Sebastian Paez

I feel like that question is a trap ...

🚨 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

How do you read from the wiff directly? (I am not super familiar with the state of SDKs for wiff/wiff2, thanks beforehand)

I think @ypriverol.bsky.social might have some hard data on this one

In 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)

Well that is false ... I calculated it for 120 TB, not 380 ... so it would actually be ~ 475 USD/month

Couldnt 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...

On our way to #USHUPO25! Poor @jspaezp.bsky.social spending a crosscountry flight sitting between not-on-bluesky-Andrea and me 😂 🙏

It 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)

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!

A screenshot of Atuin Desktop

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

bsky is descending into degeneracy D:
bsky.app/profile/ucdp...

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.

@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 !!

@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 ?

Just 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)

Why did the project name have a space ? What kind of savagery is that? :P

# 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}")

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...

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

This is a movie of actin filaments in a cultured cell. I like watching it and I hope you do to.

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...

I 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?

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...

Some of us like writting the software a lot more than any of those :P

@pride-ebi.bsky.social is now here. Now you can delete your X account if you are in proteomics.

#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

That is what the personal GCP/AWS account is for ... For the massive proteomics raw data fun :)

You 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

It 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.