Jug 2.5.0 is out! Jug is a Python framework for parallel & reproducible computation. Write plain Python, run it across many processes or machines with no message-passing code. pip install jug --upgrade (Or use the conda-forge packages with conda/pixi)

I will be speaking at BrisJAMS next week!

New Year updates from the group with a focus on Anil Pokhrel who is working on metagenomics for food security! bigdatabiology.substack.com/p/bdb-lab-ja...

It's time for the 2025 Gibbons Lab Research Roundup! Yeehaw! 🤠 @isbscience.org In these dark times, let the joy of scientific discovery and trainee success be your balm ❤️‍🩹 🧵...

Today I had the pleasure of meeting the 🇵🇹 Microbiome HD Lab Great to see Bich Ngoc Do's work on the Portuguese gut resistome data using argNorm (github.com/BigDataBiolo... by @bigdatabiology.bsky.social). Impressive, methodical research! @anasalmeida.bsky.social thank you for the invitation!

🔬 Call to create junior research groups at the Institut Pasteur Focus: Infectious diseases, host-microbe interactions, vaccines Special interest: AI methodologies 📅 Deadline: Feb 9, 2026 👥 2-12 years post-PhD Apply now 📝 research.pasteur.fr/en/call/crea... #JobOpportunity #Research

New version of macrel released (v1.6.0) The biggest change is internal, using a much better approach to saving and loading models (thus removing the dependency on particular versions of scikit-learn) A few other bugfixes were included github.com/BigDataBiolo...

I would like to thank all co-authors: Yiqian Duan, Fernando Gil, Alexei Chklovski, Nithya Kruthi, Shaojun Pan, Sofia Forslund, Susanne Lau, Ulrike Löber, Xing-Ming Zhao, and especially @luispedrocoelho.bsky.social And of course, all the dog owners and the main characters of this story 🐶

September 2025 updates! A focus on Anna's preprint, but several other updates too, including Faith Adegoke joining us to work on AMR and several other preprints bigdatabiology.substack.com/p/bdb-lab-se...

Finally, the results of my postdoc at the @bigdatabiology.bsky.social lab in Shanghai see the light! The work includes my three favorite things research-wise: 🦠 microbiome, 🧬 long-reads, and 🐶 dogs. See our new preprint: www.biorxiv.org/content/10.1...

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort https://www.biorxiv.org/content/10.1101/2025.09.17.676595v1

Full thread will come later, but @annacusco.bsky.social's preprint on the dog pet gut microbiome is out! Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases doi.org/10.1101/2025...

New paper in collaboration with the @asantoslopez.bsky.social lab! www.biorxiv.org/content/10.1...

Quarterly updates from the Lab! This June, the focus is on Alexandre Areias Castro, who is working on metabolic modeling of the microbiome with the aim of giving us a new view on microbial composition, focused of "functional roles" instead of taxonomy bigdatabiology.substack.com/p/bdb-lab-up...

New version of argNorm! Will be available frombioconda & funcscan in the next few days We fixed how NCBI genes were being handled. It is a fundamentally more principled way and should fix a few corner cases (particularly if data has been run through hARMonization) pypi.org/project/argn...

Anyone from Europe wants to spend 2 years in sunny Queensland working on the global microbiome? Get in touch (even if all you have right now is a vague idea, just email early)! We also have a lot of friends in Europe for the return phase. marie-sklodowska-curie-actions.ec.europa.eu/calls/msca-p...

An tutorial by our own Alexandre on metabolic modeling areias03.github.io/blog/intro-t...

ArgNorm 0.8.0 released! More information including English language names for outputs and a bugfix for handling abricate+resfinder outputs argnorm.readthedocs.io/en/latest/wh...

🚨PhD position in AI in Microbiology! We’re looking for a PhD researcher passionate about developing automated systems for microbiological research. 🌍 More info & apply: jobs.vib.be/j/109363/phd... @vibmicrobes.bsky.social @vibai.bsky.social

Updates from the group (newsletter, sent 4x/year) Focusing on #ExtremelyOpenScience this quarter bigdatabiology.substack.com/p/bdb-lab-ma...

SemiBin v2.2.0 released! This includes a lot of minor fixes rather than any big new features Generally speaking, SemiBin v2.2.0 is more robust, will fail in fewer corner cases and will give you better error messages when it does. semibin.readthedocs.io/en/latest/wh...

