Scientific Literature: searching, ranking, storage

Dealing with scientific literature has been one important theme in Chemical blogspace. For example, ranking articles and how to store your personal PDF archive has been topics of discussion. In this blog I will summarize bits of the discussion, and my personal view on things.

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A Blue Obelisk corner in Chemical Blogspace

I just finished setting up a Blue Obelisk section for Chemical blogspace, as future replacement for the current Planet Blue Obelisk (unless someone wants to take over that webpage). The only thing really missing is a RSS feed for recent posts for just the Blue Obelisk member blogs (BTW, just email me if you want to be listed as BO member with your blog too; the BO community is very open!).

less than 1 minute read

Finding email with Strigi in .tar backups

Now that my CUBIC desktop machine is shutting down, I made the necessary backups, among a mail.tar for my mail correspondence of about a year. About 500MB in size for almost 8700 files. Strigi is a perfect tool to help me find messages in this archive, as it will recurse into the .tar archive, and even into email attachements. I created an index just for the archive with:

less than 1 minute read

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:

less than 1 minute read

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.

1 minute read

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:

less than 1 minute read

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.

less than 1 minute read