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Mike Schatz

@mikeschatz.bsky.social

4.7K followers 870 following 180 posts

Bloomberg Distinguished Professor at Johns Hopkins University. http://schatz-lab.org

schatz-lab.org

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Mike Schatz @mikeschatz.bsky.social · Jun 2

Today (June 1) marks the 20th anniversary of Galaxy! Thanks to all the developers, admins, researchers, trainers, educators, students and more that have made up this amazing community. Here is to the next 20 years! @galaxyproject.bsky.social @jxtxfoundation.bsky.social galaxyproject.org

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Reposted by Mike Schatz

Rob Patro @robp.bsky.social · 11h

Have you recently completed (or finishing soon) a PhD in CS or a related discipline? Do you want to do research advancing the theory & practice of algorithmic genomics & build tools that people love to use? I'll be looking to hire a postdoc! Official ad coming soon:
docs.google.com/document/d/1...

Postdoc Description.docx

Title: Postdoctoral Associate Summary statement: The postdoctoral research associate is responsible for developing novel computational methodology for high-throughput sequence genomics tasks, as well ...

docs.google.com

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Mike Schatz @mikeschatz.bsky.social · 16d

After vibe coding a little swift this summer, I feel totally validated by this post! holdtherobot.com/blog/xcode-i...

Xcode is the Worst Piece of Professional Software I Have Ever Used | Hold The Robot

The compiler is unable to type-check this expression in reasonable time; try breaking up the expression into distinct sub-expressions

holdtherobot.com

Mike Schatz @mikeschatz.bsky.social · 21d

Easy! We dont we change the USA to the metric system too while we are at it!

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Mike Schatz @mikeschatz.bsky.social · 22d

zcat reads.fq | paste - - - - | awk '{print $2}'

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Mike Schatz @mikeschatz.bsky.social · 23d

This is amazing

Bede Constantinides @bedec.bsky.social · 29d

Zstandard's --long range mode works wonders for assemblies, but needs uninterrupted single line sequences.

*AllTheBacteria 661k, multiline fasta*
gzip (pigz): 751GB
zstandard --long: 641GB (30% original size)

*Single line fasta*
gzip (pigz): 700GB
zstandard --long: 232GB (10% original size)

Reposted by Mike Schatz

Galaxy Project @galaxyproject.bsky.social · 28d

after a long effort, gathering a lot of input from many people, we finaly put it all together:
Ten Common Misconceptions About Galaxy (and Why They Are Wrong!)
https://www.preprints.org/manuscript/202509.0823
Thank you very much to all people involved !

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Reposted by Mike Schatz

Heng Li @lh3lh3.bsky.social · 29d

minimap2.com is potentially a phishing site. Please don't use anything from that website.
github.com/lh3/minimap2...

Phishing site : minimap2.com · Issue #1316 · lh3/minimap2

Not sure how to label this one, but I have come across a website minimap2.com which appears to be AI generated but is serving it's own copy of the Github repository. If you search the address or em...

github.com

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Reposted by Mike Schatz

Galaxy Project @galaxyproject.bsky.social · Sep 8

🎉 Big news! Galaxy Training Network workflows are now automatically registered on WorkflowHub.
Easier discovery, citation, & direct Galaxy execution → boosting FAIR & accessible training!

training.galaxyproject.org/training-mat...

GTN is now integrated with WorkflowHub

Thanks to a collaborative effort between the teams at Galaxy Training Network (GTN), WorkflowHub, and Australian BioCommons, GTN workflows are now registered automatically with WorkflowHub. The existi...

training.galaxyproject.org

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Mike Schatz @mikeschatz.bsky.social · Sep 3

I dont think this is totally up to date, but I bet this still generally reflects the overall distribution in capacity: enseqlopedia.com/ngs-mapped/

NGS Mapped - Enseqlopedia

enseqlopedia.com

Mike Schatz @mikeschatz.bsky.social · Sep 3

Ten trillion years ago we tried to track this down from and predicted we should be about exabyte range now, but I have not tried to revise this estimate since. journals.plos.org/plosbiology/...

Big Data: Astronomical or Genomical?

