iiinova — where your digital self keeps evolving

Reposted by Tessa Pierce Ward, PhD

Titus Brown @titus.idyll.org · 08/09/2025

There are two recent papers that use sourmash in creative ways - and it gladdens my heart! pubmed.ncbi.nlm.nih.gov/40812187/ by @silask.bsky.social et al looks cleverly at human gut subspecies. www.biorxiv.org/content/10.1... by @rayanchikhi.bsky.social et al counts billions of k-mers. Super neat!

pubmed.ncbi.nlm.nih.gov

Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research - PubMed

Microbial strains within a single species can exhibit distinct functional characteristics due to variations in gene content and often show individual specificity, which can obscure unbiased associatio...

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Reposted by Tessa Pierce Ward, PhD

Amy D Willis @amydwillis.bsky.social · 29/06/2025

We had a last minute cancellation for STAMPS -- a phenomenal course on microbiome data analysis. Woods Hole, MA, July 14-24 2025. If you or *anyone* you know is interested to attend, please email Titus &/or me... and we'll do what we can!!! Thx for sharing widely! 🤞❤️

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Reposted by Tessa Pierce Ward, PhD

Joshua Weitz @joshuasweitz.bsky.social · 23/06/2025

The #SCIMaP team announces a major update: an analysis of the economic impacts of the White House's NIH FY26 budget. Bottom-line, we estimate $46B in total economic loss, 202K lost jobs, and impacts in communities nationwide. Interactive map and shareable report: scienceimpacts.org/fy26 a 🧵

Economic loss due to NIH budget cuts by congressional district, scienceimpacts.org/fy26

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Reposted by Tessa Pierce Ward, PhD

Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 05/06/2025

My HPC team at UC Davis is hiring! Looking for an experienced sysadmin to help build and maintain clusters (hardware and software). HPC experience great, but if you’re an experienced sysadmin and willing to learn, please apply! careerspub.universityofcalifornia.edu/psc/ucdavis/...

careerspub.universityofcalifornia.edu

An error has occurred.

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Reposted by Tessa Pierce Ward, PhD

Titus Brown @titus.idyll.org · 15/05/2025

Another super cool bioinformatics tool (this one using pyani and sourmash) - genomeRxiv, for exploring multiscale taxonomic relationships between genomes. From @borisvinatzer.bsky.social group, by Reza Mazloom, and also with Lenny Heath - all at VT.

genomerxiv.cs.vt.edu

GenomeRxiv

A pure CSS toggle switch for form input checkboxes

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Reposted by Tessa Pierce Ward, PhD

Jesse Raab @jraab.bsky.social · 21/02/2025

For whatever reason, the US government have decided the US should no longer lead in science. Great economic opening for other countries, but really bad for America. This could be stopped by a handful of majority senators. That they aren't doing it tells you they want us to cede 70 years of building

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Reposted by Tessa Pierce Ward, PhD

Deborah Blum @deborahb.bsky.social · 06/01/2025

As we start the new year, I would like to remind everyone that it is now almost 120 years since the US decided consumer protection - by which I mean regulation - mattered. Given the upcoming presidential inauguration, let's talk about how that happened - and why it's so important. (A thread)

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Titus Brown @titus.idyll.org · 27/12/2024

Hi all, here's my passion project for December - a Web site for ~realtime DNA sample screening/composition analysis. Let me know what you think!

ivory.idyll.org

Announcing: the chill-filter Web site - DNA sample composition at a glance!

what's in my sample, dude?

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Titus Brown @titus.idyll.org · 16/12/2024

Regularly tempted to write in my NIH grants innovation section: "Funding software that already exists and works well would be highly innovative for the NIH." (I bet half the panel would break down ROFL, but I'm also highly skeptical that I'd get a good score, or that the PO would be amused.)

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Reposted by Tessa Pierce Ward, PhD

Ketan Joshi @ketanjoshi.co · 08/12/2024

40% of the mass of everything transported by a ship in 2023 was a fossil fuel. That stat paired with this new study shines a pretty harsh spotlight on how obscenely bad-faith the right-wing concern trolling around offshore wind + whales is www.seattletimes.com/seattle-news...

seattletimes.com

UW study finds leading cause of whale deaths

New research shows that the top threat to whales around the globe has changed. But it wouldn't take much to reduce the risk, researchers say.

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Reposted by Tessa Pierce Ward, PhD

David Shiffman, Ph.D. 🦈 @whysharksmatter.bsky.social · 04/12/2024

I've been putting off sending a professional email since July because I've dreaded the response. I sent it today, and received a reply of "no worries that's fine" in about three minutes. I will learn nothing from this.

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Pierre Peterlongo @pierrepeterlongo.bsky.social · 11/11/2024

🧬🔍There are 50 petabases of freely-available DNA sequencing data. We introducing Logan Search which allows you to search for any DNA sequence in minutes, bringing Earth’s largest genomic resource to your fingertips. 🏔️ logan-search.org 🏔️ #Genomics #Bioinformatics #OpenScience

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Tessa Pierce Ward, PhD @bluegenes.bsky.social · 02/12/2024

This was an interesting take on software dev, and gave me a generalized perspective on some of the challenges we've faced with sourmash over time. www.baldurbjarnason.com/2022/theory-.... Thanks @luizirber.bsky.social for sharing!

baldurbjarnason.com

Theory-building and why employee churn is lethal to software companies

Web dev at the end of the world, from Hveragerði, Iceland

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Tessa Pierce Ward, PhD @bluegenes.bsky.social · 30/11/2024

These grapes were beautiful, inside and out.

