George Bouras
@gbouras13.bsky.social
📤 1174
📥 336
📝 60
Bioinformatics @ University of Adelaide - phages, microbes and more
pinned post!
Phold's manuscript is now available
@narjournal.bsky.social
thanks to
@susiegriggo.bsky.social
@npbhavya.bsky.social
@vijinim.bsky.social
@linsalrob.bsky.social
@martinsteinegger.bsky.social
@milot.bsky.social
@eunbelivable.bsky.social
& others not on bsky
#phagesky
academic.oup.com/nar/article/...
add a skeleton here at some point
3 months ago
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George Bouras
Pedro Beltrao
19 minutes ago
We have updated the yeast AlphaFold3 co-folding map. The 15GB docker also has an updated streamlit app that is more responsive and easier to search through if you want to just browse the results. There will be many false positives ! We added known interactions for those wanting to filter.
add a skeleton here at some point
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reposted by
George Bouras
Sam Horsfield
1 day ago
ggCaller v1.5.0 is out! We've removed the integrated clustering to enable users to benefit from new Panaroo features. Now, ggCaller generates GFFs that can be used with any clustering method. But for fans of an integrated ggCaller pangenome workflow read on...
github.com/bacpop/ggCal...
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GitHub - bacpop/ggCaller: Bifrost graph gene caller.
Bifrost graph gene caller. Contribute to bacpop/ggCaller development by creating an account on GitHub.
https://github.com/bacpop/ggCaller
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reposted by
George Bouras
naturepoker
2 days ago
#Archaeasky
folks - I'm curious. How do you feel about the dorado polish bacteria mode for your archaeal ONT long read assembled genomes? I know it holds up well with bacteria, but archaea's always been a bit funny. 💻🧬
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reposted by
George Bouras
Hasindu Gamaarachchi
3 days ago
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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reposted by
George Bouras
Jim Shaw
4 days ago
Myloasm, our long-read metagenome assembler, is now published! w/
@mgmarin.bsky.social
and
@lh3lh3.bsky.social
Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback.
rdcu.be/famFj
add a skeleton here at some point
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reposted by
George Bouras
Martin Steinegger 🇺🇦
15 days ago
AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions 📄
research.nvidia.com/labs/dbr/ass...
🌐
alphafold.ebi.ac.uk
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George Bouras
EMBL-EBI
15 days ago
You asked, we listened. Millions of AI-predicted protein complex structures are now available in the
#AlphaFold
Database. This spans homodimers from 20 of the most studied species, including humans, as well as the World Health Organization’s priority pathogens list.
www.ebi.ac.uk/about/news/t...
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George Bouras
Dr Andrew Lonsdale
21 days ago
Some background to this, and an example I think of Phil's attitudes towards fostering students and encouraging others. I never got a chance to meet Phil in person, but will share his act of generosity that helped myself and
@hdashnow.bsky.social
and I think had in indelible mark on our careers. 1/8
add a skeleton here at some point
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reposted by
George Bouras
Anton Bushuiev
26 days ago
ProteinTTT is now easy to run on Hugging Face Spaces and Google Colab. We’ll also be presenting the paper at ICLR 2026 🇧🇷 🤗 Hugging Face Space:
huggingface.co/spaces/pimen...
⚙️ Google Colab:
colab.research.google.com/drive/1l_h7c...
🧵👇
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reposted by
George Bouras
Michael Hall
26 days ago
Until joining
@loolibear.bsky.social
's lab in July, I embarrassingly hadn't had much experience with plasmids. So when I started, Leah said "here you go, have a look at this dataset". What a fun ride this has been. Preprint out today and thread below
www.medrxiv.org/content/10.6...
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Novel transposon Tn8026 acts as a global driver of transmissible linezolid resistance in Enterococcus via a linear plasmid
Linezolid is a critical last-resort antimicrobial for multidrug-resistant Enterococcus faecium , particularly against vancomycin-resistant lineages where therapeutic options are severely limited. Whil...
https://www.medrxiv.org/content/10.64898/2026.03.04.26347163v1
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reposted by
George Bouras
Torsten Seemann
about 1 month ago
Joining the All-The-Bacteria project provides an annualised return on investment of 8.9% bacterial genomes.
add a skeleton here at some point
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reposted by
George Bouras
Zamin Iqbal
about 1 month ago
Courtesy of
@martibartfast.bsky.social
, we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025.
allthebacteria.readthedocs.io/en/latest/ov...