This perspective considers the growth of genomics over the next ten years and assesses the computational needs that we will face relative to other "Big Data" activities such as astronomy, YouTube, and...

journals.plos.org

Mike Schatz @mikeschatz.bsky.social · Sep 3

My strong belief is there is much more sequencing going on in private companies (especially diagnostics) than academic work so just looking at SRA/ENA will substantially undercount

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Mike Schatz @mikeschatz.bsky.social · Sep 3

This is a hard number to track. Illumina, PacBio, & ONT are publicly traded companies so you can get an estimate of instruments & reagents sold from their disclosures, but that doesnt mean they are actively being used by their customers at full capacity.

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Reposted by Mike Schatz

Brian Umberger @brianumberger.bsky.social · Aug 28

Please repost!

We have an open rank, tenure-line faculty position in biomechanics in the School of Kinesiology at the University of Michigan Ann Arbor. At U-M we have great colleagues, exceptional resources, and biomechanics can be found all across the campus. #BiomechSky

Tenure-track Faculty Position in Biomechanics (Open Rank), University of Michigan, Ann Arbor, MI, USA - Biomch-L

The School of Kinesiology (http://kines.umich.edu) at the University of Michigan invites applications and nominations for a tenure-track faculty position at the level of Assistant Professor, Associate...

biomch-l.isbweb.org

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Mike Schatz @mikeschatz.bsky.social · Aug 26

Scholarships available for Genome Informatics - just include a brief summary on your open science work plus your conference abstract. If you have already paid to register, we will work with CSHL to refund you the $$$. Apply today! jxtxfoundation.org/news/2025-6-... @jxtxfoundation.bsky.social

JXTX + CSHL 2025 Genome Informatics Scholarship

JXTX + CSHL 2025 Genome Informatics Scholarships

jxtxfoundation.org

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Reposted by Mike Schatz

Ben Langmead @benlangmead.bsky.social · Aug 26

📢🚨📢🚨 Genome Informatics deadline extended to September 8! meetings.cshl.edu/meetings.asp....
Please spread the word. If you are like me and had at least one abstract that wasn't quite ready by last week's deadline, you get another swing. See you there!

Genome Informatics

Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

meetings.cshl.edu

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Mike Schatz @mikeschatz.bsky.social · Aug 26

Genome Informatics abstract deadline now Sept 8! h/t @benlangmead.bsky.social meetings.cshl.edu/meetings.asp...

Genome Informatics

Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

meetings.cshl.edu

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Mike Schatz @mikeschatz.bsky.social · Aug 26

Checking out the new JHU student center! Super impressive inside! @jhu.edu

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Reposted by Mike Schatz

JHU Computer Science @jhucompsci.bsky.social · Aug 22

Johns Hopkins researchers including @mikeschatz.bsky.social & @vikramshivakumar.bsky.social have developed Uncalled4, a new software toolkit that can detect epigenetic changes—chemical modifications to normal DNA and RNA that control which genes are turned off and on—with unprecedented accuracy.

Researchers build a smarter tool for reading genetic code

The Hopkins team’s new, open-source software dramatically improves scientists’ ability to detect genetic modifications that control gene activity.

www.cs.jhu.edu

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Reposted by Mike Schatz

Galaxy Project @galaxyproject.bsky.social · Aug 18

🎉 Galaxy has passed 21,000 citations on Google Scholar!
A huge thank you to the global community of researchers who use and advance Galaxy for open, reproducible science.

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Mike Schatz @mikeschatz.bsky.social · Aug 15

Amazing line up! So sad to miss it

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Mike Schatz @mikeschatz.bsky.social · Aug 9

This popped up in my feed today: adele.pollux.casa/gemlog/2025-...

Human check

adele.pollux.casa

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Mike Schatz @mikeschatz.bsky.social · Aug 7

Just started! openai.com/live/

Mike Schatz @mikeschatz.bsky.social · Aug 7

Individual academics probably don’t have enough clout to apply any real pressure although if we band together we maybe do. This could be a good topic for GA4GH or another society to address

Mike Schatz @mikeschatz.bsky.social · Aug 7

Another dimension to this is when code should be directly interacting with files vs leveraging an API. As datasets get increasingly large I see API based access becoming more popular, especially for data in the cloud

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Mike Schatz @mikeschatz.bsky.social · Aug 7

And as much as I hate fastq, at least it doesnt have vendor lock in. As recently as yesterday I was fighting with cbcl files that could only be converted by bcl-convert (closed source/closed binary from Illumina)

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