How to install SemiBin using pixi (including GPU support) Pixi is conda modernized and makes everything easier youtu.be/kqp8qV4S8dk

We are looking for PhD students! Fully funded studentships available to work on a range of topics, from small proteins to developing computational tools to study the global microbiome

ArgNorm version 0.7.0 released! A lot of improvements, including an update to CARD v4, support for AMRFinderPlus 4, an updated manual curation for many genes argnorm.readthedocs.io/en/latest/wh...

Check out @biorxivpreprint.bsky.social on healthy urinary microbiome from BacTdrugs - Luísa Peixe lab led by Svetlana U. Perović

NGLess tutorial (in 4 languages) English:

Assembling multiple metagenomes using NGLess

Our YouTube channel has videos on our work including tutorials on our tools and we are happy to do them on request as well (if you have a question that we think others would like to see answered as well) Like & subscribe to keep up to date

Congratulation to the #MVIF #34 winners!!! 💐 Vedanth Ramji (@bigdatabiology.bsky.social) 💐 Kurtis Budden Besides the fame, there's a $200 prize to the prize winners, so make sure to vote and to submit an abstract for next time!

How to obtain amino acid versions of GMGCv1 subcalogs

"A global survey of eco-evolutionary pressures acting on horizontal gene transfer" by Marija Dmitrijeva et al. https://buff.ly/3DDBBgj

The antimicrobial peptides (AMPs) of the global microbiome! From 72 diffferent habitats (the best current sampling of the global microbiome) we obtained almost 1 million candidate AMPs https://buff.ly/404s9Ky

Our paper on nurturing a #PositiveResearchCulture within your #research #team published by @wellcometrust.bsky.social gives useful tips for your lab. As well as making you a good team leader, nurturing culture pays off in building your science: 1/11 wellcomeopenresearch.org/articles/9-3...

News from our lab for the past quarter, focusing on new lab members! bigdatabiology.substack.com/p/bdb-lab-ja...

A catalogue of small proteins from the global microbiome! As part of our ongoing efforts to understand small proteins in prokaryotes, we catalogued almost 1 billion sequences

Check out Vedanth's video to learn more about what argNorm is https://buff.ly/3ZWwY8y

SemiBin2 Tutorial

Yiqian presenting at MicrobiomeVIF earlier in 2024

Review paper with Celio Dias Junior and De La Fuente Upenn How mining small peptides from (meta)genomes is different from mining full-sized enzymes and how we need new methods and approaches (AI/ML instead of sequence alignment) https://buff.ly/3ONEr4w

In June, @luispedrocoelho.bsky.social found found 863,498 molecules that can potentially kill infectious microbes and become the source of antibiotics. And they're all from the natural world! https://buff.ly/3D8ZoV5

Check out our #extremelyopenscience episodes for the year as we wrap up 2024!!

For more information on long-term sustainability of software in bioinformatics that @luispedrocoelho.bsky.social presented at BOSC2024, read more in the @plos.org journals.plos.org/ploscompbiol...

If you are interested in Sustainable Research Software. Luis recorded his presentation from BOSC2024. Have a watch! https://buff.ly/3ZKhKVo

Revisiting when argNorm became part of nf-core/funcscan! Great work from Vedanth to get this integrated

Back in August, A/P @luispedrocoelho.bsky.social , presented at ISME's conference in South Africa. Luis spoke about microbes and the microbiome to local school children of Cape Town. To find out more about CMR's exciting research, reach out.

Have you seen the GMSC manuscript published in @naturecomms.bsky.social (open access)? We constructed a small protein catalog from the global microbiome

Check out our Youtube channel where we post tutorials on our tools, highlights of our work, and other content.

Every 3 months, we send out an update email. Subscribe on Substack to get the updates (we really only send 4 emails per year). This was our September update:

Check out this review featuring A/Prof Luis Pedro Coelho, which highlights recent advancements and current challenges in the field of orthology-based research.

CMR Director Prof Gene Tyson sat down with journalist Elissa Lawrence to discuss one of his favourite topics: the human microbiome. Read more about Prof Tyson’s career as a microbial ecologist and his hopes for the future of microbiome science.