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Overview — AllTheBacteria documentation
https://allthebacteria.readthedocs.io/en/latest/overview.html
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reposted by
George Bouras
Zamin Iqbal
about 1 month ago
@wytamma.bsky.social
's WASM tools have transformed my experience of teaching Python to first year undergraduate biologists this year. Since last year, I've been teaching ~400 undergrads how to code (functions, lists, dictionaries, loops) over (one hour intro lecture +) two 2-hour practicals. 1/n
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George Bouras
Rob Edwards
about 1 month ago
The
@isvm-society.bsky.social
is organising monthly
#virus
of
#microbes
(including
#phage
). Nominate a speaker and register for the upcoming events at
isvm.org/ivom/
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iVoMs – ISVM
https://isvm.org/ivom/
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Super happy that the AllTheBacteria hypothetical proteins are now in AFDB - hopefully we can start to understand the function of some of them at least 😁
add a skeleton here at some point
about 1 month ago
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reposted by
George Bouras
Zamin Iqbal
about 1 month ago
Delighted to see over 17 million new protein structure predictions from novel proteins in AllTheBacteria are now integrated into the AlphaFold Database at
@ebi.embl.org
! Huge work from
@gbouras13.bsky.social
@oschwengers.bsky.social
and friends to generate these.
www.ebi.ac.uk/about/news/u...
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AlphaFold Database welcomes community datasets
Latest AlphaFold Database update adds high-value datasets for microbial and viral proteins, generated by specialist communities
https://www.ebi.ac.uk/about/news/updates-from-data-resources/alphafold-database-community-datasets/
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George Bouras
Spyros Lytras
about 2 months ago
Our paper on inferring context dependent entropy using protein language models is officially out in NAR Genomics & Bioinformatics! 🧬🤖 with Adam Strange, Jumpei Ito, and
@systemsvirology.bsky.social
academic.oup.com/nargab/artic...
details below...
#NARGAB
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Inferring context-specific site variation with evotuned protein language models
Abstract. Multiple sequence alignments (MSAs) have been traditionally used for making inferences about site-specific diversity in proteins. Recent advancem
https://academic.oup.com/nargab/article/8/1/lqag018/8468463
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reposted by
George Bouras
John Lees
about 2 months ago
How do bacterial pangenomes evolve, what controls their dynamics, why do they exist? Fitting a mechanistic model to 450 species from
allthebacteria.org
suggesting fast vs slow gene exchange (i.e. amount of MGEs) is a major differentiating factor, correlated with phylogeny rather than lifestyle
add a skeleton here at some point
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reposted by
George Bouras
Zamin Iqbal
about 2 months ago
A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by
@martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)
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Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods
This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.
https://www.nature.com/articles/s41592-025-02947-1
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reposted by
George Bouras
Patrick Bryant
about 2 months ago
Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure. We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
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George Bouras
Sam Horsfield
about 2 months ago
Super excited to announce the release of gene and intergenic region annotation from the largest bacterial genome and MAG datasets available, including AllTheBacteria, GTDB, SPIRE, HRGM, mOTUs and MGnify - dereplicated and available from HuggingFace
huggingface.co/AllTheBacteria
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Hugging Face – The AI community building the future.
We’re on a journey to advance and democratize artificial intelligence through open source and open science.
https://huggingface.co
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George Bouras
Ryan Wick
about 2 months ago
New blog post: ONT read QC strategies for assembly
rrwick.github.io/2026/02/05/r...
Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.
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ONT read QC strategies for assembly
a blog for miscellaneous bioinformatics stuff
https://rrwick.github.io/2026/02/05/read_qc_testing.html
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George Bouras
Oliver Schwengers
about 2 months ago
🦠🧬🖥️ Bakta v1.12.0 is out with tons of tiny improvements and bug fixes, too many to list all: - partial genes on linear seqs - improved errror handlings & runtimes - support Python 3.12 & 3.13 - ... A huge shout out and thank you to all bug reporters and contributors!
github.com/oschwengers/...
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Release v1.12 - Just do it, but don't crash · oschwengers/bakta
This is the twelfth minor release (v1.12) providing more than 10 minor improvements and many bug fixes improving runtime stability, IO compatibility, and last but not least user experience. Compati...
https://github.com/oschwengers/bakta/releases/tag/v1.12.0
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reposted by
George Bouras
Asaf Levy
2 months ago
A new paper from the lab on virus-like particles called eCISs
www.nature.com/articles/s41...
