Sebastian Paez @jspaezp.bsky.social · 26/11/2025media.tenor.coma man in a green shirt says the horror while sitting on a couchALT: a man in a green shirt says the horror while sitting on a couch 110
Reposted by Sebastian PaezYasset Perez-Riverol @ypriverol.bsky.social · 18/06/2025🚨 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 #PRIDElnkd.inLinkedInThis link will take you to a page that’s not on LinkedIn 01112
Sebastian Paez @jspaezp.bsky.social · 14/05/2025How do you read from the wiff directly? (I am not super familiar with the state of SDKs for wiff/wiff2, thanks beforehand) 110
Sebastian Paez @jspaezp.bsky.social · 06/05/2025I think @ypriverol.bsky.social might have some hard data on this one 010
Sebastian Paez @jspaezp.bsky.social · 05/03/2025In the past I have written stuff to delete things more than X years old that are not raw file and that seems to already give a pretty good compromise. pdresults, pep.xmls, maxquant .peaks and that kind of stuff are massive files. (If I recall my past life that was taking up ~75% of the space) 010
Sebastian Paez @jspaezp.bsky.social · 05/03/2025Well that is false ... I calculated it for 120 TB, not 380 ... so it would actually be ~ 475 USD/month 210
Sebastian Paez @jspaezp.bsky.social · 05/03/2025Couldnt help myself from crunching the numbers of how much this would be in the cloud ... turns out its ~ 155 bucks/month cloud.google.com/products/cal...cloud.google.comGoogle Cloud Pricing CalculatorCreate your own Custom Price Quote for the products offered through Google Cloud based on number, usage, and power of servers 110
Reposted by Sebastian PaezLindsay K Pino @lindsaykpino.com · 21/02/2025On our way to #USHUPO25! Poor @jspaezp.bsky.social spending a crosscountry flight sitting between not-on-bluesky-Andrea and me 😂 🙏 1263
Sebastian Paez @jspaezp.bsky.social · 30/01/2025It also depends on the tool/acquisition method. Some can be understood as missing at random and some cannot (or at least different ratios of the two) 010
Reposted by Sebastian PaezCharlie Marsh @crmarsh.com · 29/01/2025We’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! 35722104
Reposted by Sebastian PaezEllie Huxtable @ellie.wtf · 27/01/2025we'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 6407
Sebastian Paez @jspaezp.bsky.social · 22/01/2025bsky is descending into degeneracy D: bsky.app/profile/ucdp... 110
Reposted by Sebastian PaezMatt Foster @mattwfoster.bsky.social · 18/01/2025Anyone 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. 112
Reposted by Sebastian PaezBrett Phinney @ucdproteomics.bsky.social · 22/01/2025@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 !! 384
Sebastian Paez @jspaezp.bsky.social · 20/01/2025@swillems.bsky.social do you have any insights on this one ? From the data I've seen the pro data is a bit larger than the ultra series ... Maybe you used compression on the pro and not the ultra ? 110
Sebastian Paez @jspaezp.bsky.social · 16/01/2025Just fyi ... Lfq is something that is not supported on the releases yet but we are thinking on how to have a good implementation for it. (We have an experimental implementation .. DM me if you want to try it out) 010
Sebastian Paez @jspaezp.bsky.social · 31/12/2024Why did the project name have a space ? What kind of savagery is that? :P 110
Reposted by Sebastian PaezJeremy Howard @howard.fm · 02/12/2024I 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... 5756
Sebastian Paez @jspaezp.bsky.social · 02/12/2024Gentle 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.comadventofcode.comAdvent of Code 2024 050
Reposted by Sebastian PaezAndy Moore @aaandmoore.bsky.social · 18/11/2024This is a movie of actin filaments in a cultured cell. I like watching it and I hope you do to. 724733
Reposted by Sebastian PaezPurdue Chemistry @purduechemistry.bsky.social · 25/11/2024Congrats 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... 1217
Sebastian Paez @jspaezp.bsky.social · 25/11/2024I think it is very interesting but I was wondering why your approach does not deal explicitly with missing values (more accurately, missing values are excluded from the CV calculation). Is the assumption that all missing values are missing at random here? 120
Reposted by Sebastian PaezSebastian Raschka (rasbt) @rasbt.bsky.social · 20/11/2024The 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... 714116
Sebastian Paez @jspaezp.bsky.social · 15/11/2024Some of us like writting the software a lot more than any of those :P 020
Reposted by Sebastian PaezYasset Perez-Riverol @ypriverol.bsky.social · 13/11/2024@pride-ebi.bsky.social is now here. Now you can delete your X account if you are in proteomics. 081
Reposted by Sebastian PaezAlejandro Brenes @ajbrenes.com · 10/11/2024#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 198751
Sebastian Paez @jspaezp.bsky.social · 13/02/2024That is what the personal GCP/AWS account is for ... For the massive proteomics raw data fun :) 010
Sebastian Paez @jspaezp.bsky.social · 15/12/2023You are right! I had forgotten about that, I have only used lisp to set something up in emacs five or six operating systems ago :P 000
Sebastian Paez @jspaezp.bsky.social · 15/12/2023It is definitely odd in it's design but I think it has a lot of really interesting elements. I don't know any other language with AST as first class citizens. He is ugly but I would not call it terrible. 100
Reposted by Sebastian PaezAlex Rubinsteyn @alexr.bsky.social · 21/11/2023np.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) 274
Sebastian Paez @jspaezp.bsky.social · 19/11/2023Pretty sure that is how Andrea is doing it nowadays (just sent her a bluesky invite :P) 130
Reposted by Sebastian PaezYasset Perez-Riverol @ypriverol.bsky.social · 02/11/2023This 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. 196
Sebastian Paez @jspaezp.bsky.social · 02/11/2023Reading sage's source code is actually a very good way to learn some of the implementation details. I am not sure if I would call that "undergraduate level" though. 120
Sebastian Paez @jspaezp.bsky.social · 26/10/2023I would argue also that... if the core serves only a service role (and not mentoring) it does very little to advance the adoption of the technology. 010
Reposted by Sebastian PaezThe Black Women in Computational Biology Network @blkwomencompbio.bsky.social · 23/10/2023Hi 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.forms.gleCompBio Perspectives SurveyWHAT 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... 014
Sebastian Paez @jspaezp.bsky.social · 23/10/2023Hey there! I've never used the gui, let me make a notebook with an example workflow :) 010
Sebastian Paez @jspaezp.bsky.social · 21/10/2023I recall having a hard time learning how to use the package! It eventually worked for what I needed but it was not a smooth ride. 120
Sebastian Paez @jspaezp.bsky.social · 21/10/2023Is this for dda or día ? Lmk if you want me to make a public notebook with an example ! (Also let me know what you want to visualize from the data ...) 210
![# 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)
