chem-bla-ics: May 2007

ChemRank: ranking scientific literature

Mitch just launched ChemRank, a website where we can comment on and vote thumbs up or down for scientific articles. Good initiative I think. Some thoughts:please include the DOI for each article overview on the front page (see why)make the content opendata, e.g. using the CC licenseprovide a means to refer to other literature to back up comments and rankingprovide an API to make mashups (like that of Chemical blogspace for use in Greasemonkey scripts)make the website source code opensource (JSON, RDF come to mind)use microformats where possible (for Operator and FF3)at least provide means for tagging articlesprovide browsing by journalimport articles from Connotea/NatureNetwork/etc

Please consider there as feature requests, and not as critique.

May

Weka Decision Trees to Java Conversion

Some time ago I wrote a small Perl script to convert a decision tree created with Weka in the ARFF format to Java source code, for use in the ionization potential prediction in CDK. The advantage is that Weka is no longer used are runtime, and that there is no model that needs to be loaded and interpreted. Instead, it is simple Java code that does the work, much faster.

May

The JCIM is linking to Planet Blue Obelisk??

I use Google Analytics to analyze the visitors of my blogs and of Planet Blue Obelisk too. Now, for the past couple of weeks, the webpage of the Journal of Chemical Information and Modeling is showing up as refering site:

What is going on here ?!?! This is really no fake, but cannot find an actual link when I visit the journal webpage either...

May

Numbers are copyrighted?

I just read on Planet Blue Obelisk Peter's disturbing news (via Suber) that Wiley thinks it can copyright a set of numbers (also known as data). That is a sad milestone in scientific publishing. It reminds me of the recent internet hype about a long number recently flooding the internet (and notably del.icio.us) related to watching DVDs you legally bought. Some details can be found in this Linux Weekly News article on How Debian packages a number.

May

Added my hCard to my blog

Getting back on microformats (see yesterday), I added my hCard to the bottom of my blog:

I will likely populate it a bit more soon (after holiday in Sweden).

Now, if you had the Firefox plugin Operator installed, you would have my contact information show up in your FF toolbar, like this:

Note the 'Export Contact' button in the toolbar. This will automatically create a vCard which I can directly open in my address book (I use the KDE addressbook).

May

Microformats in chemistry...

Peter blogged some days ago about microformats and how they could be used in chemistry. Being late and a bit absent minded, I added a short comment that Chemical blogspace supports microformats for chemistry, and that chemistry is harvested from that, and actually semantically distributed again using CMLRSS.

In reply to my comment, he wrote a follow up highlighting one of blog items linked above (thanx for that!).

May

Preparing a Chemoinformatics workshop

After handing in a new draft of my PhD manuscript with my co-promotors last friday, and a week before we leave for Sweden, it is time to start finishing up the material for my one hour workshop on chemoinformatics in general and QSAR/QSPR in particular for the Bioclipse Workshop.

Pierre blogged about this movie.

May

Cb comments for InChI's

About a year ago Pedro wrote a Greasemonkey script to add comments from PostGenomic.com to table of contents of scientific journals. Noel extended it with support for Chemical blogspace (see also this earlier item). Now, the later website is maintained by me, and I extended the aggregator software with molecule support, for example to show hot molecules on the frontpage (at some point my patches will be backported into mainstream. Euan, why not invite me to London HQ in, say, June?).