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dismally.bsky.social

@dismally.bsky.social
133 followers 1.3K following 1 posts

HPC and computational biology. Somewhere in 🇦🇺.

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Adrian Jackson @adrianjhpc.bsky.social · 01/09/2026
Developing next-generation accelerators requires benchmarking them on realistic and agentic AI workloads. As part of the ARIA Scaling Compute programme, we are releasing TEAS, serving 5 models (4B to ~1T total) on 9 accelerators for 6 workloads. @epcc.bsky.social teasbench.com
teasbench.com
TEAS Benchmark
TEAS reports measured cost, accuracy, performance and energy for LLM inference across models, workloads, engines and accelerators.
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Kate Michie @kmichie.bsky.social · 28/07/2026
Excited to hear @rolanddunbrack.bsky.social talk today ( 1 pm Sydney time) on “Structural bioinformatics and AlphaFold modeling of the human kinome and its interactions” at the Australian Structural Biology Computing community meeting. Details to join the talk:
biocommons.org.au
MEETING: Australian Structural Biology Computing Community — Australian BioCommons
Join the quarterly meeting of the Australian Structural Biology Computing community. More information
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Nils Homer @nilshomer.com · 28/06/2026
🚀 new bwa-mem3 is out. Why use it? - 🏛️keep using a bwa-mem variant (avoid revalidation/reprocessing) - 🚅 1.7x faster/20% less memory than bwa-mem2 - 🧬native methylation support (asymmetric scoring) - ✅ matches bwa-mem2 output - 👊opt-in knobs to go even 2x faster bwa-mem3.readthedocs.io/en/latest/
bwa-mem3.readthedocs.io
Home - bwa-mem3
Accelerated short-read alignment, derived from bwa-mem2
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Rob Patro @robp.bsky.social · 15/06/2026
As promised, a bit more on salmon 2.0 🧵 It's a from-scratch rewrite of salmon in Rust. It provides the same workflow (index → quant → quant.sf), rebuilt to be faster, far easier to install, and a clean foundation for the next decade of development. 1/8
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Prof Christina Pagel @chrischirp.bsky.social · 01/05/2026
NHS data should be driving innovation & improvement – it’s an amazing resource We just published the sequel to our 2021 "Road to Hell" paper on using NHS data for research... things are worse! Buckle up for a long 🧵about *how COMPLETELY mad* system is for accessing NHS data for research 1/20
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Hasindu Gamaarachchi @hasindu2008.bsky.social · 28/03/2026
The pre-print for Slorado and openfish is out. biorxiv.org/content/10.6... You can do @nanoporetech.com basecalling with not just NVIDIA GPU, but also using a range of AMD GPU. Would be useful since popular GPUs are now 💸💸💸💸(& hard to buy), Work by @bonson-wong.bsky.social
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Christian Meesters @rupdecat.fediscience.org.ap.brid.gy · 26/03/2026
Did you know? We started to gather cluster profiles for Snakemake users in a little repo: github.com/snakemake/snakemake-clus… They should serve as a template for others. #HPC #Snakemake #ReproducibleComputing #SnakemakeHackathon2026
github.com
GitHub - snakemake/snakemake-cluster-profiles: The snakemake-profiles repository is an effort to create configuration profiles for executing Snakemake in specific institutional cluster or compute environments. It is meant to complement the executor plugins, which are designed for specifying execution on general architectures such as SLURM, LSF, etc.
The snakemake-profiles repository is an effort to create configuration profiles for executing Snakemake in specific institutional cluster or compute environments. It is meant to complement the exec...
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Louis Moresi @louis.moresi.info · 05/02/2026
It's an important time to learn about the monitoring of nuclear testing. Here is an article by @scienceanu.bsky.social colleague, Hrvoje Tkalčić: theconversation.com/in-the-austr... ⚒️
theconversation.com
In the Australian outback, we’re listening for nuclear tests – and what we hear matters more than ever
As the United States and Russia signal a return to nuclear testing, Australia’s remote monitoring station plays a crucial role in global verification.
