Lightnews — Scholar-powered news

Reposted by Fred Jaya

Michelle Wille @duckswabber.bsky.social · Jan 27

Between 2019 and 2023, researchers paid $8.968 billion to make papers open access. Imagine what else could be done with this money if it wasnt paid to for profit publishing companies...
👉 arxiv.org/abs/2407.16551

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Fred Jaya @fredjaya.bsky.social · Jan 19

Need way more practice but most classes I write end up having lots of things #YAGNI, or gets absorbed quickly by "god" objects 🤔🤔

Fred Jaya @fredjaya.bsky.social · Jan 19

Objects, for me, are one of those things that are conceptually easy to understand, but once you have to write your own this understanding breaks down so quickly

Ming Tommy Tang @tommytang.bsky.social · Jan 18

What the heck is an object (Seurat object?) in object-oriented programming? 🤔 Let's break it down with bioinformatics examples👇

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Reposted by Fred Jaya

Australian BioCommons @ausbiocommons.bsky.social · Jan 16

We'd love to hear from all Australian researchers who can benefit from a centralised web platform for managing, launching and monitoring their Nextflow bioinformatics pipelines! www.biocommons.org.au/seqera-service

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Fred Jaya @fredjaya.bsky.social · Jan 16

The dog when you return home after leaving for 27 minutes

Science Magazine @science.org · Jan 15

Slow-motion videos reveal tree frogs making some of the most dramatic landings in nature.

Learn more: scim.ag/4gTAurn

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Fred Jaya @fredjaya.bsky.social · Jan 15

Our team at SIH are looking for a Senior Bioinformatician!

Please repost and share with anyone that might be interested.

More details: usyd.wd3.myworkdayjobs.com/USYD_EXTERNA...

#bioinformatics #jobs #hiring

Senior Bioinformatician

Support transformative bioinformatics initiatives at Sydney Informatics Hub Full time, fixed term until December 2026 Base Salary $108,557 - $118,267 + 17% superannuation About the opportunity The Syd...

usyd.wd3.myworkdayjobs.com

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Fred Jaya @fredjaya.bsky.social · Jan 14

😍😍🥳

Fred Jaya @fredjaya.bsky.social · Jan 13

Post the best ways to wish someone a happy new years, I'll start:

A screenshot of a WhatsApp chat. The messages are:

"MERRY X'MAS" at 5:47 PM.

"HAPPY NEW YEAR" at 5:47 PM.

"MANUSCRIPT MAJOR REVISIONS" at 5:48 PM.

The response is:

"oh fuck lol" at 5:48 PM, with two blue checkmarks indicating the message has been read.

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Reposted by Fred Jaya

⚡️🔩Felsenstein's Monster🔩⚡️ @josephwb.bsky.social · Jan 9

if you are having dinner with a phylogeneticist it is rude to order basil

michael @radplanets.bsky.social · Jan 9

if you’re having dessert with a volcanologist is it rude to order lava cake

sanjana! @sanjanacurtis.bsky.social · Jan 9

if you’re having dinner with a mycologist is it rude to order mushrooms

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Fred Jaya @fredjaya.bsky.social · Jan 6

xkcd.com/323/

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Reposted by Fred Jaya

Emi Tanaka @emitanaka.org · Jan 2

Want to use your #statistics, ML/AI or #bioinformatics skills to solve problems in #agriculture?

We are seeking 3 postdocs (up to 3 years) to join at ANU Biological Data Science Institute as part of Analytics for 🇦🇺 Grains industry by 📅 19 Jan

We now also have a (WIP) website!

🌐 anu-aagi.github.io

ANU-AAGI team featuring investigators: Eric Stone, Emi Tanaka, Alan Welsh and Francis Hui

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Reposted by Fred Jaya

Ryan Wick @rrwick.bsky.social · Dec 31

New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
(1/5)

Home

A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

github.com

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Fred Jaya @fredjaya.bsky.social · Dec 24

Amazing. Meanwhile I still can't get the bootloader working on an Arch install

Niema Moshiri @niema.net · Dec 23

Got something interesting cooking up... 👀 @robert.bio

R36S handheld video game device compiling Minimap2

Minimap2 help message on ArkOS 2.0 on an R36S handheld video game device

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Fred Jaya @fredjaya.bsky.social · Dec 24

holy shit @rpodonnell.bsky.social

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Fred Jaya @fredjaya.bsky.social · Dec 23

✋

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Reposted by Fred Jaya

Michael Milton @multimeric.bsky.social · Dec 18

We're hiring a Research Computing Engineer for my team at WEHI: wehi.wd3.myworkdayjobs.com/en-US/WEHI/j.... Please send this to anyone you know who might be interested!

