Fred Jaya
@fredjaya.bsky.social
Binfie 🧬👩🏽💻 - Sydney Informatics Hub 🇦🇺
Current🐇🕳️ 🕳️: linux, nextflow, scRNA, phylogenetics, OOP/pygame
Current🐇🕳️ 🕳️: linux, nextflow, scRNA, phylogenetics, OOP/pygame
Reposted by Fred Jaya
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
👉 arxiv.org/abs/2407.16551
January 27, 2025 at 12:33 AM
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
👉 arxiv.org/abs/2407.16551
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
What the heck is an object (Seurat object?) in object-oriented programming? 🤔 Let's break it down with bioinformatics examples👇
January 19, 2025 at 7:16 AM
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
Reposted by Fred Jaya
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
January 16, 2025 at 4:15 AM
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
The dog when you return home after leaving for 27 minutes
Slow-motion videos reveal tree frogs making some of the most dramatic landings in nature.
Learn more: scim.ag/4gTAurn
Learn more: scim.ag/4gTAurn
January 16, 2025 at 12:40 AM
The dog when you return home after leaving for 27 minutes
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
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
January 15, 2025 at 3:54 AM
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
Please repost and share with anyone that might be interested.
More details: usyd.wd3.myworkdayjobs.com/USYD_EXTERNA...
#bioinformatics #jobs #hiring
Post the best ways to wish someone a happy new years, I'll start:
January 13, 2025 at 7:03 AM
Post the best ways to wish someone a happy new years, I'll start:
Reposted by Fred Jaya
if you are having dinner with a phylogeneticist it is rude to order basil
if you’re having dessert with a volcanologist is it rude to order lava cake
if you’re having dinner with a mycologist is it rude to order mushrooms
January 9, 2025 at 5:33 PM
if you are having dinner with a phylogeneticist it is rude to order basil
Reposted by Fred Jaya
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
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
January 2, 2025 at 3:37 AM
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
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
Reposted by Fred Jaya
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)
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
December 31, 2024 at 11:43 PM
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)
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)
Amazing. Meanwhile I still can't get the bootloader working on an Arch install
December 24, 2024 at 12:47 AM
Amazing. Meanwhile I still can't get the bootloader working on an Arch install
Reposted by Fred Jaya
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
#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
December 18, 2024 at 2:15 AM
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
#rse
Reposted by Fred Jaya
🐍🌲 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...
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
December 17, 2024 at 10:00 PM
🐍🌲 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...
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...
Reposted by Fred Jaya
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!
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
December 17, 2024 at 8:58 PM
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!
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!
Reposted by Fred Jaya
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.
- 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.
December 12, 2024 at 3:13 AM
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.
- 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.
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.
@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.
December 10, 2024 at 8:23 PM
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.
@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.
Reposted by Fred Jaya
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
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
December 9, 2024 at 10:29 PM
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
www.biocommons.org.au/news/biohack...
#genomics #FAIR #usegalaxy
Reposted by Fred Jaya
🎉 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
📅 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
December 10, 2024 at 4:13 AM
🎉 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
📅 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
Huge. Congrats @rpodonnell.bsky.social!!
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
December 8, 2024 at 3:58 AM
Huge. Congrats @rpodonnell.bsky.social!!
Intro to @nextflow.io training done and dusted - thanks for having us, AMSI! @ausbiocommons.bsky.social
December 5, 2024 at 7:32 AM
Intro to @nextflow.io training done and dusted - thanks for having us, AMSI! @ausbiocommons.bsky.social
Reposted by Fred Jaya
Come join us!
The ARC Training Centre in Plant Biosecurity (@arc-pbtc.bsky.social) has NINE PhD scholarships now open.
Each come with integrated placements in government or industry and professional development for future research leaders. plantbiosecuritycentre.edu.au/phd-opportun...
Each come with integrated placements in government or industry and professional development for future research leaders. plantbiosecuritycentre.edu.au/phd-opportun...
PhD Opportunities
We’re seeking outstanding PhD applicants to innovate novel approaches to prevent, respond to, and recover from plant pests and diseases that threaten the economy and environment. See the bene…
plantbiosecuritycentre.edu.au
December 5, 2024 at 6:49 AM
Come join us!