Publishing habits changes very slowly, too slowly. The whole industry is incredibly inert, which can lead to severe frustration as it did for me. But sometimes small changes can do so much. 

Linkrot, the phenomenon that URLs are not persistent, has been studied, including the in scholarly settings (see 1998, 2000, 2003, 2006, 2008, 2014, 2015, 2000, 2021, and probably many more). Indeed, scholarly publishers started introducing the following: URLs should be accompanied with an "accessed on" statement. Indeed, you can find this in many bibliographic formatting standards.

Indeed, this must change, and we already have a solution since 1996: the Internet Archive (tho the archive goes back much longer). I call all publishers to change their "Accessed on" to "Archived on".

This week the 11th edition of the World Congress on Alternatives and Animal Use in the Life Sciences is held in Maastricht. Well, virtually in Maastricht. It was originally supposed to be held last year, but, yeah, we know why. Yesterday the S67 session on "Using the Sematic Web for Rapid Integration of Publicly Available Biological Information" took place, chaired Holly Mortensen (EPA) and Penny Nymark (KI).

Our scientific knowledge dissemination system is broken. Scholars have devices a system where knowledge is encrypted in PDF and HTML and ReadCube, many of these have been deliberately obfuscated to make text and data mining hard. After all, as some claim, without prestige and high stakes, no quality science. Utter bollocks, of course. So, we're wasting enormous amounts of research money in the process. Welcome to the market economy.

The new Debian stable (bullseye) does not come with the latest Apache Groovy version. So, the packaged version still gives warnings with Java 11 and higher. You can download Groovy 3.0.8 as a binary zip file and unzip this in /opt. Easy enough. But you will also want to set it up as "alternative", which is an old Debian mechanism to have alternative versions of the same software installed. It's so old that I had to look up what to type again.

Yesterday I started a blog series around the Journal Article Tag Suite (JATS) of the Journal of Cheminformatics. JATS is the XML standard used to share articles from the journal. It can be seen as the source code of the article. The source code can be compiled to HTML, PDF, and ReadCube. Each output can be customized such as we have seen multiple HTML flavors for articles in the journal.

Delayed, because once more I had a really crowded year where a lot of things happened. Progress is being made. This post starts a series in which I use my API account to download and redistribute Springer Nature articles. Actually, I already started this earlier at https://github.com/egonw/jats and I will start with the articles that have CiTO annotation. But I intend to actually make all Journal of Cheminformatics articles available this way in the next months.
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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!
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