries and the number of active blogs per week are continuously increasing:<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://3.bp.blogspot.com/_5vhaOf2_53I/RotV5xk-B1I/AAAAAAAAAFA/lmsYrGzWspw/s1600-h/CbRise.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;" src="http://3.bp.blogspot.com/_5vhaOf2_53I/RotV5xk-B1I/AAAAAAAAAFA/lmsYrGzWspw/s320/CbRise.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5083251055467038546" /></a><br /><br />Interestingly, the blog had a very nice <a href="http://www.thechemblog.com/wp-content/uploads/2007/06/vismap.jpg">plot of the blogosphere interconnectivity</a>. It is good practice to link to many other blogs and resources in ones entries, to keep discussions going, provide further information etc. <a href="http://wwmm.ch.cam.ac.uk/blogs/murrayrust/?p=383">Like Peter</a> 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.Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com11tag:blogger.com,1999:blog-5063252723345876353.post-8757095880463114862007-06-27T23:52:00.000-07:002007-06-27T23:56:12.431-07:00RDFa Operator in action on CbI reported yesterday on my efforts (and Mike's help) to get <a href="http://chem-bla-ics.blogspot.com/2007/06/chemical-rdfa-with-operator-in-firefox.html">RDFa for chemistry going</a>. I did not have time to add the new HTML code to <a href="http://cb.openmolecules.net/">Cb</a>, but have done so now:<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://1.bp.blogspot.com/_5vhaOf2_53I/RoNbKRk-B0I/AAAAAAAAAE4/pYJMu_ppMiY/s1600-h/pubchemRDFa1.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;" src="http://1.bp.blogspot.com/_5vhaOf2_53I/RoNbKRk-B0I/AAAAAAAAAE4/pYJMu_ppMiY/s320/pubchemRDFa1.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5081005036679333698" /></a><br />Read my <a href="http://chem-bla-ics.blogspot.com/">Chem-bla-ics</a> blog for the details.Egon Willighagenhttp://www.blogger.com/profile/07470952136305035540noreply@blogger.com0