View with grape vines in the foreground and rolling hills with trees in the background. Cloudy sky with the beginnings of yellow sunset.

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Reposted by Tessa Pierce Ward, PhD

Itai Yanai @itaiyanai.bsky.social · 09/11/2024

Doing good science is 90% finding a science buddy to constantly talk to about the project.

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Reposted by Tessa Pierce Ward, PhD

George Matsumoto @georgeimatsumoto.bsky.social · 20/11/2024

🧪 🍎 📍 🌊 🦑 pathwaystoscience.org Paid Summer 2025 Undergraduate Research Placements; financial support in graduate school; tips on applications and other resources; opportunities in ocean sciences and engineering

pathwaystoscience.org

Pathways To Science | Increasing Diversity in STEM

Offering a directory of 1,000+ scholarships, fellowships, internships, and postdoc positions in STEM, with emphasis on supporting underrepresented students.

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Tessa Pierce Ward, PhD @bluegenes.bsky.social · 26/11/2024

It’s been a pleasure to co-mentor on this project, excited about the progress!

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Reposted by Tessa Pierce Ward, PhD

Wei Shen 沈伟 @shenwei356.bsky.social · 20/11/2024

Just updated taxid-changelog. Now you can track each NCBI Taxonomy taxon's detailed changes in the past 10 years😮😱😃 This is the proudest work I've done in my past 10+ year academic career, cause it's useful and funny but no one else did this, haha. github.com/shenwei356/t...

github.com

Release taxid-changelog v2024.11 · shenwei356/taxid-changelog

This version includes taxdump files of "2013-02-21", "2013-05-03", "2014-06-03","2014-07-22" $ zcat taxid-changelog.csv.gz \ | csvtk grep -f taxid -p 562 \ | csvtk cut -f -lineage-taxids \...

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Reposted by Tessa Pierce Ward, PhD

Rob Patro @robp.bsky.social · 18/11/2024

This is a very important idea, and worthwhile for those developing bioinformatics software to consider. One massive shortcoming, over which the scientists & devs have quite little control, however, is the huge dearth in funding software dev & maintenance. Software is its own product & requires $!

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Reposted by Tessa Pierce Ward, PhD

Zamin Iqbal @zaminiqbal.bsky.social · 15/11/2024

Align to AllTheBacteria with low RAM (1-2Gb) and quickly (seconds if just 1000s of hits, 15 mins for a gene present in all 2.4 million genomes) using @shenwei356.bsky.social Lexicmap. So you can basically BLAST AllTheBacteria locally - but need 3-4Tb disk for index www.biorxiv.org/content/10.1...

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Reposted by Tessa Pierce Ward, PhD

Stephen Turner @stephenturner.us · 15/11/2024

A thread with some new starter packs in genomics and bioinformatics 🧵 1/13...

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Reposted by Tessa Pierce Ward, PhD

Rob Patro @robp.bsky.social · 12/11/2024

I made a starter pack for algorithmic genomics. It's certainly incomplete, but already has a ton of awesome peeps. Let me know if you know people I should add (with a focus on algorithms and data structures in genomics) go.bsky.app/TRWCnZs

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Reposted by Tessa Pierce Ward, PhD

John Wiswell @wiswell.bsky.social · 05/10/2024

It's important to realize how long scientists have warned those in power. Climate change is not somebody's fault for not recycling beer cans. It's the result of a fraud against the public by corporations who have flooded the zone with bribes and misinformation.

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Reposted by Tessa Pierce Ward, PhD

Dan Portik @dportik.bsky.social · 24/09/2024

Don't miss out on this free #metagenomics webinar next week! PacBio HiFi sequencing on Revio can be used to generate single-contig, complete MAGs from the most difficult sample type to assemble - soil. Results for wetland and grassland soil shown here, from my talk at LAMG. bit.ly/3Tf9qJj

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Reposted by Tessa Pierce Ward, PhD

Titus Brown @titus.idyll.org · 20/02/2024

We released a nice new version of sourmash, along with a super nice new version of the branchwater plugin - faster! lower memory! more convenient! better code! more zhuzh! Hat tip to @bluegenes.bsky.social and @luizirber.bsky.social who did all the hard work here!

ivory.idyll.org

Speeding sourmash the heck up

Faster things are always nice, right?

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Reposted by Tessa Pierce Ward, PhD

Harriet Alexander @nekton4plankton.bsky.social · 16/11/2023

So branchwater.sourmash.bio is really awesome... Check it out metagenome pals. I queried 700k+ metaG in <2 minutes. 💻🧬🧪 Major HT to @luizirber.bsky.social @ctitusbrown.bsky.social @bluegenes.bsky.social and others.

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Tessa Pierce Ward, PhD @bluegenes.bsky.social · 20/11/2023

Neat!! Murderbot (especially with narration by Kevin R Free) is such a comfort read for me.

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Amy H Fitzpatrick @amyhfitzpatrick.bsky.social · 31/10/2023

Do you use #wastewater for #virus surveillance? Do you mine the #SRA or #ENA looking for novel viruses? Please fill out this survey about #metadata ec.europa.eu/eusurvey/run... #ReTweet #BioHackEU23 #ElixirEurope

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Sherri Rose @sherrirose.bsky.social · 27/09/2023

I'm hiring an Open Science Rigor & Reproducibility Software Developer at Stanford! Great mix of work developing best practices, coding, and independence to propose new initiatives. careersearch.stanford.edu/jobs/open-sc... Hybrid & remote eligible within the United States. #stats #academicsky

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