iiinova — where your digital self keeps evolving

Greg Caporaso @cap-lab.bio · 02/07/2025

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".

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Reposted by Greg Caporaso

QIIME 2 @qiime2.org · 12/12/2024

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

forum.qiime2.org

QIIME 2 2024.10 is now available!

The QIIME 2 2024.10 release is now available! Thanks to everyone involved for their hard work! 🙌🏼 🎉 As a reminder, our next planned QIIME 2 release is scheduled for April 2025 (QIIME 2 2025.4), but p...

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Greg Caporaso @cap-lab.bio · 14/11/2024

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....

microbiomejournal.biomedcentral.com

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...

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Reposted by Greg Caporaso

QIIME 2 @qiime2.org · 14/11/2024

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...

doi.org

Upcycling Human Excrement: The Gut Microbiome to Soil Microbiome Axis (supporting data)

This archive contains the supporting data and code for Meilander et al., 2024: Upcycling Human Excrement: The Gut Microbiome to Soil Microbiome Axis. Clicking the links below will open the correspon...

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Greg Caporaso @cap-lab.bio · 12/04/2024

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.

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Reposted by Greg Caporaso

QIIME 2 @qiime2.org · 19/02/2024

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!

forum.qiime2.org

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...

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Reposted by Greg Caporaso

Sean Gibbons 🦠💩 @gibbological.bsky.social · 08/12/2023

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...

youtube.com

2023 ISB Microbiome Series

Share your videos with friends, family, and the world

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Reposted by Greg Caporaso

Michael Love @mikelove.bsky.social · 30/11/2023

Provenance is so important

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Reposted by Greg Caporaso

Lina Kim @linathekim.bsky.social · 30/11/2023

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

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Greg Caporaso @cap-lab.bio · 29/11/2023

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...

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

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Greg Caporaso @cap-lab.bio · 18/11/2023

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...

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Greg Caporaso @cap-lab.bio · 18/11/2023

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.

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Greg Caporaso @cap-lab.bio · 13/11/2023

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.

Condor perched on a rock in front at Grand Canyon.

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