Kai Blin
@kblin.bsky.social
Microbiology PhD, co-author of antiSMASH, Open Source geek, views are my own. @kblin@scholar.social
Made the rookie mistake of opening linkedin. Saw a professor from Princeton claim that the step from manual coding to vibe coding is the same control vs. productivity tradeoff as C to Python, assembler to C, or machine code to assembler. 1/n
January 3, 2026 at 10:55 PM
Made the rookie mistake of opening linkedin. Saw a professor from Princeton claim that the step from manual coding to vibe coding is the same control vs. productivity tradeoff as C to Python, assembler to C, or machine code to assembler. 1/n
Dear journal editor: Inviting me to review a paper on Christmas Eve and then sending a nag email about that on the 26th is the best way to get me to decline that invitation. If your system is being stupid automatically, get a better automated system. Tell the publisher to use those APCs for it.
December 28, 2025 at 12:10 PM
Dear journal editor: Inviting me to review a paper on Christmas Eve and then sending a nag email about that on the 26th is the best way to get me to decline that invitation. If your system is being stupid automatically, get a better automated system. Tell the publisher to use those APCs for it.
Welcome to another member of the antiSMASH ecosystem of tools. When @marnixmedema.bsky.social and I were putting together antiSMASH version 1.0 15 years ago, I don't think our wildest dreams would have predicted where our little tool would go.
Merry X-SMASH!
My first first author paper is out on bioRxiv! 🖥
We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫
1/8
My first first author paper is out on bioRxiv! 🖥
We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫
1/8
December 26, 2025 at 3:38 PM
Welcome to another member of the antiSMASH ecosystem of tools. When @marnixmedema.bsky.social and I were putting together antiSMASH version 1.0 15 years ago, I don't think our wildest dreams would have predicted where our little tool would go.
Reposted by Kai Blin
Once in a while, you publish an article that fundamentally redefines your research area. I believe this is one of those moments. I huge thanks to all contributors. 🎉
Merry X-SMASH!
My first first author paper is out on bioRxiv! 🖥
We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫
1/8
My first first author paper is out on bioRxiv! 🖥
We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫
1/8
December 25, 2025 at 11:55 AM
Once in a while, you publish an article that fundamentally redefines your research area. I believe this is one of those moments. I huge thanks to all contributors. 🎉
Reposted by Kai Blin
A little Christmas gift for the molecular biology nerds! I love the simplicity of this idea: very useful (and small) plasmid selection system that alleviates the need for antibiotics in molbio and bioprocesses. Elegant work by my former PhD student, lab, and colleagues: doi.org/10.1021/acss...
tRNA-Mediated Plasmid Stabilization for Antibiotic-Free Applications in Escherichia coli
Plasmids are essential tools in molecular biology and biotechnology. In research laboratories, it is common to use antibiotic selection markers to ensure that plasmids are stably maintained in a cellu...
doi.org
December 24, 2025 at 7:39 AM
A little Christmas gift for the molecular biology nerds! I love the simplicity of this idea: very useful (and small) plasmid selection system that alleviates the need for antibiotics in molbio and bioprocesses. Elegant work by my former PhD student, lab, and colleagues: doi.org/10.1021/acss...
Apparently, all my Sonos speakers at home decided some days ago to automatically crank their volume up in the middle of the night to make sure that you really wake up in the morning.
A bit of digging shows that there's a log file on a device web page to debug which source is responsible. 1/?
A bit of digging shows that there's a log file on a device web page to debug which source is responsible. 1/?
November 20, 2025 at 8:32 AM
Apparently, all my Sonos speakers at home decided some days ago to automatically crank their volume up in the middle of the night to make sure that you really wake up in the morning.
A bit of digging shows that there's a log file on a device web page to debug which source is responsible. 1/?
A bit of digging shows that there's a log file on a device web page to debug which source is responsible. 1/?
Our old, stupid on purpose robot vacuum died. It's been hard to resist the urge to buy a more fancy, feature-rich model. But while I don't share the complete disdain of many people in tech have for "smart" devices, local control of those devices is important for me.
1/2
1/2
November 4, 2025 at 11:36 PM
Our old, stupid on purpose robot vacuum died. It's been hard to resist the urge to buy a more fancy, feature-rich model. But while I don't share the complete disdain of many people in tech have for "smart" devices, local control of those devices is important for me.
1/2
1/2
Ah, Monday morning emails. Occasionally, they come with problems that are already solved. Friday evening: got invited to review a paper. Sunday evening: got uninvited for not responding within 48 hours.
I'm aware editors have a hard time finding reviewers, but some clearly aren't really trying.
I'm aware editors have a hard time finding reviewers, but some clearly aren't really trying.
November 3, 2025 at 7:18 AM
Ah, Monday morning emails. Occasionally, they come with problems that are already solved. Friday evening: got invited to review a paper. Sunday evening: got uninvited for not responding within 48 hours.
