Chemical SciencesJekyll

chem-bla-ics

Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.
Home PageAtom Feed
language
Published

Publishing grant proposal is still not very common. The proposal published in Research Ideas and Outcomes) (doi:10.3897/rio.10.e124884) for the NWO Open Science grant for the CDK is, however, not the first and hopefully not the last. Interestingly, it is already cited in (the German) Wikipedia. It is used there to support a statement which tools use the Chemistry Development Kit.

Published

We recently got awarded our second NWO Open Science grant (OSF23.2.097), this time for the Chemistry Development Kit (CDK). “We” here is me and Alyanne de Haan, René van der Ploeg, and Marc Teunis from Hogeschool Utrecht. The proposal has been submitted for public dissemination in RIO Journal, like we did with the first NWO Open Science grant.

Published

During the Open Science Retreat I organized a short session where we looking into typing citation intentions using a new nanopublication template. First, let’s describe nanopublications (originally used in doi:10.3233/ISU-2010-0613) a bit. Scholia gives a nice overview of (macro?)publications on the topic.

Published

Last week I attended the Open Science Retreat (#osr24nl) in a quite and relaxing region in North-Holland. The meeting was how I like all meetings to be (and I count myself lucky many of my meetings are like this): open, welcoming, constructive, diverse, and intellectually challenging. Not all scientific meetings are like this and it is easy to end up going to obligatory meetings where the discussions are of a different level.

Published

My research is about the interaction of (machine) representation and the impact on the success of data analysis (matchine learning, chemometrics, AI, etc). See the posts about molecular chemometrics. This got me into FAIR: making data interoperable and being able to (really) reuse data is the starting point of doing research.

Published

Just before the end of the year, the Wikidata subsetting: approaches, tools, and evaluation paper by Seyed Amir Hosseini Beghaeiraveri et al. got published (doi:10.3233/SW-233491). I am really excited our group (i.e. Ammar and Denise) has been able to contribute to this. I think it also is a great example of the power of hackathons to bring together people.

Published

This week the next WikiPathways NAR Database issue paper was published (doi:10.1093/nar/gkad960). It is the next paper in a series of papers about the evolution of the Open Science project for making biological pathways available in a Open and FAIR way. This year, it described that significant move away from MediaWiki.

Published

Two weeks ago the write up of a week-long scientific discussions around artificial intelligence for natural product drug discovery in Leiden at the Lorentz Center got published (doi:10.1038/s41573-023-00774-7, free PDF). Sadly, the meetings was still during the (partial) lockdown, and I think my contribution could have been more extensive.

Published

This paper got published in July already, but I had not had the time yet to blog about this exciting work by Irini Furxhi and Ammar Ammar: A data reusability assessment in the nanosafety domain based on the NSDRA framework followed by an exploratory quantitative structure activity relationships (QSAR) modeling targeting cellular viability (doi:10.1016/j.impact.2023.100475) The study has two sides to it: first, it looks into how far we