Sebastian Paez
@jspaezp.bsky.social
Data scientist @ Talus Bio.
Kind of into data, proteomics, open source and biology.
Kind of into data, proteomics, open source and biology.
Reposted by Sebastian Paez
🚨 Has PRIDE helped your research?
Take 15 mins to tell funders why open data matters!
📊 Fill out the EMBL-EBI 2025 survey 👉
www.surveymonkey.com/r/QGFMBH8?ch...
Your feedback helps keep PRIDE open, FAIR & impactful.
🙏 Please share!
#FAIR #OpenData #Proteomics #MassSpectrometry #PRIDE
Take 15 mins to tell funders why open data matters!
📊 Fill out the EMBL-EBI 2025 survey 👉
www.surveymonkey.com/r/QGFMBH8?ch...
Your feedback helps keep PRIDE open, FAIR & impactful.
🙏 Please share!
#FAIR #OpenData #Proteomics #MassSpectrometry #PRIDE
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
June 18, 2025 at 6:02 AM
🚨 Has PRIDE helped your research?
Take 15 mins to tell funders why open data matters!
📊 Fill out the EMBL-EBI 2025 survey 👉
www.surveymonkey.com/r/QGFMBH8?ch...
Your feedback helps keep PRIDE open, FAIR & impactful.
🙏 Please share!
#FAIR #OpenData #Proteomics #MassSpectrometry #PRIDE
Take 15 mins to tell funders why open data matters!
📊 Fill out the EMBL-EBI 2025 survey 👉
www.surveymonkey.com/r/QGFMBH8?ch...
Your feedback helps keep PRIDE open, FAIR & impactful.
🙏 Please share!
#FAIR #OpenData #Proteomics #MassSpectrometry #PRIDE
Reposted by Sebastian Paez
On our way to #USHUPO25! Poor @jspaezp.bsky.social spending a crosscountry flight sitting between not-on-bluesky-Andrea and me 😂 🙏
February 21, 2025 at 5:15 PM
On our way to #USHUPO25! Poor @jspaezp.bsky.social spending a crosscountry flight sitting between not-on-bluesky-Andrea and me 😂 🙏
Reposted by Sebastian Paez
We’re building a new static type checker for Python, from scratch, in Rust.
From a technical perspective, it’s probably our most ambitious project yet. We’re about 800 PRs deep!
From a technical perspective, it’s probably our most ambitious project yet. We’re about 800 PRs deep!
January 29, 2025 at 5:18 PM
We’re building a new static type checker for Python, from scratch, in Rust.
From a technical perspective, it’s probably our most ambitious project yet. We’re about 800 PRs deep!
From a technical perspective, it’s probably our most ambitious project yet. We’re about 800 PRs deep!
Reposted by Sebastian Paez
we've been working hard on addressing early beta feedback for Atuin Desktop
in the past week
- dark mode (y'all kept asking)
- improved collaboration UX
- custom terminal fonts
- fixed several sync & performance issues
in the past week
- dark mode (y'all kept asking)
- improved collaboration UX
- custom terminal fonts
- fixed several sync & performance issues
January 27, 2025 at 2:17 PM
we've been working hard on addressing early beta feedback for Atuin Desktop
in the past week
- dark mode (y'all kept asking)
- improved collaboration UX
- custom terminal fonts
- fixed several sync & performance issues
in the past week
- dark mode (y'all kept asking)
- improved collaboration UX
- custom terminal fonts
- fixed several sync & performance issues
Reposted by Sebastian Paez
Anyone recommend a cheapish reader for scanning 2d barcodes? Best if it could scan an entire plate of Matrix tubes. Also looking at used/refurbished options specific for these or similar plates, if there’s anything that is highly recommended.
January 18, 2025 at 3:27 PM
Anyone recommend a cheapish reader for scanning 2d barcodes? Best if it could scan an entire plate of Matrix tubes. Also looking at used/refurbished options specific for these or similar plates, if there’s anything that is highly recommended.
Reposted by Sebastian Paez
@michaellazear.bsky.social & @jspaezp.bsky.social I'm Running Sage on a dual Epyc 128 thread box w/ 2TB memory (I think) . Searching 19 ddaPASF files directly with built in timsRUST!! Dang this is screaming fast !!
