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Pat Schloss @patschloss.bsky.social · Sep 3

"Live free or die"... hmmm.

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Pat Schloss @patschloss.bsky.social · Aug 31

more officially this: www.nlm.nih.gov/pubs/techbul...

NCBI To Discontinue Sequence Read Archive and Peptidome. NLM Technical Bulletin. 2011 Jan–Feb

The NLM Technical Bulletin is your source to stay informed about NLM products and services.

www.nlm.nih.gov

Pat Schloss @patschloss.bsky.social · Aug 31

I recall it being pretty serious at the time, it wasn't an intellectual exercise. See the discussion in pmc.ncbi.nlm.nih.gov/articles/PMC...

The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection

The 19th annual Database Issue of Nucleic Acids Research features descriptions of 92 new online databases covering various areas of molecular biology and 100 papers describing recent updates to the da...

pmc.ncbi.nlm.nih.gov

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Pat Schloss @patschloss.bsky.social · Aug 30

My google skills are failing... Back in 2011, NCBI (started to?) close the SRA. The SRA is still with us. Anyone know of any articles from around then about how they saw the light? For those that this is news to...

genomebiology.biomedcentral.com/articles/10....

Closure of the NCBI SRA and implications for the long-term future of genomics data storage - Genome Biology

genomebiology.biomedcentral.com

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Pat Schloss @patschloss.bsky.social · Aug 15

I know things are hard right now. But, if you are going to review proposals submitted to a special PA, please at least read the PA before reviewing proposals submitted to the PA. I mean, if it says no biological questions allowed, don't ding me for not proposing to answer biological questions.

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Pat Schloss @patschloss.bsky.social · Aug 13

CONGRATS!

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Pat Schloss @patschloss.bsky.social · Jul 31

I'm offering a new workshop that's part instruction, part group coaching. This program will focus on the design principles we should consider when generating visuals. There won't be any coding so don't let that hold you back shop.riffomonas.org/products/tra...

Transform your data visualizations in 5 weeks - no judgement, no code

shop.riffomonas.org

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Pat Schloss @patschloss.bsky.social · Jul 31

my pleasure - thanks for the shout out!

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Pat Schloss @patschloss.bsky.social · Jul 25

Mary and I danced to a piano version of "Where Is My Mind" at her wedding two years ago. All the other the Gen X dads all appreciated the choice www.youtube.com/watch?v=90Fp...

Maxence Cyrin - Where is my mind - Official 2018 Video (The Pixies Piano cover)

YouTube video by Maxence Cyrin

www.youtube.com

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Reposted by Pat Schloss

Vaughn Cooper @vscooper.micropopbio.org · Jun 8

Sharing the most significant work from my group, led by the @evolvingstem.bsky.social team.

Come for the discoveries of how Pseudomonas adapts in biofilms, stay for the story of how they were discovered by thousands of young scientists in grades 9-12. 🧪🧫🧬🧵

www.biorxiv.org/content/10.1...

Student-led experimental evolution reveals novel biofilm regulatory networks underlying adaptations to multiple niches

We established a research-education partnership known as EvolvingSTEM that provides secondary school students the opportunity to conduct authentic research experiments centered on microbial evolution....

www.biorxiv.org

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Pat Schloss @patschloss.bsky.social · Apr 16

May I also now apologize for the roughly 2543 times I have said "Harvard sucks".

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Pat Schloss @patschloss.bsky.social · Apr 16

If you've been putting off learning how to make plots in R with ggplot2, then have I got what you need! I'll be teaching a zoom-based workshop on just that subject. This will be a one day all ggplot2 workshop on May 9th shop.riffomonas.org/products/int...

Introduction to ggplot2 and the grammar of graphics

shop.riffomonas.org

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Pat Schloss @patschloss.bsky.social · Apr 16

If the folks at @umich.edu need help with web design I'm sure the designers of harvard.edu would be happy to help

Harvard University

Harvard University is devoted to excellence in teaching, learning, and research, and to developing leaders who make a difference globally.

harvard.edu

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Pat Schloss @patschloss.bsky.social · Mar 3

en.wikipedia.org/wiki/Altered...

Altered Schaedler flora - Wikipedia

en.wikipedia.org

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Pat Schloss @patschloss.bsky.social · Feb 27

Just to be clear... there are two editorials. I appreciate the love for the other one on supporting science, but I don't want this one on diversifying science to get lost

Pat Schloss @patschloss.bsky.social · Feb 27

My editorial simultaneously published in all of @asm.org's journals addresses the ongoing effort by the administration to halt efforts to diversify science. It should be obvious from ASM Journals' efforts over the years, but we aren't fans journals.asm.org/doi/10.1128/...