#rse

Research Computing Engineer

Job Title Research Computing Engineer Job Description An opportunity is available for a Research Computing Engineer to join the Research Computing Platform at Australia’s pre-eminent biomedical resear...

wehi.wd3.myworkdayjobs.com

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Reposted by Fred Jaya

Katherine Caley @katherinecaley.bsky.social · Dec 17

🐍🌲 piqtree: IQ-TREE2 meets Python via cogent3! 🤝⚡️

The developers of IQ-TREE2 and cogent3 have joined forces to bring the power of IQ-TREE2 to Python users as piqtree.

piqtree exposes selected IQ-TREE2 capabilities within Python, using the cogent3 library as the interface...

piqtree: IQ-TREE2 meets Python via cogent3 · iqtree piqtree · Discussion #145

The developers of IQ-TREE2 and cogent3 have joined forces to bring the power of IQ-TREE2 to Python users as piqtree. piqtree exposes selected IQ-TREE2 capabilities within Python, using the cogent3 ...

github.com

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Reposted by Fred Jaya

Ryan Wick @rrwick.bsky.social · Dec 17

New release of Canu - first one in over 3 years!
github.com/marbl/canu/r...

The notes say this will be the very last release. Many thanks to its devs Brian Walenz and @sergek.bsky.social. Canu may be a bit old and it's certainly not fast, but it makes good assemblies and so I still use it!

Release Canu v2.3 · marbl/canu

These are release notes for Canu version 2.3, which was released on December 17th, 2024. Canu is specialized for assembly of single-molecule sequences. Full documentation can be found at http://can...

github.com

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Reposted by Fred Jaya

Alex Swarbrick @alexswarbrick.bsky.social · Dec 12

Jobortunities: Shortly advertising for 2 positions, both working on the Breast Cancer Atlas, in Sydney.
- Wet lab research assistant: mol bio +/- pathology desirable
- Comp. Research Assistant: scRNA-Seq, spatial transcriptomics and ML
Details to follow, DM or email if you are a great fit.

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Fred Jaya @fredjaya.bsky.social · Dec 10

2025 🟩🟩🟩👀👀?? @katherinecaley.bsky.social

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Fred Jaya @fredjaya.bsky.social · Dec 10

What started off as
@katherinecaley.bsky.social
and I seeing peoples github contributions and being like "wow, so coool...", turned out to become a year (mostly) of developing (mostly) good version control/software engineering habits.

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Reposted by Fred Jaya

Australian BioCommons @ausbiocommons.bsky.social · Dec 9

Last month 18 keen 🇦🇺🧪 scientists gathered to work into the night to join ELIXIR's #BioHackEU24 Read how they got stuck in shaping global #bioinformatics advancements while networking locally and abroad 👇
www.biocommons.org.au/news/biohack...

#genomics #FAIR #usegalaxy

Australian Outpost of BioHackathon Europe connects researchers to help shape global bioinformatics advances — Australian BioCommons

A group of researchers passionate about fungal and plant genomics gathered at ANU to enhance their bioinformatics skills, learn about the powerful tools and workflows available on Galaxy Australia, an...

www.biocommons.org.au

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Reposted by Fred Jaya

rladiessydney.bsky.social @rladiessydney.bsky.social · Dec 10

🎉 Join us for our final R-Ladies Sydney event of 2024!

📅 When: Wednesday, December 18, 5:30 PM

📍 Where: Moore College, 1 King Street, Newtown

🎯 What: A casual social catch-up to network with fellow R enthusiasts, celebrate the year, and build new connections.

👉 RSVP here: bit.ly/3BaR32J

EOY In-Person R-Ladies Meetup: Share, Learn, and Connect!, Wed, Dec 18, 2024, 5:30 PM | Meetup

Join us for our final R-Ladies event of the year! This in-person gathering is a fantastic opportunity to: * Practice presenting your R-focused projects or work in a suppor

meetup.com

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Fred Jaya @fredjaya.bsky.social · Dec 8

Huge. Congrats @rpodonnell.bsky.social!!

Ryan P. O’Donnell @rpodonnell.bsky.social · Dec 7

The first chapter of my PhD has finally been published in Systematic Biology! “Discordance Down Under: Combining phylogenomics & fungal symbioses to detangle difficult nodes in a diverse tribe of Australian terrestrial orchids” - advance access link below 1/🧵

academic.oup.com

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Fred Jaya @fredjaya.bsky.social · Dec 5

Intro to @nextflow.io training done and dusted - thanks for having us, AMSI! @ausbiocommons.bsky.social

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