January 22, 2025 at 2:43 AM
@michaellazear.bsky.social & @jspaezp.bsky.social I'm Running Sage on a dual Epyc 128 thread box w/ 2TB memory (I think) . Searching 19 ddaPASF files directly with built in timsRUST!! Dang this is screaming fast !!
Reposted by Sebastian Paez
I used a few starter packs to help connect with my communities, but after a couple of weeks I noticed nearly all the posts I'm interested in are from folks that follow me back.
So I created an nb to unfollow non-mutual follows. Code in alt text, or here:
colab.research.google.com/drive/1V7QjZ...
So I created an nb to unfollow non-mutual follows. Code in alt text, or here:
colab.research.google.com/drive/1V7QjZ...
![# Remove bsky non-mutual follows
from fastcore.utils import *
from fastcore.xtras import *
from atproto import Client
from fastprogress.fastprogress import master_bar, progress_bar
cli = Client()
pv = cli.login('youruser', 'yourpass')
did = pv.did
pv.posts_count,pv.followers_count,pv.follows_count
def at_paged(did, meth):
"Return all pages of results from some method"
resp = None
while True:
resp = meth(did, cursor=resp.cursor if resp else None)
yield resp
if not resp.cursor: return
posts = L(at_paged(did, cli.get_author_feed)).attrgot('feed').concat()
posts[-2].post.record
fws = L(at_paged(did, cli.get_follows))
frs = L(at_paged(did, cli.get_followers))
following = fws.attrgot('follows').concat()
followers = frs.attrgot('followers').concat()
len(following),len(followers)
to_unfollow = set(following.attrgot('did')) - set(followers.attrgot('did'))
len(to_unfollow)
followd = {o.did:o.viewer.following for o in following}
for fdid in progress_bar(to_unfollow):
try: cli.unfollow(followd[fdid])
except Exception as e: print(f"Could not unfollow {fdid}: {e}")](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:ihze7dasblwewgunyesfbm23/bafkreia2oxxpu274ex3axg22mhfkhj5eusbpnusllc7a5g3jcojtyxqd4q@jpeg)
December 2, 2024 at 9:24 PM
I used a few starter packs to help connect with my communities, but after a couple of weeks I noticed nearly all the posts I'm interested in are from folks that follow me back.
So I created an nb to unfollow non-mutual follows. Code in alt text, or here:
colab.research.google.com/drive/1V7QjZ...
So I created an nb to unfollow non-mutual follows. Code in alt text, or here:
colab.research.google.com/drive/1V7QjZ...
Gentle reminder that 2024 advent of code is up (yes I am a nerd and you can be one as well <3)!
Daily programming puzzles at Advent of Code #AdventOfCode adventofcode.com
Daily programming puzzles at Advent of Code #AdventOfCode adventofcode.com
Advent of Code 2024
adventofcode.com
December 2, 2024 at 3:02 AM
Gentle reminder that 2024 advent of code is up (yes I am a nerd and you can be one as well <3)!
Daily programming puzzles at Advent of Code #AdventOfCode adventofcode.com
Daily programming puzzles at Advent of Code #AdventOfCode adventofcode.com
Reposted by Sebastian Paez
This is a movie of actin filaments in a cultured cell. I like watching it and I hope you do to.
November 18, 2024 at 5:50 AM
This is a movie of actin filaments in a cultured cell. I like watching it and I hope you do to.
Reposted by Sebastian Paez
Congrats to Professor Graham Cooks who just surpassed 100,000 citations and hit the 150 h-index! More photos and story: www.chem.purdue.edu/media/news/2...
November 25, 2024 at 7:49 PM
Congrats to Professor Graham Cooks who just surpassed 100,000 citations and hit the 150 h-index! More photos and story: www.chem.purdue.edu/media/news/2...
Reposted by Sebastian Paez
The Llama 3.2 1B and 3B models are my favorite LLMs -- small but very capable.
If you want to understand how the architectures look like under the hood, I implemented them from scratch (one of the best ways to learn): github.com/rasbt/LLMs-f...
If you want to understand how the architectures look like under the hood, I implemented them from scratch (one of the best ways to learn): github.com/rasbt/LLMs-f...
November 20, 2024 at 8:33 AM
The Llama 3.2 1B and 3B models are my favorite LLMs -- small but very capable.