How bacteria evolved thousands of precision nanoinjectors? Some bacteria don’t secrete toxins — they inject them using phage-derived machines called extracellular contractile injection systems (eCISs).
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A comprehensive catalogue of receptor-binding domains in extracellular contractile injection systems - Nature Communications
Extracellular contractile injection systems (eCISs) are bacteriophage tail-derived toxin delivery complexes that are present in many prokaryotes. Here, the authors present an analysis of eCIS tail fib...
https://www.nature.com/articles/s41467-026-68710-y
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reposted by
George Bouras
Martin Steinegger 🇺🇦
2 months ago
FoldMason is out now in
@science.org
. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and
@milot.bsky.social
. 📄
www.science.org/doi/10.1126/...
🌐
search.foldseek.com/foldmason
💾
github.com/steineggerla...
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Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
https://www.science.org/eprint/4QQQFGCSQEGFJVGUESWN/full?activationRedirect=/doi/full/10.1126/science.ads6733
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George Bouras
Hasindu Gamaarachchi
2 months ago
slow5tools v1.4.0 released
github.com/hasindu2008/...
Many bit profiles for ex-zd lossy compression added by @hiruna72, who reduced 275TB of historical @nanopore rawdata at @GenTechGp to 172TB. guide to lossy archive:
hasindu2008.github.io/slow5tools/a...
paper:
doi.org/10.1101/gr.2...
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Release slow5tools-v1.4.0 · hasindu2008/slow5tools
What's Changed slow5tools skim supports the new auxiliary field open_pore_level introduced in latest ONT pod5 slow5tools degrade has new profiles added (by @sashajenner and @hiruna72) and are docu...
https://github.com/hasindu2008/slow5tools/releases/tag/v1.4.0
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reposted by
George Bouras
Jim Shaw
2 months ago
Announcing a new tool for "denoising" long-read amplicon sequences: savont. Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay. 1/4
github.com/bluenote-157...
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GitHub - bluenote-1577/savont: Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads
Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont
https://github.com/bluenote-1577/savont
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reposted by
George Bouras
Dongwook Kim
2 months ago
Can ever-increasing sequence databases improve phylogenetic reconstruction of a gene family? Our new preprint introduces AmpliPhy, a pipeline that automates homolog enrichment to improve gene tree inference, built on a robust phylogenomic benchmark scheme. 🧵1/n 📃
doi.org/10.64898/2026.01.26.701724
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AmpliPhy improves gene trees by adding homologs without affecting alignments
In phylogenomics, gene tree reconstruction depends on multiple sequence alignment (MSA) and tree inference, and ongoing work continues to improve inference quality. Denser taxon sampling has been associated with improved gene tree inference, suggesting that adding homologs could be a practical route to higher accuracy as sequence databases continue to expand. However, adding sequences can influence multiple steps of typical inference pipelines, and little is known on its specific effect on the multiple sequence alignment, tree reconstruction, and rooting steps. We performed a large-scale empirical benchmark to quantify how homolog enrichment affects alignment and phylogenetic inference. Using an enrichment-impoverishment design and a measure of tree accuracy based on taxonomic congruence, we found that enrichment consistently improves tree inference quality, while effects on alignment quality are marginal. We show that this improvement is associated with accurate root placement on enriched trees when sensitive homolog search is accompanied. Notably, much of the benefit can be retained with relatively compact alignments produced by sequence addition. Building on these observations, we provide a tool, AmpliPhy, which efficiently improves phylogenetic reconstruction of protein families through homolog enrichment. The AmpliPhy open-source pipeline software is available at https://github.com/DessimozLab/ampliphy. ### Competing Interest Statement The authors have declared no competing interest. Swiss National Science Foundation, https://ror.org/00yjd3n13, 216623, 10005715
https://doi.org/10.64898/2026.01.26.701724
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reposted by
George Bouras
Rob Edwards
2 months ago
New 2026 iVoM series coming up! Each session includes SCR and 3 ECRs, & plenty of opportunities to interact with the speakers and ask questions. Sign up for links/updates:
docs.google.com/forms/d/1hAB...
First up: Viral Biotechnologies Wed, 28 th January at 17:00 CET / 11:00 EST / 08:00 PST
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Registration form for iVoM4
After submitting this form, you will receive the instructions to join our webinars at the email address you provide.
https://docs.google.com/forms/d/1hABmyJirdMcyrHfWX_1y0vibB_iiQFN6CdeaVqyDlCs/viewform?edit_requested=true#settings
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reposted by
George Bouras
Ryan Wick
2 months ago
New blog post with some thoughts on
@nanoporetech.com
and their recent announcement that the P2 Solo will be discontinued:
rrwick.github.io/2026/01/21/p...
