Lightnews — Scholar-powered news

Reposted

Larry Hunter @proflhunter.bsky.social · 6d

I donate to them, and I think everyone who can should. donate.wikimedia.org

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Chuck Wendig @chuckwendig.bsky.social · 14d

And away we go -- apple review number two:

THE SWEETIE

Apple Review #2: Sweetie

Today, a real clown nose of an apple: New Zealand’s Sweetie. It’s small and red and sucks. I’d love to leave my review right there but fine, I’ll go deeper. It’s a Gal…

terribleminds.com

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Javier Santoyo @jsantoyo.bsky.social · 16d

Competencies for bioinformatics core facility scientists: extension of the ISCB competency framework for bioinformatics. #Bioinformatics #CoreFacility #BioinformaticsCompetencies @bioinfoadv.bsky.social
academic.oup.com/bioinformati...

Competencies for bioinformatics core facility scientists: extension of the ISCB competency framework for bioinformatics

AbstractMotivation. The competency framework of the International Society of Computational Biology (ISCB) provides a benchmark for capturing the knowledge,

academic.oup.com

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daily bunnies 🐇✨ @dailybunnies.bsky.social · Sep 1

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Polly Nator @madeincleveland.bsky.social · Aug 28

Remember when COVID vaccines were first available? Remember how they saved lives and helped us move toward normalcy? Remember how relieved and grateful we were? Remember how amazing our healthcare workers were? Remember how science rescued us?

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Jen @ladyjenpool.bsky.social · Aug 15

Hey, as a librarian I have to tell you

You don't have to finish a book that doesn't interest you. Life's too short for that. Not your jam? You have my permission to move on to the next book.

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Stephen Turner @stephenturner.us · Aug 15

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RandomWhiteGuy @thereelrandom.bsky.social · Aug 13

My wife shared this with me and I’m tellin you… it’s worth the read.

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Sam Wilson @samwilson.bsky.social · Jul 28

Can’t wait to introduce bird-based storage into my backup system

A twitter post explaining how you can “save PNGs to birds” by converting a drawing of a bird into a spectrogram then playing it to a starling who sung it back, reproducing the PNG.

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mmarchin.bsky.social @mmarchin.bsky.social · Jul 24

Daniel Huson - sketch, capture, and layout phylogenies using phylosketch2 github.com/husonlab/phy... #ISMBECCB2025 #biovis seems handy!

GitHub - husonlab/phylosketch2: Sketch phylogenetic trees and networks

Sketch phylogenetic trees and networks. Contribute to husonlab/phylosketch2 development by creating an account on GitHub.

github.com

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mmarchin.bsky.social @mmarchin.bsky.social · Jul 24

scooby - multimodal (rna/atac) profiles from dna at sc resolution. builds on borzoi. @lauradmartens.bsky.social #ISMBECCB2025 #regsys

mmarchin.bsky.social @mmarchin.bsky.social · Jul 24

original ad for human genome volunteers! #ISMBECCB2025 #HITSEQ @tobiasmar.bsky.social

newspaper ad for 20 volunteers for the human genome project

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Carl T. Bergstrom @carlbergstrom.com · Jul 23

"We"?

The problem is, *we* aren't building these systems. A very small number of very wealthy companies, controlled by a nearly-as-small group of even more wealthy men, are building these systems.

And none of the incentives align with "helping people draw their own, more accurate conclusions".

The adoption of LLMs is happening, for good or bad. If we build these systems with the explicit aim of helping people draw their own, more accurate conclusions about the world — and in so doing earn their trust — we may find ourselves in a more participatory, democratic society. This might mean systems that prioritize veracity, expose their own reasoning (not just conclusions), meet people where they are without condescension or overload, and are not overconfident.

