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Antonio Camargo proslijedio/la je Tweet
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Antonio Camargo proslijedio/la je Tweet
Check this out: it's Bowtie2 running in the browser using WebAssembly!

This is still preliminary (I disabled SIMD and threads) but I'd like to figure out how this could be useful as a sandbox on the web; ideas are welcome! #bioinformatics#webassembly cc@BenLangmeadpic.twitter.com/63iR55ikArHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
Antonio Camargo proslijedio/la je Tweet
"On the performance and design of BioSequences compared to the Seq language" https://biojulia.net/post/seq-lang/ ht
@luizirberHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
All the code is available in GitHub and everyone is invited to collaborate and report bugs.https://github.com/apcamargo/RNAsamba/ …
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We also provide users with a web interface, making it easy for anyone to use RNAsamba in their research projects. https://rnasamba.lge.ibi.unicamp.br/ pic.twitter.com/lGN4gI0E0S
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Despite using a complex model, RNAsamba is much faster than other neural network-based alternatives. To achieve that, part of the code was written in
@rustlang (and I'm eager to see more#bioinformatics tools being written in Rust!)pic.twitter.com/ldHeTyK0Jb
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In our evaluations, RNAsamba outperformed other state-of-the-art tools for
#lncRNA discovery in multiple independent datasets. We also show that it can be used to identify truncated mRNAs and sORFs.pic.twitter.com/xnQEClxLPl
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We are excited to announce that we just published our paper describing RNAsamba, a neural network-based annotation tool to classify mRNAs/lncRNAs using sequence information. https://academic.oup.com/nargab/article/2/1/lqz024/5701461 …
#Bioinformatics#MachineLearning#DeepLearningPrikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
Antonio Camargo proslijedio/la je Tweet
New blog post: "Oxidizing sourmash: PR walkthrough" https://blog.luizirber.org/2020/01/10/sourmash-pr/ … I chose a small sourmash PR and added details about my though process. I think this PR is interesting because it is moving code from
@python to@rustlang, touching all the layers in sourmash.Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
Antonio Camargo proslijedio/la je Tweet
Do you want to try new software, but don't want to mess with your operating system packaging/installation? Why not contribute a recipe for the new software to
@condaforge?Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
Antonio Camargo proslijedio/la je Tweet
Aesthetics are important, but the main point of a figure is NOT to make the paper look pretty. When adding a figure to a paper, think hard about how the visual cues help the reader understand a result. Published network hairballs, for example, rarely covey anything useful to me.
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Antonio Camargo proslijedio/la je Tweet
sourmash 3.0.0 released! Officially migrated from C++ to
#RustLang
Release notes: https://sourmash.readthedocs.io/en/v3.0.1/release-notes/sourmash-3.0.html …
PyPI: https://pypi.org/project/sourmash/3.0.0 …
$ pip install sourmash==3.0.0
Bioconda:
$ conda install -c conda-forge -c bioconda sourmash=3.0.0Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
Antonio Camargo proslijedio/la je Tweet
Ever wondered who is to blame for all the gaps in your genome assembly? Our
@biorxivpreprint led by@valentina_peona evaluates what's been previously hiding in gaps and how sequencing technologies succeed/struggle with repeat/GC-rich regions. https://www.biorxiv.org/content/10.1101/2019.12.19.882399v1 …#transposonpic.twitter.com/tz5dJUv39g
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Antonio Camargo proslijedio/la je Tweet
In praise of "night science": What is the question?https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1902-1 …
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Antonio Camargo proslijedio/la je Tweet
So, pretty happy with Rust for performance, Python for analysis/integration, and how it is stitched together now. Once sourmash 3.0 is released I will post more info in my blog. This thread was longer than expected (but hopefully it makes some sense =]) (10/10)
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Antonio Camargo proslijedio/la je Tweet
The sourmash master branch has been oxidized. Rust has landed. I repeat, rust has landed. https://github.com/dib-lab/sourmash/pull/424 … cc
@luizirber :)Hvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
Antonio Camargo proslijedio/la je Tweet
#HematologyTweetstory 10: how did the 5 major#nucleobases get their names? This is slightly tangential to hematology, admittedly, but is a cool story that I’ve been aching to tell since I went through an intense etymology phase many years ago (still have lots of dusty books)./1pic.twitter.com/F8C8RgIE7r
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Antonio Camargo proslijedio/la je Tweet
Very excited to announce my latest WebAssembly project:
http://bam.bio
It's a playground for samtools, a genomics CLI that I ported from C to #WebAssembly so it can run directly in the browser!pic.twitter.com/qgWP1z9G02Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi -
Antonio Camargo proslijedio/la je Tweet
MetaEuk predicts eukaryotic proteins from metagenomes. They extract millions of yet unknown proteins from marine metagenomes
@TaraOcean_ . Preprint: https://www.biorxiv.org/content/10.1101/851964v1 … Code: https://github.com/soedinglab/metaeuk … The proteins can be searched at https://search.mmseqs.com pic.twitter.com/C2h4KfqAZV
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Antonio Camargo proslijedio/la je Tweet
Deciphering eukaryotic gene-regulatory logic with 100 million random promoters https://go.nature.com/2Lgbw90 pic.twitter.com/VeztN2HkMK
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