Rich recently blogged about the limitations of the two-atom bond representation often used in chemoinformatics, triggered by the four ferrocene entries in PubChem . In reply to himself, Rich described FlexMol , an XML language that can describe bond systems that involve more than two atoms.
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.
Here’s a quick update on my blog about SMILES, CAS and InChI in blogs: Greasemonkey last sunday. The original download was messed up :( You can download a new version at userscripts.org. This new version also supports chem:compound, for any chemical.
As follow up on my Including SMILES, CML and InChI in blogs blog last week, I had a go at Greasemonkey. Some time ago already, Flags and Lollipops and Nodalpoint showed with two cool mashups (one Connotea/Postgenomic and one Pubmed/Postgenomic) that userscripts are rather useful in science too. I can very much recommend the PubMed/Postgenomic mashup, as PubMed has several organic chemistry journals indexed too!
I just found out that a review article that I wrote earlier this year got printed: Molecular Chemometrics (DOI:10.1080/10408340600969601), with my personal view on the interplay between chemoinformatics and chemometrics.
The blogs ChemBark and KinasePro have been discussing the use of SMILES, CML and InChI in Chemical Blogspace (with 70 chemistry blogs now!). Chemists seem to prefer SMILES over InChI, while there is interest in moving towards CML too. Peter commented. Any incorporation of content other than images and free text requires some HTML knowledge, but this can be rather limited.
Peter blogged about the h-index, which is a measure for ones scientific impact. He used Google Scholar, but I do not feel that that database is clean enough. I believe a better source would be the ISI Web-of-Science. Therefore, I composed a list of h-indices of my own, ordered by value.
Because no one picked up my Chemo::Blogs suggestion, I will now officially claim the blog series title. However, unlike the original Bio::Blogs series, I will not summarize interesting blogs, but just spam you with websites I recently marked as toblog on del.icio.us. Semantics and Text Mining Evan Prodromou wrote about RDFa vs microformats.
Contributions to open data do not have to be large, as long as many people are doing it. The Wikipedia is a good example, and PubChem accepts contributions of small databases too (I think). The result can still be large and rather useful, even scientifically.
Recently I discussed JUnit testing from within Eclipse , and blogged at several occasions about it in other situations. I cannot stress enough how useful unit testing is: it adds this extra set of eyeballs to make bugs shallow. And it does that, indeed. Ensuring that you actually test all the code you write, however, is not easy.