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P2 Solo announcement and the trade-offs of a more stable ONT
a blog for miscellaneous bioinformatics stuff
https://rrwick.github.io/2026/01/21/p2_solo.html
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reposted by
George Bouras
Milot Mirdita
2 months ago
My time in
@martinsteinegger.bsky.social
's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org
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Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning
Mirdita Lab builds scalable bioinformatics methods.
https://mirdita.org/
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George Bouras
Torsten Seemann
2 months ago
🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup. libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements.
#unix
github.com/ebiggers/lib...
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GitHub - ebiggers/libdeflate: Heavily optimized library for DEFLATE/zlib/gzip compression and decompression
Heavily optimized library for DEFLATE/zlib/gzip compression and decompression - ebiggers/libdeflate
https://github.com/ebiggers/libdeflate
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George Bouras
naturepoker
3 months ago
Heng Li's lab is looking for a postdoc, "algorithms for sequence alignment, pangenome representation, application of pangenome data structures, or other projects". C/C++/rust proficiency needed.
hlilab.github.io/vacancies
💻🧬
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HLi Lab - Vacancies
Openings
https://hlilab.github.io/vacancies
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Phold's manuscript is now available
@narjournal.bsky.social
thanks to
@susiegriggo.bsky.social
@npbhavya.bsky.social
@vijinim.bsky.social
@linsalrob.bsky.social
@martinsteinegger.bsky.social
@milot.bsky.social
@eunbelivable.bsky.social
& others not on bsky
#phagesky
academic.oup.com/nar/article/...
add a skeleton here at some point
3 months ago
1
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reposted by
George Bouras
Brian Naughton
3 months ago
Releasing alignism, a small tool that I have found useful for doing multiple sequence alignment in browser.
hgbrian.github.io/alignism/
- The hard work was done by the awesome biowasm team! - Does tree building too - V fast compared to e.g., muscle on EBI - Not tested that much!
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reposted by
George Bouras
Torsten Seemann
3 months ago
💾 snp-dists 1.2.0 Major upgrade to this distance matrix tool - huge performance gains from multithreading (-j), max distance short circuiting (-x) and lower triangle output (-L).
#bioinformatiocs
#microbiology
#genomics
github.com/tseemann/snp...
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Release Go the distance even faster · tseemann/snp-dists
Speed major fix to CPU parallelisation - far better scaling -x maxdiff option to short-circuit distant pairs -L option to only calculate the lower triangle of the matrix (2x faster) Features -t ...
https://github.com/tseemann/snp-dists/releases/tag/v1.2.0
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reposted by
George Bouras
Torsten Seemann
3 months ago
💾 any2fasta 0.8.1 is released! The FASTA format is now 40 years old (Pearson & Lipman) and any2fasta makes it easy for your scripts and pipelines that accept FASTA to also accept other formats, even if compressed! eg. .gbk.gz
#bioinformatiocs
#microbiology
#genomcs
github.com/tseemann/any...
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Release Next time I'll try to be FASTA · tseemann/any2fasta
New features Option -k is keep processing even when some inputs fail option -g to include GBK version suffix option s to strip desc from>id desc in ID lines Support for PDB protein structure forma...
https://github.com/tseemann/any2fasta/releases/tag/v0.8.1
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reposted by
George Bouras
Torsten Seemann
3 months ago
💾 mlst 2.25.0 has been released! Fixed a bug that missed alleles in increasingly larger schemes like senterica (thanks
@microbiologikat.bsky.social
) and updated the databases.
#bioinformatiocs
#microbiology
#genomics
github.com/tseemann/mls...
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Releases · tseemann/mlst
:id: Scan contig files against PubMLST typing schemes - tseemann/mlst
https://github.com/tseemann/mlst/releases
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reposted by
George Bouras
Zamin Iqbal
3 months ago
Hey folks, am looking for examples of circularised/full plasmid sequences from "unusual " bacterial species, sequenced since 2020 (as independent validation for a plasmid identification tool that was trained on refseq2020+plsdb). Any tips?
