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Nicholas Cooley

@npcooley.bsky.social
159 followers 215 following 40 posts

R, Bioinformatics, Organic Chemistry, and oh look a bird! github.com/npcooley

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Nicholas Cooley @npcooley.bsky.social · 21/09/2026
Hi folks! We are running a Developer Survey for Bioconductor through the end of september! If you want to have a say in our priorities and infrastructure choices, please give us your feedback and opinions! survey link: forms.gle/WWCZAX7uuPfr...
forms.gle
Bioconductor developer survey
Thank you for taking the time to complete this Bioconductor developer survey. For the purposes of this survey, "developer" includes package developers as well as contributors involved in documentation...
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Nicholas Cooley @npcooley.bsky.social · 21/09/2026
Bioconductor's September Developer Forum is taking place this thursday at 4pm UTC! Join us for Andrew Ghazi presenting on approaches for improving R packages! Registration Link: us06web.zoom.us/meeting/regi...
us06web.zoom.us
Welcome! You are invited to join a meeting: September Developer Forum. After registering, you will receive a confirmation email about joining the meeting.
This talk will focus on approaches for improving R packages. First we'll go over identifying and managing heavy dependencies using havel and rlang. Then we'll cover examining performance with bench an...
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Nicholas Cooley @npcooley.bsky.social · 26/08/2026
Join us tomorrow for Bioconductor's August developer forum! We'll have Sebastian Fischer talking about {anvl} and GPU access in R! lnkd.in/p/evtbmntQ
lnkd.in
📢 Join the August Bioconductor Developers' Forum! Interested in high-performance computing for R? This month's Developers' Forum will introduce {anvl}, an array computing framework that s...
📢 Join the August Bioconductor Developers' Forum! Interested in high-performance computing for R? This month's Developers' Forum will introduce {anvl}, an array computing framework that supports auto...
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Nicholas Cooley @npcooley.bsky.social · 25/06/2026
We are holding our monthly Bioconductor Developer Forum today at 4pm UTC! www.linkedin.com/posts/biocon...
linkedin.com
#bioconductor | Bioconductor
🧬 Upcoming Bioconductor Developers' Forum 📅 June 25, 2026 🕓 4 PM UTC 🎤 Szabolcs Horvát Topic: igraph: Complex network analysis across multiple programming languages As Bioconductor continues to exp...
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Nicholas Cooley @npcooley.bsky.social · 17/06/2026
Join us for this month's developer forum, coming up next week!
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Nicholas Cooley @npcooley.bsky.social · 07/12/2024
Back on my bullshit. (emailing ridiculous questions about edirect to the nlm support email at weird hours)
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MU-Peter Shimon 🀄 @mu-peter.bsky.social · 25/04/2024
☀️ Fiat lux! Evidence for a single origin of bioluminescence in Octocorallia and infers the age of occurrence to around the Cambrian era, approximately 540 Mya Evolution of bioluminescence in Anthozoa with emphasis on Octocorallia 🧪 royalsocietypublishing.org/doi/10.1098/...
Phylogeny of Octocorallia with bioluminescent ancestral states. Newly time-calibrated tree adapted from McFadden et al. [19] using UCE data. Traits were defined as bioluminescent (species or genus-level record), non-bioluminescent (negative record) or unknown (no record). Taxon branches are colour coded based on known genus-level depth ranges (green, shallow < 200 m; purple, deep > 200 m; blue, shallow/deep range spans both). Ancestral depth range estimates are from electronic supplementary material, figure S4. The two major clades represent the orders Malacalcyonacea (purple) and Scleralcyonacea (pink).
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Nicholas Cooley @npcooley.bsky.social · 16/04/2024
We found ourselves wondering why some closely related genomes had very different rates of pseudogenization, and whether those rate differences were real or not. It turns out there was a whole lot to that story, and it's finally published!
bmcgenomics.biomedcentral.com
Many purported pseudogenes in bacterial genomes are bona fide genes - BMC Genomics
Background Microbial genomes are largely comprised of protein coding sequences, yet some genomes contain many pseudogenes caused by frameshifts or internal stop codons. These pseudogenes are believed ...
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Nicholas Cooley @npcooley.bsky.social · 12/04/2024
Who has two thumbs and wasted almost a week of work because they forgot that the default genetic code wasn’t the bacterial genetic code? This guy!
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Nicholas Cooley @npcooley.bsky.social · 21/02/2024
For anyone interested, we’re hosting a special session on Scalable Analysis for Big Biological data at GLBio here in Pittsburgh this summer! I believe applications close this Friday! We’d love to hear your large scale compute stories! www.iscb.org/glbio2024/programme-sc…
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Nicholas Cooley @npcooley.bsky.social · 17/01/2024
Doing bioinformatics work is basically just an endlessly repeating version of that Doctor Who meme where someone asks the Doctor ‘is 4 a lot?’ and he replies ‘Depends on the context!’ with new and exciting values and contexts.
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Nicholas Cooley @npcooley.bsky.social · 25/12/2023
Type 2 fun accomplished!
Triumph Completion notification for Solo-ing Warlord's Ruin in Destiny 2.
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Per-Ola Norrby @peonor.bsky.social · 12/12/2023
We need a chemist to work on high throughput synthesis at AstraZeneca in Gothenburg careers.astrazeneca.com/job/gothenbu...
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Nicholas Cooley @npcooley.bsky.social · 07/12/2023
Solidarity forever.
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Marnix Medema @marnixmedema.bsky.social · 05/12/2023