I'm aware editors have a hard time finding reviewers, but some clearly aren't really trying.
I'm aware editors have a hard time finding reviewers, but some clearly aren't really trying.
I'm being pulled into a medical discussion that is a bit outside of my horizon, but maybe someone here can point me at some papers. A family member is hospitalised with pneumonia and seems to show adverse reactions to some of the antibiotics used.
1/?
1/?
October 27, 2025 at 1:37 PM
I'm being pulled into a medical discussion that is a bit outside of my horizon, but maybe someone here can point me at some papers. A family member is hospitalised with pneumonia and seems to show adverse reactions to some of the antibiotics used.
1/?
1/?
Reposted by Kai Blin
Bacterial telomeres are common, just not so much in RefSeq 'complete' genomes. But they can be added by the new tool David Faurdal wrote. I am thrilled to see this out as a preprint here: www.biorxiv.org/content/10.1... @tilmweber.bsky.social @thombooth.bsky.social
October 15, 2025 at 10:04 AM
Bacterial telomeres are common, just not so much in RefSeq 'complete' genomes. But they can be added by the new tool David Faurdal wrote. I am thrilled to see this out as a preprint here: www.biorxiv.org/content/10.1... @tilmweber.bsky.social @thombooth.bsky.social
Reposted by Kai Blin
Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬
And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
October 10, 2025 at 1:02 PM
Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬
The joy of being a bioinformatics person I'd that you'll get both of these
Threw away the pellet
In honour of spooky month, share a 4 word horror story that only someone in your profession would understand.
rm -rf ~/
rm -rf ~/
October 12, 2025 at 3:39 PM
The joy of being a bioinformatics person I'd that you'll get both of these
Reposted by Kai Blin
Bioinformaticians / computational biologists take note - know where you should take your OS tool chain from and do not introduce backdoors.
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:44 AM
Bioinformaticians / computational biologists take note - know where you should take your OS tool chain from and do not introduce backdoors.
Manuscript submitted. Now we only need to get that grant proposal done, and then I’ll just stay in bed for a week to catch up on all the sleep I lost in the past weeks.
September 15, 2025 at 8:06 PM
Manuscript submitted. Now we only need to get that grant proposal done, and then I’ll just stay in bed for a week to catch up on all the sleep I lost in the past weeks.
Dear Microsoft, I open your tools when I absolutely have to. When I do, I need to get work done. I never, ever want to leave a review on how much I’m enjoying that experience. Just sod off with that irritating pop up.
September 15, 2025 at 5:33 PM
Dear Microsoft, I open your tools when I absolutely have to. When I do, I need to get work done. I never, ever want to leave a review on how much I’m enjoying that experience. Just sod off with that irritating pop up.
Reposted by Kai Blin
⏰ Just 7 days left for our Glycopeptide Renaming Challenge!
💡 Share your best name idea and win 500€
👉 More info and submission here: docs.google.com/forms/d/1ym9...
#secmet #NaturalProducts #Antibiotics #NamingChallenge #Glycopeptides @gdwantibiotics.bsky.social @marghesosio.bsky.social
💡 Share your best name idea and win 500€
👉 More info and submission here: docs.google.com/forms/d/1ym9...
#secmet #NaturalProducts #Antibiotics #NamingChallenge #Glycopeptides @gdwantibiotics.bsky.social @marghesosio.bsky.social
Naming Challenge: Help Redefine the Glycopeptide Family!
We are excited to launch a naming competition inspired by the recent preprint "Phylogenetic distance and structural diversity directing a reclassification of glycopeptide antibiotics" (https://www.bio...
docs.google.com
September 8, 2025 at 12:14 PM
⏰ Just 7 days left for our Glycopeptide Renaming Challenge!
💡 Share your best name idea and win 500€
👉 More info and submission here: docs.google.com/forms/d/1ym9...
#secmet #NaturalProducts #Antibiotics #NamingChallenge #Glycopeptides @gdwantibiotics.bsky.social @marghesosio.bsky.social
💡 Share your best name idea and win 500€
👉 More info and submission here: docs.google.com/forms/d/1ym9...
#secmet #NaturalProducts #Antibiotics #NamingChallenge #Glycopeptides @gdwantibiotics.bsky.social @marghesosio.bsky.social
Reposted by Kai Blin
So the LLM synthesizes a result from various sources (that may be made up or misquoted) and then you "double-check" the sources?
Sounds like the LLM is using you as research assistant.
Sounds like the LLM is using you as research assistant.
September 8, 2025 at 1:55 PM
So the LLM synthesizes a result from various sources (that may be made up or misquoted) and then you "double-check" the sources?
Sounds like the LLM is using you as research assistant.
Sounds like the LLM is using you as research assistant.