#microsky
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reposted by
George Bouras
Oliver Schwengers
4 months ago
Honestly, as a micro binfie, I couldn't feel more honored than to be entrusted with this! 😃 Prokka has served so many so well, and deeply inspired me how to write Bakta. I'm thankful to be part of this open science com, and will do my best to meet these high quality standards. Thanks Torsten! 🦠💻
add a skeleton here at some point
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reposted by
George Bouras
Torsten Seemann
4 months ago
💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because
@oschwengers.bsky.social
already has an excellent replacement called Bakta you can migrate to.
#bioinformatics
#microbiology
#genomics
github.com/tseemann/pro...
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Release Heading into the sunset · tseemann/prokka
The future This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...
https://github.com/tseemann/prokka/releases/tag/v1.15.6
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reposted by
George Bouras
Torsten Seemann
4 months ago
💾 Shovill 1.4.1 has been released! The best way to de novo assemble microbial genomes from Illumina FASTQ. Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking.
#bioinformatiocs
#genomics
#microbiology
github.com/tseemann/sho...
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Releases · tseemann/shovill
⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads - tseemann/shovill
https://github.com/tseemann/shovill/releases
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reposted by
George Bouras
Kevin K. Yang 楊凱筌
4 months ago
Enzyme Engineering Database (EnzEngDB): a platform for sharing and interpreting sequence–function relationships across protein engineering campaigns
@francescazfl.bsky.social
@jsunn-y.bsky.social
@francesarnold.bsky.social
@arianemora.bsky.social
Paper:
doi.org/10.1093/nar/...
DB:
enzengdb.org
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reposted by
George Bouras
Evelien Adriaenssens
4 months ago
I'm proud to share the latest methods work from my group. Led by
@revathykri.bsky.social
we wrote a book chapter on how we process and analyse viromes. Thanks to co-authors
@rikhaagmans.bsky.social
@ryancook94.bsky.social
& Alise Ponsero
link.springer.com/protocol/10....
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Virome Analysis
Viruses are omnipresent and the most abundant biological entities on the planet. They play a critical role in shaping the ecology and evolution of all life forms. This chapter provides methods to perf...
https://link.springer.com/protocol/10.1007/978-1-0716-5009-7_14
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reposted by
George Bouras
Hasindu Gamaarachchi
4 months ago
Cornetto v0.2.0 is now released for using programmable selective nanopore sequencing for genome assembly. GitHub:
github.com/hasindu2008/...
Paper:
nature.com/articles/s41...
Datasets:
hasindu2008.github.io/cornetto/doc...
... and a banner made by Ira Deveson referring to ‘no boring bits’.
add a skeleton here at some point
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reposted by
George Bouras
Torsten Seemann
4 months ago
💾 ABRicate 1.2.0 has been released! This 'oversight' lasted 6 years, but with help from
@finlaym.bsky.social
we got CI working and updated all the databases.
#bioconda
#conda
#bioinformatics
#microbiology
#genomics
github.com/tseemann/abr...
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Releases · tseemann/abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes - tseemann/abricate
https://github.com/tseemann/abricate/releases
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reposted by
George Bouras
Torsten Seemann
4 months ago
This poster design was the hard work of
@wytamma.bsky.social
who is implementing Snippy-NG. You should follow him now - an amazing ECR who produces a lot of very cool stuff.
add a skeleton here at some point
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15
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reposted by
George Bouras
Vijini Mallawaarachchi
4 months ago
🚀 Just launched: GraphBin Visualise (WASM) a browser-based visualisation tool for comparing initial metagenomic binning results vs refined results from GraphBin - all running in your browser, no backend required. (1/n)
#bioinformatics
#metagenomics
#binning
#webapp
#pyiodide
#webassembly
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GitHub - metagentools/graphbin-visualise-wasm-app: GraphBin Visualise WebAssembly App
GraphBin Visualise WebAssembly App. Contribute to metagentools/graphbin-visualise-wasm-app development by creating an account on GitHub.
https://github.com/metagentools/graphbin-visualise-wasm-app
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reposted by
George Bouras
Wytamma
4 months ago
Workshop landing page with demos here ->
wasmodic.github.io
add a skeleton here at some point
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reposted by
George Bouras
Feargal Ryan
4 months ago
That’s a wrap! Huge thank you to everyone who joined us for
#ABACBS2025
& a big shout-out to the Adelaide bioinfo community who worked their butts off. Couldn’t have asked for a better crew or a better venue than Adelaide Oval.
@wessidepraxis.bsky.social
@linsalrob.bsky.social
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