Here's a link to a quick article I wrote about how we're making changes to the #qiime2 documentation ecosystem, and introducing the #qiime2 Library "Stacks".

This announcement is a little late (we're just starting to use bluesky), but #QIIME 2 2024.10 was release this October! Lots of exciting new features with many more still on the way!

forum.qiime2.org/t/qiime-2-20...

#microbiome
#bioinformatics
#microbiomesky

Reposting, to share on #microbiomesky.

I'd also love to be in.

The dissertation pulling all of this together will be defended next week by Jeff Meilander at Northern Arizona University. DM if you'd like the Zoom link!

Microbiome science of human excrement composting Abstract. Linear waste management systems are unsustainable and contribute to environmental degradation, economic inequity, and health disparities. Among t

And finally, if you're ready for the deep-dive, check out our literature review, just accepted at ISME Journal:
doi.org/10.1093/isme...

All of the data, including the interactive visualizations, are linked in the corresponding Zenodo archive here:
zenodo.org/records/1388...

Upcycling Human Excrement: The Gut Microbiome to Soil Microbiome Axis Human excrement composting (HEC) is a sustainable strategy for human excrement (HE) management that recycles nutrients and mitigates health risks while reducing reliance on freshwater, fossil fuels, a...

Then, if you're still interested, check out our new pre-print presenting results from our first experiment (the :
arxiv.org/abs/2411.04148

Microbiome multi-omics can accelerate human excrement composting research - Microbiome In this editorial, we discuss the need for a new, long-term strategy for managing human excrement (feces and urine) to facilitate health equity and promote environmental sustainability. Human excremen...

My lab has some publications and pre-prints out on a new-to-us topic: microbiomes of Human Excrement Composting (yep, you read that right: 💩➡️🌻).

If you're interested, start here with a two-page editorial introducing the topic and why we care:
microbiomejournal.biomedcentral.com/articles/10....

Do you use Zenodo for archiving QIIME 2 data for publications? We now support loading QIIME 2 Results (Artifacts and Visualizations) directly from Zenodo with QIIME 2 View.

Check out the links in this Zenodo record, which references data from a new @cap-lab.bio pub:
doi.org/10.5281/zeno...

I'm excited to share a new pre-print (𝐀𝐬𝐬𝐞𝐬𝐬𝐢𝐧𝐠 𝐄𝐧𝐠𝐫𝐚𝐟𝐭𝐦𝐞𝐧𝐭 𝐅𝐨𝐥𝐥𝐨𝐰𝐢𝐧𝐠 𝐅𝐞𝐜𝐚𝐥 𝐌𝐢𝐜𝐫𝐨𝐛𝐢𝐨𝐭𝐚 𝐓𝐫𝐚𝐧𝐬𝐩𝐥𝐚𝐧𝐭; arxiv.org/abs/2404.07325) by Chloe Herman et al. which discusses approaches that have been applied to quantify donor #microbiome engraftment extent and presents recommendations for your #FMT work.

QIIME 2 2024.2 is now available! The QIIME 2 2024.2 release is now available! Thanks to everyone involved for their hard work! 🙌🏼 🎉 As a reminder, our next planned QIIME 2 release is scheduled for May 2023 (QIIME 2 2023.5), but plea...

Happy Monday! Start your week off w/ a new QIIME 2 release: @qiime2 2024.2. There's a lot in this one, including new parallel actions in the shotgun distribution, a fancy new visualizer (summarize-plus), for summarizing feature tables & performance enhancements and minor fixes throughout. Enjoy!

2023 ISB Microbiome Series Share your videos with friends, family, and the world

The course lectures & symposium talks from the 2023 @isbsci.bsky.social Virtual Microbiome Series are now edited & posted to YouTube! If you have students who need a crash course in 16S data analysis or community-scale metabolic modeling, send them here: www.youtube.com/playlist?lis...

Provenance is so important

Ever wonder how your collaborators analyzed your data? Maybe pull out your hair trying to reverse-engineer their code? Never fear, Provenance Replay is here!

(Please process your microbiome data responsibly.)

🦠🧪🧬🖥️ #metasci

Definitions of Reproducible, Replicable, Robust, and Generalizable in the context of data analysis.

QIIME 2 Provenance Replay auto-generates the code for creating QIIME 2 results from QIIME 2 results & builds "bioinformatics reproducibility supplements" for your papers. Our goal is to make it easy for you to perform reproducible, replicable & robust bioinformatics.

doi.org/10.1371/jour...

Exciting times to be at NAU! This semester we shared that we're creating a School of Medicine & will begin recruiting MD students & in 2025 we will be an R1!

Many new faculty, PhD, & other open positions on the horizon - keep NAU on your radar if you're looking!

news.nau.edu/r1-designati...

Today I'm writing a compiler that generates assembly code to pass to the assembler I wrote last week ( github.com/gregcaporaso... ) which will then pass machine instructions (1s and 0s!) to the CPU I built (virtually) the week before and down it goes to the logic gates I built a few weeks before.

Currently reading The Elements of Computing Systems: Building a Modern Computer from First Principles nand2tetris.org. This is the most fun I've had with a computer in a long time. 6 projects down, 6 to go, and I've already learned so much.

Condor perched on a rock in front at Grand Canyon.

Hello BlueSky! It seems like a lot of folks I follow share their birding pics here, so I figured I may as well start there (even though I'm not really a birder).

This is a California Condor I spotted at Grand Canyon, and thanks to its tag (01) and condorspotter.com I know it's a 12 year old male.