A call for healing and unity | mBio

Executive orders signed since 20 January 2025 aim to end programs intended to diversify the scientific workforce via equitable and inclusive practices and processes; cut federal funding for research and innovation; and stifle scientific communications. They represent a stunning reversal of policies that have been the bedrock of the U.S. scientific research enterprise and its leadership in the world, and therefore not surprisingly they have been met with a number of legal challenges. Some of the executive orders have been blocked by temporary restraining orders, and others are pending judicial review.

journals.asm.org

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Pat Schloss @patschloss.bsky.social · Feb 27

My editorial simultaneously published in all of @asm.org's journals addresses the ongoing effort by the administration to halt efforts to diversify science. It should be obvious from ASM Journals' efforts over the years, but we aren't fans journals.asm.org/doi/10.1128/...

A call for healing and unity | mBio

Executive orders signed since 20 January 2025 aim to end programs intended to diversify the scientific workforce via equitable and inclusive practices and processes; cut federal funding for research and innovation; and stifle scientific communications. They represent a stunning reversal of policies that have been the bedrock of the U.S. scientific research enterprise and its leadership in the world, and therefore not surprisingly they have been met with a number of legal challenges. Some of the executive orders have been blocked by temporary restraining orders, and others are pending judicial review.

journals.asm.org

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Pat Schloss @patschloss.bsky.social · Feb 27

The @asm.org Journals Committee has published a response to the recent disruptions in science in the US... A call for the United States to continue investing in science | mBio journals.asm.org/doi/10.1128/...

A call for the United States to continue investing in science | mBio

The U.S. life science research mission is critical not only to human health and understanding the natural world but also to agriculture and food production, technological innovations, socioeconomic pr...

journals.asm.org

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Pat Schloss @patschloss.bsky.social · Feb 21

Hey folks! Over the past few weeks I've been posting videos recreating several of W.E.B. DuBois's "data portraits" from the 1900 Paris Exhibition in #Rstats using only {tidyverse} and {showtext}. I have 4 up now and there will be 4 more over the next 2 weeks www.youtube.com/playlist?lis...

DuBois recreations - YouTube

www.youtube.com

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Reposted by Pat Schloss

Jo Handelsman, PhD @johandelsman.bsky.social · Feb 13

"Make America Great Again. Make America Healthy Again. These were promises made by candidate Trump in his campaign to be president of the United States of America. What in this campaign platform should have prepared us for a war on discovery?"

Guest column: “The war on discovery” is antithesis of campaign pledge to make America great again - Wisconsin Technology Council

By Jo Handelsman MADISON, Wis. – Make America Great Again. Make America Healthy Again. These were promises made by candidate Trump in his campaign to be president of the United States of America. What...

wisconsintechnologycouncil.com

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Pat Schloss @patschloss.bsky.social · Jan 27

Folks can check out how I'd make this visualization with ggplot2 here (another from the same article will be available on Thursday): youtu.be/RCo85v7zt08

Visualizing changes in kindergarten vaccination rates with dplyr and ggplot2 (CC336)

YouTube video by Riffomonas Project

youtu.be

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Pat Schloss @patschloss.bsky.social · Jan 14

Every bit of this package was developed as part of my Riffomonas YouTube channel. You can watch its development through this playlist www.youtube.com/playlist?lis...

R package development - YouTube

Join Pat as he creates a new R package

www.youtube.com

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Pat Schloss @patschloss.bsky.social · Jan 14

Happy to share that a manuscript describing my {phylotypr} R package has been released on Microbiology Resource Announcements. {phylotypr} is an R-based implementation of the naive Bayesian classifier, aka the RDP classifier: journals.asm.org/doi/epdf/10....

phylotypr: an R package for classifying DNA sequences

You have to enable JavaScript in your browser's settings in order to use the eReader.

journals.asm.org

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Pat Schloss @patschloss.bsky.social · Jan 8

That's a classic! I knew exactly what it was without clicking the link 🤓

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Pat Schloss @patschloss.bsky.social · Jan 7

My first thing on this platform (what are the things called?).

Pat Schloss @patschloss.bsky.social · Jan 7

What's your favorite plot that you've seen recently?
What's the most 🔥💩 plot that you've seen recently?

I'm getting headaches looking through 42 part figures that are full of over bolded prism plots, 58 by 287 heat maps with attached dendrograms, or balls of yarn attempting to show interactions

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Pat Schloss @patschloss.bsky.social · Jan 7

What's your favorite plot that you've seen recently?
What's the most 🔥💩 plot that you've seen recently?

I'm getting headaches looking through 42 part figures that are full of over bolded prism plots, 58 by 287 heat maps with attached dendrograms, or balls of yarn attempting to show interactions

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