We are looking for a new colleague to work on ML/AI in bioinformatics! Come join WUR Bioinformatics as assistant/associate professor in a wonderful scientific ecosystem. Please RT! www.academictransfer.com/en/335162/as...
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Nicholas Cooley @npcooley.bsky.social · 03/12/2023
It’s usually easy for me to forget that I’m colorblind, but some things, like trying to find the red tabbed connectors for the lights on our Christmas tree, definitely remind me.
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Jeremy Kamil @macroliter.bsky.social · 21/11/2023
🧪 3 tenure-track microbiome faculty job openings in Hawaii! 🌞 🏄🏽‍♀️ 🍄 🧫 🧬 🦃
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Nicholas Cooley @npcooley.bsky.social · 29/11/2023
Staring blankly into the abyss when suddenly the abyss says snidely “I see you forgot to add a progress bar to this function.”
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Nicholas Cooley @npcooley.bsky.social · 22/11/2023
Back on my bullshit (submitting a couple thousand jobs on the first day of vacation, so I can neurotically check in on them when I’m supposed to be relaxing).
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Kevin Verhoff @kevinverhoff.bsky.social · 31/10/2023
Happy Halloween! Reminder to slow the F down if you’re driving today!
A chart showing the number of pedestrian deaths in the US by day of the year. There is a big spike, particularly for kids, on Oct 31st.
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Curtis Suttle @virosphere.bsky.social · 27/10/2023
Please share: @UBCScience is searching for 15 TT faculty in diverse areas of expertise science.ubc.ca/about/careers. Included are 2 positions in Quantitative and Environmental Science as part of a hiring cluster for black faculty; you will join 6 current UBC faculty science.ubc.ca/blackscholars.
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Nicholas Cooley @npcooley.bsky.social · 28/10/2023
In hindsight, reading a grant review on a Saturday morning was not my best life choice.
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Keith Robison @omicsomics.bsky.social · 21/10/2023
Summer 2024 bioinformatics internship at @Ginkgo in the NGS group. Spectacular opportunity 🧬🖥️ www.linkedin.com/jobs/view/37...
linkedin.com
Ginkgo Bioworks, Inc. hiring NGS Bioinformatics Intern (2024) in United States | LinkedIn
Posted 6:28:59 PM. **Please note this is an internship role for 3 months, full-time hours, from end of May -…See this and similar jobs on LinkedIn.
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Nicholas Cooley @npcooley.bsky.social · 18/10/2023
🎵fall is here 🎵
A picture looking down the Mon River towards the Birmingham Bridge and downtown Pittsburgh.
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Nicholas Cooley @npcooley.bsky.social · 28/09/2023
Someone made it two months without an ear infection.
A bernese mountain dog laying on a tile floor.
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Nicholas Cooley @npcooley.bsky.social · 24/09/2023
Found a smol buddy napping by a walking path today.
A small snake curled up in the grass.
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Kathleen (Katie) Ferris @ferrisifolius.bsky.social · 20/09/2023
Calling all prospective PhD students! I am recruiting students for Fall 2024 to study the genetics of adaptation & speciation in alpine Monkeyflowers!!!! Check out my website (link below) for my contact info and details about the lab. Please RePost!!!!! kathleengferristulane.wordpress.com
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Nicholas Cooley @npcooley.bsky.social · 17/09/2023
Cheers to volunteer tomatoes!
A colander full of small and medium sized tomatoes.
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Nicholas Cooley @npcooley.bsky.social · 15/09/2023
Back on my bullshit (submitting a manuscript late in the afternoon on a Friday).
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Nicholas Cooley @npcooley.bsky.social · 13/09/2023
I'm not sure what sins I committed in a previous life, but the amount of times I'm stuck trying to shorten an axis label where the most straightforward word to abbreviate is 'cumulative' is staggering.
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Amanda Warr @amandatron89.bsky.social · 06/09/2023
So it would seem DNA extracted from ileum contents are ~80% host. This is annoying. Anyone got a favourite host depletion method for me? Samples have already been frozen. 🧬 🖥 #microbiome
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Dr. Lauren E. Fuess @laurenfuess.bsky.social · 30/08/2023
My reach here isn't great yet, so maybe people can help spread the word. We're hiring a postdoctoral scholar as part of an NSF planning grant to support a bioinformatics research center in global change ecology at TXST. Details here: fuesslab.wp.txstate.edu/opportunities/ Apply by 9/15!
fuesslab.wp.txstate.edu
opportunities – Symbiommunity Lab
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Nicholas Cooley @npcooley.bsky.social · 05/09/2023
Carneros isn’t bad.
View of a vineyard sprawling out over small rolling hills.
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Nicholas Cooley @npcooley.bsky.social · 31/08/2023
Back on my bullshit (submitting half a million jobs on a friday afternoon when I'm supposed to be on vacation).
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Nicholas Cooley @npcooley.bsky.social · 26/08/2023
If you’re a Pittsburgher, don’t sleep on the aviary!
A bird named Malcolm at the Pittsburgh aviary, posing very regally and showing off his bright colors.
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Nicholas Cooley @npcooley.bsky.social · 08/08/2023
“I should probably plan my next project better, so that I’m not running entirely on vibes.” I say to myself as I think about prospective projects entirely in terms of vibes.
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Matt Hartings @matthartings.bsky.social · 05/08/2023
Hey Chemsky, anyone know of academic programs that teach classes or do applied work in chemistry of art preservation/restoration
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