Reposted by Jackson Burns
🐍 Want to publish your own Python package?
Join pyOpenSci’s 2-hour online workshop Nov 6:
✔️ Build your first package fast
✔️ Learn the core files (pyproject.toml, docs, metadata)
✔️ Publish to PyPI with confidence
📅 Nov 6, 2025 | Online
🎟️ bit.ly/PythonPackaging
Join pyOpenSci’s 2-hour online workshop Nov 6:
✔️ Build your first package fast
✔️ Learn the core files (pyproject.toml, docs, metadata)
✔️ Publish to PyPI with confidence
📅 Nov 6, 2025 | Online
🎟️ bit.ly/PythonPackaging
September 22, 2025 at 3:51 PM
🐍 Want to publish your own Python package?
Join pyOpenSci’s 2-hour online workshop Nov 6:
✔️ Build your first package fast
✔️ Learn the core files (pyproject.toml, docs, metadata)
✔️ Publish to PyPI with confidence
📅 Nov 6, 2025 | Online
🎟️ bit.ly/PythonPackaging
Join pyOpenSci’s 2-hour online workshop Nov 6:
✔️ Build your first package fast
✔️ Learn the core files (pyproject.toml, docs, metadata)
✔️ Publish to PyPI with confidence
📅 Nov 6, 2025 | Online
🎟️ bit.ly/PythonPackaging
The emperor has no clothes
An assessment of DNA language models concludes:
◼️ They do not offer compelling gains over baseline models
Their performance is inconsistent and requires much more compute.
arxiv.org/abs/2412.05430
◼️ They do not offer compelling gains over baseline models
Their performance is inconsistent and requires much more compute.
arxiv.org/abs/2412.05430
June 24, 2025 at 12:03 AM
The emperor has no clothes
This is the golden age of science informatics!
Run BioEmu in Colab - just click "Runtime → Run all"! Our notebook uses ColabFold to generate MSAs, BioEmu to predict trajectories, and Foldseek to cluster conformations.
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...
Thanks @jjimenezluna.bsky.social for the help!
🌐 colab.research.google.com/github/sokry...
📄 www.biorxiv.org/content/10.1...
Google Colab
colab.research.google.com
March 30, 2025 at 1:51 PM
This is the golden age of science informatics!
Reposted by Jackson Burns
The new #RDKit blog post is an update of an older tutorial on displaying fingerprint bits.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
RDKit blog - Rendering fingerprint bits
Visualizing the meaning of fingerprint bits
greglandrum.github.io
March 29, 2025 at 7:49 AM
The new #RDKit blog post is an update of an older tutorial on displaying fingerprint bits.
greglandrum.github.io/rdkit-blog/p...
greglandrum.github.io/rdkit-blog/p...
Just started using Zarr - literally unbelievably good.
Your friendly neighborhood #chunked, #compressed, & #cloud-ready #n-dimensional array format is now verified as @zarr.dev on @bsky.app!
Visit us at zarr.dev for more info!
Visit us at zarr.dev for more info!
Zarr
Have beautiful data in Zarr? Show us on Bluesky!
zarr.dev
March 24, 2025 at 1:59 PM
Just started using Zarr - literally unbelievably good.
Reposted by Jackson Burns
Are you interested in getting involved in peer review of software? We need more editors!
We are looking for folks with a background in #physics and also people with more stats / analytics background.
Join our team. support the #opensource tools that drive #science
📢 Apply here: buff.ly/PKSpJ47
We are looking for folks with a background in #physics and also people with more stats / analytics background.
Join our team. support the #opensource tools that drive #science
📢 Apply here: buff.ly/PKSpJ47
forms.gle
March 6, 2025 at 5:20 PM
Are you interested in getting involved in peer review of software? We need more editors!
We are looking for folks with a background in #physics and also people with more stats / analytics background.
Join our team. support the #opensource tools that drive #science
📢 Apply here: buff.ly/PKSpJ47
We are looking for folks with a background in #physics and also people with more stats / analytics background.
