Mitja M. Zdouc

Finally, a shout out to all contributors to #MIBiG and a special thanks to the co-authors of this Position article in #bib, especially to @catarinacarolina.bsky.social, @kblin.bsky.social, and @marnixmedema.bsky.social ! It was a great pleasure working with you on this piece! (8/8)

MIBiG 5.0 Annotathons Registration Form Planned for spring 2026

Speaking of MIBiG hackathons: iteration 5.0 it is planned for spring 2026 and registrations are open! Please sign up if you are interested and feel free to share with your colleagues! (7/8) forms.gle/JKsf3XL3d1XN...

In our Position article, we analyze the outcomes of our strategy and compare it with related biocuration frameworks. Our biocuration strategy can be used as inspiration for related community-driven efforts. We will also implement lessons learned in future MIBiG hackathons (6/8)!

Flow diagram of workflow used in the MIBiG biocuration framework.

This framework uses social and technical workflows to facilitate the creation of high-quality annotations, combining #Kanban boards for work coordination with controlled data input via a dedicated submission portal, using motivational strategies inspired by insights from social sciences (5/8).

To this end, we developed a new framework for community-driven biocuration, and successfully applied it during the MIBiG 4.0 annotation hackathons, mobilizing 267 researchers who collectively invested over 4,000 hours into biocuration (4/8).

One such initiative is #MIBiG. Founded in 2015, it has become the gold standard database for #biosynthetic gene clusters due to the tireless efforts of the #secmet #naturalproducts community. However, the biocuration efforts were mostly organized ad hoc, lacking a organizational framework (3/8).

#Biocuration is essential to transform unstructured biological data into machine-readable and structured resources. While institutional databases (e.g. #UniProt) can afford professional biocuration, many smaller initiatives rely on volunteer efforts (2/8).

Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0 Abstract. Biocuration is essential to transform molecular sequence data into standardized, machine-readable resources. Such curated datasets enable compara

Have you ever used a #bioinformatics #database and were frustrated by its lack of coverage? Did you ever think about starting your own resource? We just published a new strategy for community-driven #biocuration, based on our experiences with the #MIBiG database (1/8)! doi.org/10.1093/bib/...

Congratulations to this great work, happy to have contributed a little bit :)

MITE training session registration form Registration form for mailing list

Working on tailoring enzymes and want to learn more about the MITE database? We are organizing a hands-on training session on how use the DB and create new entries: October 30th and November 4th 10-11 am Amsterdam time. Sign up here: forms.gle/KHPqe9XV1RRg... See you there! #secmet #natprod

Astral really is creating top notch tools!

Inspired by discussions with @adafede.bsky.social and @skepteis.bsky.social :)

Interested in Python programming and good software engineering practices? Check out my newest blog post where I introduce a "modern Python" GitHub repository template and talk about my motivation for its creation! mmzdouc.github.io/posts/2025/1...

@skepteis.bsky.social

Are you building applications using docker? In my recent blog post, I am investigating git's curious behavior when used as a subprocess inside a containerized Flask application. You can read more here: mmzdouc.github.io/posts/2025/1...

Hopefully this will be a wakeup call for journals which still accept images of gels or western blots as experimental evidence 🙃

Typo: it should be mite.bioinformatics.nl

Great to see PhyloNaP out! Great tool, and it also connects to mite.bioinformatic.nl! #openscience #collaboration

Again, thanks a lot to all the contributors and especially @adafede.bsky.social @skepteis.bsky.social @jjjvanderhooft.bsky.social @marnixmedema.bsky.social @catarinacarolina.bsky.social @jorgenavarro.bsky.social @nadineziemert.bsky.social @tilmweber.bsky.social @kblin.bsky.social

MITE training session registration form Registration form for mailing list

MITE is created by the natural products community, for the community! If you are interested in learning more about using MITE or even contributing to it, make sure to sign up for the mailing list! We will organize a first training session for MITE soon-ish (mid-October)! forms.gle/9NUe2aovynTV...

MITE can be queried in various ways to get information about tailoring enzymes, their pathways, and associated organisms. Its already being used by @antismash.bsky.social and MIBiG, and we foresee its use in machine learning applications for enzyme reaction prediction and classification!

The MITE database is a curated, crowd-sourced, and expert-reviewed database of tailoring enzymes, capturing catalytic reactions, substrate specificities, genomic context, and cross-references to existing resources (e.g. MIBiG, Rhea, UniProt).

Aaand it's out! Meet MITE - the natural product tailoring enzyme database, just published in @narjournal.bsky.social! MITE DB captures the substrate- and reaction-specificity of tailoring enzymes, allowing to capture this information in a human- and machine-readable way! doi.org/10.1093/nar/...

Next at @vaam-microbes.bsky.social Workshop, Leo Dumjahn talks about the opportunistic pathogen Chromobacterium haemolyticum and the cyclic lipopeptides it uses as virulence factors.

Next at the @vaam-microbes.bsky.social Workshop, Valerie Rebhahn is talking about the cyanobacterial aetokthonotoxin and its mode of action in uncoupling the oxidative phosphorylation in mitochondria.

In today's third talk at @vaam-microbes.bsky.social Workshop at @freieuniversitaet.bsky.social, Nico Brüssow talks about the lanthipeptide II RiPP nostolanthin A which apparently oligomerizes - a very unusual property in RiPPs.

Next at VAAM Workshop at @freieuniversitaet.bsky.social , Alexandra Eckart from HIPS talking about her discoveries of tenacious bacteria isolated from Hydractinia echinata hydroids.

@mitjare.bsky.social kicking off the second day of the VAAM Workshop at @freieuniversitaet.bsky.social talking about the phyllosphere, its bacterial inhabitants and the natural products they produce - including surfactants!

Super interesting perspective!

If you are interested, make sure to apply! I have been working with Marnix, Justin, and Daniel over the last few years and they are awesome!