If you want to understand how the architectures look like under the hood, I implemented them from scratch (one of the best ways to learn): github.com/rasbt/LLMs-f...
If you want to understand how the architectures look like under the hood, I implemented them from scratch (one of the best ways to learn): github.com/rasbt/LLMs-f...
Reposted by Sebastian Paez
@pride-ebi.bsky.social is now here. Now you can delete your X account if you are in proteomics.
@pride-ebi.bsky.social is now here. We will communicate with our users, submitters and the proteomics community. We hope we can be added to the MS package created by @alejandrobrenes.bsky.social.
November 13, 2024 at 2:10 PM
@pride-ebi.bsky.social is now here. Now you can delete your X account if you are in proteomics.
Reposted by Sebastian Paez
#teamMassSpec here is a starting pack in case you just moved over, or in case you've been absent for a while. This is #proteomics or #massspec related. The pack is not comprehensive but it's a start.
go.bsky.app/HH7kqEh
go.bsky.app/HH7kqEh
November 10, 2024 at 3:46 PM
#teamMassSpec here is a starting pack in case you just moved over, or in case you've been absent for a while. This is #proteomics or #massspec related. The pack is not comprehensive but it's a start.
go.bsky.app/HH7kqEh
go.bsky.app/HH7kqEh
Reposted by Sebastian Paez
np.random.rand is all you need (to publish well stratified survival curves in NEJM)
Works best if random features are sparse and you have more features than samples
(requires "supervised" feature selection on full dataset)
Works best if random features are sparse and you have more features than samples
(requires "supervised" feature selection on full dataset)
November 21, 2023 at 9:16 PM
np.random.rand is all you need (to publish well stratified survival curves in NEJM)
Works best if random features are sparse and you have more features than samples
(requires "supervised" feature selection on full dataset)
Works best if random features are sparse and you have more features than samples
(requires "supervised" feature selection on full dataset)
Reposted by Sebastian Paez
This is Big for #quantms team. Let me explain some of the big improvements:
- Sage integration thanks to @michaellazear.bsky.social
- Bruker and library based DIA support thanks to @jspaezp.bsky.social
- Major improvements in LFQ pipeline and pmultiqc reports.
- Lot of bugs fixed from version 1.1.1.
- Sage integration thanks to @michaellazear.bsky.social
- Bruker and library based DIA support thanks to @jspaezp.bsky.social
- Major improvements in LFQ pipeline and pmultiqc reports.
- Lot of bugs fixed from version 1.1.1.
Pipeline release! nf-core/quantms v1.2.0 - nfcore/quantms v1.2.0 - Thimphu!
Please see the changelog: https://github.com/nf-core/quantms/releases/tag/1.2.0
Please see the changelog: https://github.com/nf-core/quantms/releases/tag/1.2.0
November 2, 2023 at 8:15 PM
This is Big for #quantms team. Let me explain some of the big improvements:
- Sage integration thanks to @michaellazear.bsky.social
- Bruker and library based DIA support thanks to @jspaezp.bsky.social
- Major improvements in LFQ pipeline and pmultiqc reports.
- Lot of bugs fixed from version 1.1.1.
- Sage integration thanks to @michaellazear.bsky.social
- Bruker and library based DIA support thanks to @jspaezp.bsky.social
- Major improvements in LFQ pipeline and pmultiqc reports.
- Lot of bugs fixed from version 1.1.1.
Reposted by Sebastian Paez
Hi there! We're on a mission to capture >= 100 responses from computational biologists in our first CompBio Perspectives Survey. It takes just ~2 minutes to complete and you can find here: forms.gle/D8h9FyJ1eX6Y...
Feel free to also pass along to others in your network.
Feel free to also pass along to others in your network.
CompBio Perspectives Survey
WHAT IS THIS SURVEY?
We're on a mission to learn from at least 100 computational biologists' professional experiences.
This is a brief survey The Black Women in Computational Biology Network (BWCB) i...
forms.gle
October 23, 2023 at 2:05 PM
Hi there! We're on a mission to capture >= 100 responses from computational biologists in our first CompBio Perspectives Survey. It takes just ~2 minutes to complete and you can find here: forms.gle/D8h9FyJ1eX6Y...
Feel free to also pass along to others in your network.
Feel free to also pass along to others in your network.