Last week I worked on my Groovy Cheminformatics book and made a first release for CDK 2.3 (doi:10.5281/zenodo.3590374). One of the new features is that the Groovy code runs on the command line without having to download or install something first:

There is yet plenty to migrate from the older paper version and, for example, the Depiction chapter is still missing.

Autumn has been hard. Due to an unfortunate combination of events, the workload was hardly bearable. Half December it started to slow down, but not enough. That said, I had a pleasant two weeks in October, when I attended four meetings in two weeks time. Busy as well, but inspiring. Normally, I blog about meetings I attend, but I haven't had time for that yet. In fact, that has become more common in the past few years.

Hi all, I'm looking for a postdoc with good organizational and programming skills and wants to develop new ontologies to make nanosafety data more FAIR:

I do not want to make it a habit to send out blog messages about preprints (you see them on your BiGCaT website) and wait with blogging until the article is formally published, but since I have mentioning this preprint to so many people know, it's likely worth checking out.

I'm happy to have been able to contribute to this story by Andrew Su's team and the many other people involved, as I do think Wikidata is a game changer.

Apparently, some culprits have found a way to escape the otherwise impressive spam detection by Google, and managed to spam Google Scholar:

Now, Google Scholar has a long history of learning with a serious paper looks like, and I'm sure they will learn to recognize this kind of spam too. If not, it will be the end of Google Scholar, I'm afraid.

It giet oan! That it a Frisian phrase for something unlike is going to happen, like and particularly related to the Elfstedentocht.

ChemCuration 2019 is a go. The website is online, the Twitter account and hashtag are ready, we got a poster prize, and here is the call for posters!

On December 3 the first ChemCuration conference will take place. ChemCuration 2019 is a one day, online-only conference around data curation and curated data in the chemistry domain.

Now that the ChemCuration 2019 online poster conference is nearing, and my upcoming talks about chemistry in Wikidata (also needing curation), and the much longer process of curation of metabolite (-like) structures in WikiPathways, I decided that something I tweeted earlier this week is actually quite useful, and therefore something I should really write up in my lab notebook.

Glucuronide is an example (biological) functional group.

Update: there are two articles, one a news item and the other the interview. I uphold my comments here. They are clearly co-published and should be seen as one event (another intended pun).

I find it very disturbing what role newspapers have in the selection of research to fund. Of course, most of this is indirectly, but claiming that a newspapers decides what is fundable and what is not, is crossing a line.
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Forget about Python being the prime data analysis platform: there are plenty of alternatives and R has been one of them. With CRAN, rOpenSci, Bioconductor (doi:10.1186/gb-2004-5-10-r80) the platform has three efforts where you can publish your R work. I think of them as scholarly journals: the peer review is strong with them. Anyways, over the years I did my share of R coding (a good bit of my PhD is written in R) and contributed to a few R packages.

First, if you like to learn more about Scholia, check this list of previous posts.

Now, yesterday I had to invite reviewers for a submission to the Journal of Cheminformatics. This can be hard, and is harder when more authors are involved, from multiple institutes. Existing tools by publishers (including SpringerNature) do not exceed in detecting possible CoIs. In fact, they already have trouble finding authors with expert knowledge. This is where I come in.
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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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