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Luiz Irber
@
luizirber
Davis, CA
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Computer Science PhD candidate at @ucdavis, DIB lab minion, @thecarpentries enthusiast,
Rustacean and Pythonista.
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7.283
Tweetovi
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1.678
Pratim
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1.001
Osobe koje vas prate
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Taylor Reiter
@ReiterTaylor
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7 h |
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For one of the pipelines I'm working on, I recently used Salmon to quantify proteins in a metagenome...and I'm not sure if this was a very bad idea. I would love to hear if this is a very bad idea, or if it's ok. taylorreiter.github.io/2020-02-04-How… Pipeline here: github.com/taylorreiter/2…
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Rayan Chikhi
@RayanChikhi
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21 h |
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#dsb2020, @CamilleMrcht presents our work (REINDEER) for querying abundances of sequences within large collections of datasets. pic.twitter.com/hrQVPCIjGs
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indygreg
@indygreg
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9 h |
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This thread turned into a meaningful change to Rust compiler error output: github.com/rust-lang/rust…. The Rust community is amazing. Thank you @ekuber! twitter.com/indygreg/statu…
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Dr Isabela Le Bras
@oceanslebrasi
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14 h |
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My new paper with @fstraneo @fmkdejong and @np_holliday is out in GRL! agupubs.onlinelibrary.wiley.com/doi/epdf/10.10…
We found a fast-track into the boundary current for a new "upper intermediate" water mass formed by convection in the Irminger Sea pic.twitter.com/ZQQV58dvZ2
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JOSS
@JOSS_TheOJ
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18 h |
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Just published in #JOSS_theOJ: 'ReferenceSeeker: rapid determination of appropriate reference genomes' doi.org/10.21105/joss.…
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Luiz Irber
@luizirber
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4. velj |
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I'm using byteorder now, but Nom seems easier to maintain/extend/verify. Not sure I need async-await/streaming for now, but will keep in mind =]
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Mo Torres
@motorresx
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29. ožu |
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A natural extension of learning about the "United States" and "Latin America" as separate entities, as if the entire continent (the Americas) doesn't share a singular history of colonialism, genocide, and slavery...
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Mo Torres
@motorresx
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29. ožu |
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If "Latinos" aren't all the same race in Latin America, why would we expect them to be in the United States?
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Luiz Irber
@luizirber
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3. velj |
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done =]
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Michael R. Crusoe
@biocrusoe
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3. velj |
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Attention @rustlang users, want easy #CommonWL export for your apps? Speak up here! github.com/clap-rs/clap/i…
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Luiz Irber
@luizirber
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3. velj |
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(sorry)
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Erik Garrison
@erikgarrison
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2. velj |
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I've pulled those changes into another repo: github.com/ekg/fastix. (It's areally simple replacement for an awk script I kept writing.) Thanks for the tips! Working my way up to a real application...
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Luiz Irber
@luizirber
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1. velj |
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But looking pretty good! Some minor things to improve:
- run `cargo fmt` in the code (PR #1 adds checks for that in CI)
- make it 2018 edition, so you don't need most of the `extern crate` declarations in main.rs
- `cargo clippy` also has many suggestions =]
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Luiz Irber
@luizirber
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1. velj |
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OK, added two: one for CI, and another with some scaffolding for a test. Both are similar (err, pretty much the same =P) to PRs I made for @erikgarrison's gaffy tool a week ago: github.com/ekg/gaffy/pull…
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Luiz Irber
@luizirber
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1. velj |
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PRs incoming =]
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Luiz Irber
@luizirber
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1. velj |
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and maybe milksnake would work with C/C++ code too? Intriguing.
Deployment-wise, I like that we have one wheel per platform in sourmash:pypi.org/project/sourma… (since the wrapped cffi doesn't depend on the CPython API directly), and you don't need one wheel per Python version.
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Luiz Irber
@luizirber
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1. velj |
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Oh, I never thought about numba, this opens so many interesting venues...
But I agree about cython & cffi being nicer to use. I use cffi (thru milksnake), as in github.com/luizirber/2018…. I like that milksnake takes care of building Rust shared lib, and I can focus on using cffi
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Rob Patro
@nomad421
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1. velj |
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@luizirber our lab's first tool in #rustlang --- github.com/COMBINE-lab/Te… ! We'd love any rust advice / feedback you might have :)
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Russell Neches
@ryneches
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1. velj |
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Calling all scientists with relevant domain experience. There are 313 results on @biorxivpreprint for "coronavirus" right now. Almost none of them have attached reviews. Let's fix that by Monday morning. Who's with me? #CommunityReview #CoronavirusOutbreak pic.twitter.com/EOd2IPS7r2
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Luiz Irber
@luizirber
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1. velj |
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that plays a small part, but mostly happy to see awesome people working together
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