Oh, look, the mandatory cybersecurity training that makes us log in via our SSO solution that enforces MFA is coming up with a threat scenario that only works if we weren’t using SSO with enforced MFA…
September 1, 2025 at 9:37 AM
Oh, look, the mandatory cybersecurity training that makes us log in via our SSO solution that enforces MFA is coming up with a threat scenario that only works if we weren’t using SSO with enforced MFA…
The recent video about DeltaDB by @t3.gg makes me realise how much I'm older than Theo. While the gripes about git are certainly valid, it's clear to me that Theo didn't work pre-git, and how much worse merge conflicts were back then. The line about svn being proprietary tells me he never used it.
August 29, 2025 at 2:54 PM
The recent video about DeltaDB by @t3.gg makes me realise how much I'm older than Theo. While the gripes about git are certainly valid, it's clear to me that Theo didn't work pre-git, and how much worse merge conflicts were back then. The line about svn being proprietary tells me he never used it.
This is one of my favourite genres of social media comedy.
August 16, 2025 at 8:36 PM
This is one of my favourite genres of social media comedy.
Sure, Journal of Stem Cell Research and Therapy, I would love to be on your editorial board, seeing how I have no clue about the topic at all….
August 14, 2025 at 9:15 AM
Sure, Journal of Stem Cell Research and Therapy, I would love to be on your editorial board, seeing how I have no clue about the topic at all….
Reposted by Kai Blin
📢 The Carpentries is in Forbes!
Our Directors @drkariljordan.bsky.social @erinstellabecker.bsky.social were interviewed by @jdrakephd.bsky.social for Forbes on The Carpentries' decision to withdrew from the $1.5M science grant due to new federal DEI rules: www.forbes.com/sites/johndr...
Our Directors @drkariljordan.bsky.social @erinstellabecker.bsky.social were interviewed by @jdrakephd.bsky.social for Forbes on The Carpentries' decision to withdrew from the $1.5M science grant due to new federal DEI rules: www.forbes.com/sites/johndr...
Nonprofit Refuses $1.5M Science Grant Due To New Federal DEI Rules
A coding nonprofit turned down a $1.5M NSF grant after new DEI restrictions, highlighting the clash between federal policy and scientific community values.
www.forbes.com
August 13, 2025 at 2:59 PM
📢 The Carpentries is in Forbes!
Our Directors @drkariljordan.bsky.social @erinstellabecker.bsky.social were interviewed by @jdrakephd.bsky.social for Forbes on The Carpentries' decision to withdrew from the $1.5M science grant due to new federal DEI rules: www.forbes.com/sites/johndr...
Our Directors @drkariljordan.bsky.social @erinstellabecker.bsky.social were interviewed by @jdrakephd.bsky.social for Forbes on The Carpentries' decision to withdrew from the $1.5M science grant due to new federal DEI rules: www.forbes.com/sites/johndr...
Reposted by Kai Blin
AI slop and the destruction of knowledge irisvanrooijcogsci.com/2025/08/12/a...
AI slop and the destruction of knowledge
This week I was looking for info on what cognitive scientists mean when they speak of ‘domain-general’ cognition. I was curious, because the nuances are relevant for something I am researching at t…
irisvanrooijcogsci.com
August 12, 2025 at 10:12 PM
AI slop and the destruction of knowledge irisvanrooijcogsci.com/2025/08/12/a...
Reposted by Kai Blin
Ever wondered why some antibiotics are made by Streptomyces on agar plates but not in liquid cultures? Read this work on redox control of antibiotic biosynthesis. Led by katienoble241.bsky.social and Rebecca Devine, and in collaboration with @barriewilks.bsky.social
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
journals.asm.org
August 7, 2025 at 4:30 PM
Ever wondered why some antibiotics are made by Streptomyces on agar plates but not in liquid cultures? Read this work on redox control of antibiotic biosynthesis. Led by katienoble241.bsky.social and Rebecca Devine, and in collaboration with @barriewilks.bsky.social
journals.asm.org/doi/10.1128/...
journals.asm.org/doi/10.1128/...
Reposted by Kai Blin
Over at Microbiology Resource Announcements (an @asm.org journal) we'd like to be publishing more public databases and tools, including short open source software announcements. We even have a call out!
We hope you might conisder us for your work (more in link).
journals.asm.org/journal/mra/...
We hope you might conisder us for your work (more in link).
journals.asm.org/journal/mra/...
Microbial Databases, Software Tools, and Web Services
Publish your microbial database or software tool in MRA to gain recognition, citations, and community trust.
journals.asm.org
July 28, 2025 at 4:08 PM
Over at Microbiology Resource Announcements (an @asm.org journal) we'd like to be publishing more public databases and tools, including short open source software announcements. We even have a call out!
We hope you might conisder us for your work (more in link).
journals.asm.org/journal/mra/...
We hope you might conisder us for your work (more in link).
journals.asm.org/journal/mra/...