Biology, ACPs, lipids, cheminformatics, and Dagstuhl

Already 3 months ago I visited Dagstuhl for the second time. The weather was much better than in the January right before the start of the pandemic. The first I attended the Computational Metabolomics meeting, with the focus From Cheminformatics to Machine Learning, one of the things we concerned ourselves with was how to do computation with compound classes (see Section 3.6 and this online book). We know how to handle SMILES and we know how to the substructure searching with SMARTS, but what if you have compound classes or lipid classes? Biology is a greasy business. 1 minute read

BridgeDb NWO grant update #2: building up momentum

Last month I reported on the start of the NWO Open Science grant and it is time for an update. First, our grant now has a grant number, 203.001.121. For a project that is about identifiers, having a project identifier is a big deal. 1 minute read

BridgeDb NWO grant update #1: first steps

Last year, Denise, Tina, Marvin, and I received an NWO Open Science grant (203.001.121) to improve the long running BridgeDb project, originally developed by Martijn van Iersel (see doi:10.1186/1471-2105-11-5). Helena joined our group as research software engineer and will work part-time on this grant. We started two weeks ago, so time for an update of results: 1 minute read

BioHackathon Europe 2021 #1: CiTO annotations in BioHackrXiv

Serendipity. I did not plan this hack at the BioHackathon Europe 2021 but it happened anyway. Based on earlier work in the Journal of Cheminformatics, extending on the work by Krewinkel et al. I looked into the idea of using the Lua filter for BioHackrXiv, a preprint server for BioHackathons. Actually, I started by looking at the Citation Styling Language file used by the BioHackrXiv tools. But that was just wrong. 1 minute read

Scholarly journals should use "Archived on" instead of "Accessed on"

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. 1 minute read

Downloading all currently released BridgeDb identifier mapping databases

The BridgeDb project (doi:10.1186/1471-2105-11-5) (and ELIXIR recommended interoperability resource) has several aims, all around identifier mapping: 2 minute read

Bioclipse git experiences #2: Create patches for individual plugins/features

This is a series of two posts repeating some content I wrote up back in the Bioclipse days (see also this Scholia page). They both deal with something we were facing: restructuring of version control repositories, while actually keeping the history. For example, you may want to copy or move code from one repository to another. A second use case can be a file that must be removed (there are valid reasons for that). Because these posts are based on Bioclipse work, there will be some specific terminology, but the approach I regularly apply in other situations. 2 minute read