Jekyll2026-08-31T19:33:33+00:00https://chem-bla-ics.linkedchemistry.info/feed/by_tag/biohackrxiv.xmlchem-bla-icsChemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.Egon WillighagenAll BioHackrXiv preprints and BioHackathon RSS feeds2025-06-22T00:00:00+00:002025-06-22T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2025/06/22/all-biohackrxiv-preprints-and-biohackathon-rss-feedsOne thing I was still missing in BioHackrXiv was a place with an overview of: 1. all biohackathons, 2. all preprints linked to a biohackathon, 3. an RSS feed for new papers of a biohackathon. Of course, there is the BioHackrXiv discover service, but the biohackathon is not a metadata field and I cannot filter based on it. And, of course, there is Scholia, but not all preprints are notable (so far, a good number had CiTO annotation that at least made them somewhat notable). Thus, they are not all listed in this venue page and neither on this overview of collections of preprints linked to BioHackathon Europe meetings.

Additionally, it also does not have an RSS feed, and we should indeed be using RSS more. So, I hacked something up and impressions were positive. Based on Jekyll and the experiences I had with this blog, I modelled individual articles as blog posts and biohackathons as tags. That automatically gave me the RSS feeds:

It’s still very much in progress, but it’s now live at index.biohackrxiv.org:

Extras

Some extra goodies already there include:

The overview of biohackathons looks like this (the tag size follows the number of preprints for that biohackathon):

]]>Egon WillighagenNew preprint: “BioHackEU24 report: ORCID and ROR identifiers in BioHackrXiv reports”2025-03-23T00:00:00+00:002025-03-23T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2025/03/23/orcid-and-rorWhile this was not the primary hack project during the ELIXIR BioHackathon Europe last autumn, but I really like BioHackrXiv and I got the question if I could have a look at getting the ORCID logo in generated PDF. The ORCID was already in the YAML metadata of report markdown, so it sounded easy. Well, it was a big more complicated, but all the nicer to now have the project report online (doi:10.37044/osf.io/p9u42_v1). And once the ORCID was working, adding the Research Organisation Registry ID was not much harder. Cool to see both used in other recent BioHackrXiv reports!

]]>Egon WillighagenBioHackathon Europe 2021 #1: CiTO annotations in BioHackrXiv2021-11-15T00:00:00+00:002021-11-15T00:00:00+00:00https://chem-bla-ics.linkedchemistry.info/2021/11/15/biohackathon-europe-2021-1-citoSerendipity. 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.

Long story short: it worked! Thanks to the encouragements from Pjotr and Tazro and suggestions from Lars and some code on how to dump a Lua data structure to stdout.

In the Markdown/BibTeX combination you would normally write [@bibtexkey] to add the reference to the article with the given key in the .bib file. To type the citation (to state the intention why you cite that source), for example because you use a method in it, you write [@usesMethodIn:bibtexkey]. This is different from how it currently works for the Journal of Cheminformatics, where the intention cannot be given at citation level yet. You can even use more than one intention, e.g. [@usesMethodIn:extends:bibtexkey].

If you want to try it, just create a compatible Markdown file with BibTeX file in a new GitHub repository, and post the repository URL on this cool preview website.

Here’s what the created PDF could look like:

]]>Egon Willighagen