Join our team. support the #opensource tools that drive #science
📢 Apply here: buff.ly/PKSpJ47
Currently making a slide deck in markdown and I've never felt so powerful
February 11, 2025 at 6:37 PM
Currently making a slide deck in markdown and I've never felt so powerful
Cool application of a foundation model to drug design
Looking at TabPFN with Polaris datasets macinchem.org/2025/02/06/l... #cheminformatics
Looking at TabPFN – Macs in Chemistry
macinchem.org
February 7, 2025 at 12:26 AM
Cool application of a foundation model to drug design
polaris is an amazing tool with a similarly amazing development team! Try it out today if you work in Computer Aided Drug Discovery world
Big milestone for @polarishub.io. We merged our first external contribution, thanks to @fastprop.bsky.social! 🎉
github.com/polaris-hub/...
#opensource #benchmarking #ml #drugdiscovery
github.com/polaris-hub/...
#opensource #benchmarking #ml #drugdiscovery
`Subset.as_dataframe()` hides targets instead of raising an error by JacksonBurns · Pull Request #258 · polaris-hub/polaris
Changelogs
Subset.as_dataframe() would raise an error when called on a test set (which hides its targets), this PR allows method to work, just doesn't return targest
Checklist:
Was this PR...
github.com
February 4, 2025 at 7:13 PM
polaris is an amazing tool with a similarly amazing development team! Try it out today if you work in Computer Aided Drug Discovery world
Reposted by Jackson Burns
🚨 Extension Alert: The intermediate leaderboard submission deadline for the antiviral challenge has been extended to midnight on February 7th!
Don't miss this chance to see how you stack up against other participants! Submit your results today: polarishub.io/competitions
Don't miss this chance to see how you stack up against other participants! Submit your results today: polarishub.io/competitions
January 31, 2025 at 2:04 PM
🚨 Extension Alert: The intermediate leaderboard submission deadline for the antiviral challenge has been extended to midnight on February 7th!
Don't miss this chance to see how you stack up against other participants! Submit your results today: polarishub.io/competitions
Don't miss this chance to see how you stack up against other participants! Submit your results today: polarishub.io/competitions
Reposted by Jackson Burns
This is obviously how scientific articles should be, and if we had an open ecosystem designed for users rather than profit, we would have had this years ago. Time to dump commercial publishers and their paywalls.
Want to see a quick demo of the technology that might replace citations in scientific papers?
Goodbye citations, hello embeds.
I was just hoping for links in scientific papers, but this is even better!
Goodbye citations, hello embeds.
I was just hoping for links in scientific papers, but this is even better!
The future of academic citations: Embeds
Citations are dead. Long live embeds! In the future, you won't use traditional citations in scientific articles. You'll directly embed the snippet of science...
youtu.be
January 16, 2025 at 7:37 PM
This is obviously how scientific articles should be, and if we had an open ecosystem designed for users rather than profit, we would have had this years ago. Time to dump commercial publishers and their paywalls.
I highly suggest all my followers working with Python to follow @pyopensci.org - great resources for packaging your code for improved reproducibility
January 2, 2025 at 12:41 AM
I highly suggest all my followers working with Python to follow @pyopensci.org - great resources for packaging your code for improved reproducibility
Thank you to everyone who read and cited my papers last year - proud to say that I received 10 citations in 2024! Double digits for the first time🎉
January 2, 2025 at 12:25 AM
Thank you to everyone who read and cited my papers last year - proud to say that I received 10 citations in 2024! Double digits for the first time🎉
Reposted by Jackson Burns
It is roughly 10 lines of code to go from 1 GPU to N GPUs with pytorch DDP. Pointing this out so that everyone is aware and doesn't shy away from scaling their code
December 30, 2024 at 7:36 PM
It is roughly 10 lines of code to go from 1 GPU to N GPUs with pytorch DDP. Pointing this out so that everyone is aware and doesn't shy away from scaling their code
Reposted by Jackson Burns
That C-C and C-N coupling are now viewed as boring (comparable to amide bond formation!!) is a testament to the work that Buchwald, Hartwig, and many others have done in the past 20 years.
