Rogue Scholar Posts

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WikidataWikipathwaysChemical Sciences
Published in chem-bla-ics

A good number of years ago, a colleague and I explored if we could get access to the Retraction Watch Database, but we could not afford it. We have been using data on retractions for curate our databases, like WikiPathways. A database should not contain knowledge based on (only) a retracted article. Wikidata, btw, has a small number (499) of statements supported by retracted articles.

BioinfoChemical Sciences
Published in chem-bla-ics

With a year of preparation and two years of thinking, on September 1st 2024 the Department of Bioinformatics, aka BiGCaT, merged with two other departments to form the Department of Translational Genomics (see also this LinkedIn announcement). This merger creates many new opportunities while it strenghtens our bioinformatics research.

PublishingChemical Sciences
Published in chem-bla-ics

I wish I could say I remember the first citation to one of my research articles. I do not. But I do remember the excitement to see why someone was citing my research. What I do remember is that I got a comment around the same time along the lines of this: “why would anyone cite your article if they can download the results for free?” (about open science cheminformatics research). Other times.

Interesting ChemistryChemical Sciences
Published in Henry Rzepa's Blog

This is another in the C&E News list of candidates for the Molecule of the Year, Molecular shuttle in a box [cite]10.1002/anie.202318829[/cite] Mirror-image cyclodextrin [cite]10.1038/s44160-024-00495-8[/cite] Molecular shuttle in a box [cite]10.1002/anie.202318829[/cite] Rule-bending strained alkene [cite]10.1126/science.adq3519[/cite] First soluble promethium complex [cite]10.1038/s41586-024-07267-6[/cite]

Chemical Sciences
Published in Jeremy Monat, PhD

Exploring other cheminformatics toolkits besides the RDKit, I wanted to try EPAM Indigo Toolkit. The Indigo Toolkit is free and open-source with Apache License 2.0, so it can be used in proprietary software. I was unable to find simple examples of drawing molecules in a Python Jupyter Notebook, so here’s how to do that. This post also demonstrates how to save molecular images to a file.