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mmarchin.bsky.social @mmarchin.bsky.social · Jul 24

I posted the rest of my notes from #bioinfocore on our beautiful vintage wiki for posterity: bioinfo-core.org/index.php?ti... #bioinfocore #ISMBECCB2025

ISMB 2025: BioinfoCoreWorkshop - BioWiki

bioinfo-core.org

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mmarchin.bsky.social @mmarchin.bsky.social · Jul 24

Patricial Carvajal Lopez presented about the competency framework for bioinformatics core facility scientists (and I helped!) I'll post when it's published, we're getting close : D #bioinfocore #ISMBECCB2025

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mmarchin.bsky.social @mmarchin.bsky.social · Jul 24

Carlos Prieto presented so many cool interactive tools for data visualization in 5 minutes: github.com/BioinfoUSAL #bioinfocore #ISMBECCB2025

mmarchin.bsky.social @mmarchin.bsky.social · Jul 24

@hubertr.bsky.social‬ presented during #bioinfocore about GEO uploader, trying to simplify the upload process for researchers (I kinda hate doing this, so I'll be looking at it) github.com/fgcz/geo-upl... #ISMBECCB2025

GitHub - fgcz/geo-uploader: A Python GUI for the upload of NGS data to GEO

A Python GUI for the upload of NGS data to GEO. Contribute to fgcz/geo-uploader development by creating an account on GitHub.

github.com

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mmarchin.bsky.social @mmarchin.bsky.social · Jul 24

@natbytes.bsky.social‬ presented during #bioinfocore about a clever method for optimizing clustering during single cell analysis: github.com/gladstone-in... #ISMBECCB2025

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mmarchin.bsky.social @mmarchin.bsky.social · Jul 24

Thomas Roder presented during #bioinfocore about the Assembly Curator - the goal was to get 80% of the quality of trycycler in 5% of the time: github.com/MrTomRod/ass... #ISMBECCB2025

mmarchin.bsky.social @mmarchin.bsky.social · Jul 24

@kubranarci.bsky.social‬ presented during #bioinfocore about development of the nf-core variantbenchmarking pipeline, developed for GHGA and shared with the world: nf-co.re/variantbench... #ISMBECCB2025 (comparing variant callers can be pretty messy!)

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mmarchin.bsky.social @mmarchin.bsky.social · Jul 24

#bioinfocore had an entertaining & interesting keynote from @damiandn.bsky.social yesterday sharing history from the computational imaging field which has gone before us into AI first territory. #ISMBECCB2025 sorry for the lighting, we didn't figure that out until later...

Damian presenting some AI oriented history from computational imaging

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mmarchin.bsky.social @mmarchin.bsky.social · Jul 23

at connect circles I learned that inference can be where something like 65% of the carbon footprint comes from for large genAI models. arxiv.org/html/2503.10... I also mentioned this book if anyone wants to know the impacts of other stuff. #ISMBECCB2025

Green Prompting

arxiv.org

mmarchin.bsky.social @mmarchin.bsky.social · Jul 22

deep dive on the beatles.

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mmarchin.bsky.social @mmarchin.bsky.social · Jul 22

RP: CRAWDAD R package to identify cell types and their proximity in spatial data. www.nature.com/articles/s41... github.com/JEFworks-Lab... #ISMBECCB2025

Characterizing cell-type spatial relationships across length scales in spatially resolved omics data - Nature Communications

Authors introduce CRAWDAD, an R package for quantifying cell-type spatial relationships across length scales in tissues using spatial omics data, enabling the identification of consistent as well as sample-specific celltype spatial relationships across multiple spatial omics datasets.

www.nature.com

mmarchin.bsky.social @mmarchin.bsky.social · Jul 22

EH: identifying time varying GRNs from time series scRNAseq data. pubmed.ncbi.nlm.nih.gov/40662830/ github.com/euxhenh/Marl... #ISMBECCB2025

Recovering time-varying networks from single-cell data - PubMed

The code used to train Marlene is available at https://github.com/euxhenh/Marlene.

pubmed.ncbi.nlm.nih.gov