December 18, 2024 at 3:57 PM
That C-C and C-N coupling are now viewed as boring (comparable to amide bond formation!!) is a testament to the work that Buchwald, Hartwig, and many others have done in the past 20 years.
An interesting read for all scientists publishing papers
There was this Tsai/Yuste/Shepard paper that meister famously eviscerated. markusmeister.com/2018/03/20/d... It seems that the authors never retracted the paper (or does ieee not mark retractions)? If not, does anyone know why not? @retractionwatch.com
Death of the sampling theorem?
tl;dr: A team from Columbia University led by Ken Shepard and Rafa Yuste claims to beat the 100 year old Sampling Theorem [1,2]. Apparently anti-aliasing filters are superfluous now because one can…
markusmeister.com
December 17, 2024 at 3:48 AM
An interesting read for all scientists publishing papers
LLMs aren't reasoning, and I tire of seeing articles acting like they are
December 13, 2024 at 3:32 AM
LLMs aren't reasoning, and I tire of seeing articles acting like they are
Reposted by Jackson Burns
📢 Calling all ML practitioners!
Have you been waiting for an opportunity to prove how well your model performs on a blind, newly generated and consistent test set? You now have the unique opportunity to!
Super excited to launch a first competition on @polarishub.io!
Have you been waiting for an opportunity to prove how well your model performs on a blind, newly generated and consistent test set? You now have the unique opportunity to!
Super excited to launch a first competition on @polarishub.io!
🦠 We’re excited to announce our first competition in partnership with @asapdiscovery.bsky.social and @omsf.io!
Test your skills across three sub-challenges revolving around SARS-CoV-2 and MERS-CoV Mpro🧵
Full details: polarishub.io/competitions
Blog: polarishub.io/blog/antivir...
Test your skills across three sub-challenges revolving around SARS-CoV-2 and MERS-CoV Mpro🧵
Full details: polarishub.io/competitions
Blog: polarishub.io/blog/antivir...
December 3, 2024 at 3:52 PM
📢 Calling all ML practitioners!
Have you been waiting for an opportunity to prove how well your model performs on a blind, newly generated and consistent test set? You now have the unique opportunity to!
Super excited to launch a first competition on @polarishub.io!
Have you been waiting for an opportunity to prove how well your model performs on a blind, newly generated and consistent test set? You now have the unique opportunity to!
Super excited to launch a first competition on @polarishub.io!
I want to learn fortran - any recommendations on projects to try, toolchains to use, etc.?
December 1, 2024 at 4:46 PM
I want to learn fortran - any recommendations on projects to try, toolchains to use, etc.?
My machine learning data splitting library astartes has just hit 64 stars on GitHub! ⭐
We built this to help rigorously quantify how well our models actually work - if you want to quantify how well you models extrapolates into new feature or target space, give it a look:
github.com/JacksonBurns...
We built this to help rigorously quantify how well our models actually work - if you want to quantify how well you models extrapolates into new feature or target space, give it a look:
github.com/JacksonBurns...
GitHub - JacksonBurns/astartes: Better Data Splits for Machine Learning
Better Data Splits for Machine Learning. Contribute to JacksonBurns/astartes development by creating an account on GitHub.
github.com
November 25, 2024 at 4:01 PM
My machine learning data splitting library astartes has just hit 64 stars on GitHub! ⭐
We built this to help rigorously quantify how well our models actually work - if you want to quantify how well you models extrapolates into new feature or target space, give it a look:
github.com/JacksonBurns...
We built this to help rigorously quantify how well our models actually work - if you want to quantify how well you models extrapolates into new feature or target space, give it a look:
github.com/JacksonBurns...
Graduate school is revising a paragraph seven times knowing full well that people will skim it just to get to the figures...
November 25, 2024 at 1:43 AM
Graduate school is revising a paragraph seven times knowing full well that people will skim it just to get to the figures...