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Would you be interested in organizing or speaking at meetups, writing blog posts, or promoting the project?
Are you part of any communities or organizations where you could share our project? #annotator #opencravat #bioinformatics #opensource #genomics
Continued thread
Can you help test new features or provide feedback on pre-release versions?
Would you be interested in setting up automated test cases or improving test coverage?
Would you be open to helping improve documentation or writing user guides?
Do you have skills in UI/UX design, and would you be interested in helping us improve the user interface?
#annotator #opencravat #bioinformatics #opensource #genomics
We are seeking community members interested in taking part in OpenCRAVAT's future.
Let us know if you might contribute in any of these areas:
Would you be interested in contributing code, bug fixes, or performance improvements?
Are there features or issues you’d like to help implement or debug?
Would you be willing to review pull requests or help triage GitHub issues?
#annotator #opencravat #bioinformatics #opensource #genomics
Structural motif search across the protein-universe with Folddisco
https://www.biorxiv.org/content/10.1101/2025.07.06.663357v1
I was just wondering the other day if there was already a tool to do this :) @martinsteinegger
bioRxiv · Structural motif search across the protein-universe with FolddiscoDetecting similar protein structural motifs, functionally crucial short 3D patterns, in large structure collections is computationally prohibitive. Therefore, we developed Folddisco, which overcomes this through an index of position-independent geometric features, including side-chain orientation, combined with a rarity-based scoring system. Folddisco indexes 53 million AFDB50 structures into 1.45 terabyte within 24 hours, enabling rapid detection of discontinuous or segment motifs. Folddisco is more accurate and storage-efficient than state-of-the-art methods, while being an order of magnitude faster. Folddisco is free software available at folddisco.foldseek.com and a webserver at https://search.foldseek.com/folddisco.
### Competing Interest Statement
M.S. acknowledges outside interest in Stylus Medicine. The remaining authors declare no competing interests.
National Research Foundation of Korea, https://ror.org/013aysd81, 2020M3A9G7103933, RS-2021-NR061659, RS-2021-NR056571, RS-2024-00396026, RS-2023-00250470
Novo Nordisk Foundation, https://ror.org/04txyc737, NNF24SA0092560
Just found https://genomicsclass.github.io/book/ by Rafael Irizarry and Michael Love and what a find! If you analyse genomic/transcriptomic data, that book has got you covered! #bioinformatics
genomicsclass.github.ioPH525x series - Biomedical Data Science
When you put the Lysenkos in charge:
Famed protein structure competition nears end as NIH grant money runs out
@bioinformatics @strucbio
#Bioinformatics
#StructuralBiology
Can AI help decode how antibodies recognize cancer-related proteins like HER2?
Investigating and evaluating potential antigen binding sites for monoclonal anti-HER2 antibodies: The LightDock approach. Computational and Structural Biotechnology Journal, DOI: https://doi.org/10.1016/j.csbj.2025.06.001
CSBJ: https://www.csbj.org/
Continued thread
In writing this blog post I realise how little I’ve looked at my ACGT blog site. I immediately noticed that I was still using a Twitter link in the footer and that has now been remedied!
Continued thread
Their podcast episode - which led to my reminiscing of bad bioinformatics names - can be listened to here:
https://podcasts.apple.com/gb/podcast/ep-50-software-naming/id1699223787?i=1000697540817
Apple PodcastsEP 50: Software NamingPodcast Episode · the bioinformatics lab · 03/03/2025 · 10m
I started this morning tried to tidy up some old notes files and ended up writing a new ACGT genomics blog post as a result!
This all came about when trying to find out whether a note I had was a previous blog post of mine or not. In searching the web, I came across a podcast on bad bioinformatics names by Andrew Page and Kevin Libuit and it prompted me to write:
Bad bioinformatics sofware names revisited
https://www.acgt.me/blog/2025/7/6/bad-bioinformatics-software-names-revisited
ACGTBad bioinformatics software names revisited — ACGT
https://www.europesays.com/uk/240940/ The role of untranslated region variants in Mendelian disease: a review #Bioinformatics #Biomedicine #Cytogenetics #DiseaseGenetics #GeneExpression #GeneRegulation #general #Genetics #HumanGenetics #Science #UK #UnitedKingdom
https://www.europesays.com/us/38222/ A homozygous frameshift variant in the CILK1 gene causes cranioectodermal dysplasia #Bioinformatics #Biomedicine #Cytogenetics #DiseaseGenetics #GeneExpression #general #Genetics #GeneticsResearch #HumanGenetics #LiverFibrosis #PaediatricKidneyDisease #Science #UnitedStates #UnitedStates #US
Job - Alert
Computational Scientist/ Bioinformatician (postdoc level) (m/f/d)
Deadline: 2025-07-27
Location: Germany, Regensburg, Bayern
https://www.academiceurope.com/ads/computational-scientist-bioinformatician-postdoc-level-m-f-d/
Pipeline release! nf-core/methylseq v4.0.0 - Wallace Chrysalis!
Please see the changelog: https://github.com/nf-core/methylseq/releases/tag/4.0.0
GitHubRelease Wallace Chrysalis · nf-core/methylseqnf-core/methylseq v4.0.0 Release Notes
This release introduces major new features, significant refactoring, and extensive test suite improvements. Key highlights include the addition of a targeted ...
#bioinformatics #microbiology #assembly question. I'm looking through some new archaeal genome assemblies, and some of the species show perfect assembly output except in one plasmid - always in about 1k different contigs of braided alternate paths but graph together nonetheless. Is this a biological signature of something?
Pipeline release! nf-core/drugresponseeval v1.1.0 - Drugresponseeval 1.1.0 - Humongous Zapdos!
Please see the changelog: https://github.com/nf-core/drugresponseeval/releases/tag/1.1.0
GitHubRelease Drugresponseeval 1.1.0 - Humongous Zapdos · nf-core/drugresponseevalWhat's Changed
Added
#43 Preprint is out now! Linking it in the documentation.
#42 Added authors and licenses to the python scripts.
#43 Added --no_hyperparameter_tuning flag for quick runs withou...
New Bioconductor blog post!
Written during #GBCC2025 CoFest, this post highlights recent work to bring Bioconductor tools into Galaxy, featuring training materials, wrapper examples, and ideas for tool developers.
Read more 
https://blog.bioconductor.org/posts/2025-07-03-bioc-to-galaxy/
Bioconductor community blogBringing Bioconductor to Galaxy: A CoFest Collaboration – Bioconductor community blogWritten during CoFest at GBCC2025, this post shares training materials, introduces Galaxy tool wrapping, and previews what’s next for integrating Bioconductor tools in Galaxy.
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