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James Ferguson @psy-fer.bsky.social · 07/02/2026
So i've been doing this, and spamming another thread with updates. I will move that over here now. I have built most of it. Currently testing on real data and squashing bugs and fixing performance issues.
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corrylab.bsky.social @corrylab.bsky.social · 02/02/2026
Beginning 2026 with a flipping good paper🚀 OSCA/TMEM63 proteins do double duty: they’re ion channels and mechanically activated lipid scramblases helping reshape membranes and survive mechanical stress. 👏 @yiechanglin.bsky.social @charlesdcox.bsky.social doi.org/10.1038/s414...
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Eduardo Eyras @edueyras.bsky.social · 20/01/2026
Thrilled to announce that I've been appointed Director of the ANU Shine Dalgarno Centre for RNA Innovation. Honoured to work with a world-class team advancing RNA science. Stay tuned for more exciting updates 🚀 jcsmr.anu.edu.au/research/cen... #RNA #RNAInnovation #ANU
jcsmr.anu.edu.au
The Shine-Dalgarno Centre for RNA Innovation
Image
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 10/12/2025
An energy-based model of protein conformational space can be used to predict structure from sequence, sample from the conformational landscape, rank structures, and predict mutation effects. @sokrypton.org www.biorxiv.org/content/10.6...
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Erik Thiede @erikhthiede.bsky.social · 05/12/2025
Bit belated, but our article on error analysis for MSMs is in JCTC! pubs.acs.org/doi/abs/10.1...
pubs.acs.org
Error Breakdown and Sensitivity Analysis of Dynamical Quantities in Markov State Models
Markov state models (MSMs) are widely employed to analyze the kinetics of complex systems. But despite their effectiveness in many applications, MSMs are prone to systematic or statistical errors, oft...
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Hasindu Gamaarachchi @hasindu2008.bsky.social · 16/10/2025
Benchmark comparing SLOW5 and POD5 for nanopore raw signal data has now been published at @GigaScience academic.oup.com/gigascience/.... Some plots required a log scale - RAM usage and random access time.
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Hasindu Gamaarachchi @hasindu2008.bsky.social · 14/09/2025
Cornetto v0.2.0-beta released github.com/hasindu2008/... Cornetto is not only an iterative assembly method for @nanoporetech.com, but also features some basic assembly evaluation tools that we implemented. Suggestions and feedback welcome!
github.com
GitHub - hasindu2008/cornetto: adaptive genome assembly using nanopore sequencing
adaptive genome assembly using nanopore sequencing - hasindu2008/cornetto
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Rob Patro @robp.bsky.social · 05/08/2025
🧬🖥️ I am strongly of the opinion that bioinformatics needs to move away entirely from text-based and "loosely" structured file formats for essentially any type of data. File formats should be binary-first, and designed for *correct* and *efficient* machine parsing 1/3
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Australian BioCommons @ausbiocommons.bsky.social · 17/07/2025
We're excited to announce that we have signed an MoU with @embl.org and @bioplatformsaus.bsky.social! This will accelerate life sciences innovation between Australia and Europe 👉 www.biocommons.org.au/news/mou-emb...
biocommons.org.au
Global collaboration across life science data infrastructures boosted by Australian BioCommons, Bioplatforms Australia and EMBL — Australian BioCommons
A new MoU fosters international collaboration across life sciences and strengthens Australian and European cooperation in science and technology.
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Bruno P. Kinoshita “kinow” @kinow.bsky.social · 06/06/2025
The Destination Earth Climate Digital Twin workflow is now open source! It's available from Destination Earth's GitHub org, soon with RO-Crate and uploaded to WorkflowHub. github.com/DestinE-Clim... & github.com/DestinE-Clim... #OpenSource #workflow #SciWorkflows #HPC
github.com
GitHub - DestinE-Climate-DT/Workflow: Development of the workflow in charge of evolving the ModelSV and periodically extracting the OutputSV, to produce the GSV, already projected to the observation space. This workflow, together with the one developed in DE_34080 (WP8) for the consumption of the GSV by the applications, will constitute the greater climate DT workflow.
Development of the workflow in charge of evolving the ModelSV and periodically extracting the OutputSV, to produce the GSV, already projected to the observation space. This workflow, together with ...
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Hasindu Gamaarachchi @hasindu2008.bsky.social · 03/05/2025
Realfreq, a framework for real-time base modification analysis for nanopore sequencing, is now published in Bioinformatics. Written efficiently using C, a laptop can keep up with a @nanoporetech.com MinION sequencer, and a desktop a PromethION 2 solo flowcell. academic.oup.com/bioinformati...
academic.oup.com
Realfreq: real-time base modification analysis for nanopore sequencing
AbstractSummary. Nanopore sequencers allow sequencing data to be accessed in real-time. This allows live analysis to be performed, while the sequencing is
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Matt Field @mattfield100.bsky.social · 26/02/2025
An opportunity exists for an exceptional early career bioinformatician to join the Field lab in tropical Cairns Australia, home of the Great Barrier Reef. Job offered until Dec 2026 however extension possible. Internationals welcome to apply. Closes Mar 26th! careers.jcu.edu.au/jobs/postdoc...
careers.jcu.edu.au
Postdoctoral Research Fellow, Bioinformatics - Cairns, QLD, Australia
James Cook University (JCU) is creating a brighter future for life in the Tropics and beyond, through education and research that makes a difference locally and globally.  We now have an opportunity a...
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Jorge Luis Gálvez Vallejo @jorgegalvez.bsky.social · 25/02/2025
On behalf of the Association of Molecular Modellers of Australasia, I am happy to invite you to our newly established Webinar series! Last month we had the opportunity to host Professor Debra Bernhardt where she talked about strategies and suggestions for DECRA and Discovery Project applications.
lnkd.in
LinkedIn
This link will take you to a page that’s not on LinkedIn
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Anna Trigos @annatrigos.bsky.social · 17/02/2025
First post in Bluesky! I am hiring a postdoc with a background in deep learning/AI to drive projects aimed at extracting biologically and clinically relevant information from cancer patient imaging, including PET and CT scans, and multi-omics data. careers.petermac.org/job/MELBOURN...
careers.petermac.org
Postdoctoral Researcher in Deep Learning
Postdoctoral Researcher in Deep Learning
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Ryan Wick @rrwick.bsky.social · 21/02/2025
I re-ran previous ONT basecalling benchmarks using the latest version of Dorado (thanks, @vellamike.bsky.social), and the RTX 40 series GPUs show an impressive speed boost! Check out the updated benchmark results at the bottom of this post: rrwick.github.io/2024/08/16/s...
rrwick.github.io
Spring OnION: a high-spec laptop for ONT sequencing
a blog for miscellaneous bioinformatics stuff
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Fred Jaya @fredjaya.bsky.social · 15/01/2025
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
usyd.wd3.myworkdayjobs.com
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...
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Emi Tanaka @emitanaka.org · 18/12/2024
Job alert 🔈 We are seeking 3 postdocs in #statistics, data science, machine learning, bioinformatics, quantitative biology or related discipline for the Analytics for Australian Grains Industry collaboration. #agriculture #databs See more information here: jobs.anu.edu.au/jobs/postdoc...
jobs.anu.edu.au
Postdoctoral/Research Fellow - Canberra / ACT, ACT, Australia
Classification: Academic Level A/BSalary package: $85,010 - $131,227 per annum plus 17% superannuationTerm: 3x Full-time, Fixed Term (Up to December 2027) The Position Three academic positions are ava...
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