#bioinformatics — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #bioinformatics, aggregated by home.social.
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@smaurizi The reasons to migrate to #EmergingEconomies in #DevelopingCountries, are multiplying.
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Pipeline release! nf-core/raredisease v3.0.0 - 3.0.0 - Mario!
Call and score variants from WGS/WES of rare disease patients.
Please see the changelog: https://github.com/nf-core/raredisease/releases/tag/3.0.0#diagnostics #raredisease #snv #structuralvariants #variantannotation #variantcalling #wes #wgs #nfcore #openscience #nextflow #bioinformatics
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Put together a #Julialang monitoring script to keep an eye on gradient norm spikes in ONT basecalling model training. Need to figure out if I can afford another epoch and if learning rate needs to decrease.
All done on my phone while on a warehouse shift coffee break! What a world.
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Put together a #Julialang monitoring script to keep an eye on gradient norm spikes in ONT basecalling model training. Need to figure out if I can afford another epoch and if learning rate needs to decrease.
All done on my phone while on a warehouse shift coffee break! What a world.
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Put together a #Julialang monitoring script to keep an eye on gradient norm spikes in ONT basecalling model training. Need to figure out if I can afford another epoch and if learning rate needs to decrease.
All done on my phone while on a warehouse shift coffee break! What a world.
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Put together a #Julialang monitoring script to keep an eye on gradient norm spikes in ONT basecalling model training. Need to figure out if I can afford another epoch and if learning rate needs to decrease.
All done on my phone while on a warehouse shift coffee break! What a world.
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⚛️ Can spherical voxelization improve how AI interprets protein chemistry and interactions?
🔗 SpheronizaTor: Spherical Voxelization for Interpretable Protein Microenvironment Modeling. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0076
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#StructuralBiology #Bioinformatics #ComputationalBiology #ProteinStructure #ArtificialIntelligence #ProteinEngineering #ProteinModeling
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Speaking of - anyone know if there's any documentation/literature on how ONT put together their bacterial dorado polishing model?
I know it fares well in benchmarks, but curious about non-bacterial prokaryotes. Is anyone putting together their own polishing models for test?
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Speaking of - anyone know if there's any documentation/literature on how ONT put together their bacterial dorado polishing model?
I know it fares well in benchmarks, but curious about non-bacterial prokaryotes. Is anyone putting together their own polishing models for test?
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Speaking of - anyone know if there's any documentation/literature on how ONT put together their bacterial dorado polishing model?
I know it fares well in benchmarks, but curious about non-bacterial prokaryotes. Is anyone putting together their own polishing models for test?
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Speaking of - anyone know if there's any documentation/literature on how ONT put together their bacterial dorado polishing model?
I know it fares well in benchmarks, but curious about non-bacterial prokaryotes. Is anyone putting together their own polishing models for test?
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Speaking of - anyone know if there's any documentation/literature on how ONT put together their bacterial dorado polishing model?
I know it fares well in benchmarks, but curious about non-bacterial prokaryotes. Is anyone putting together their own polishing models for test?
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"Empirically determined baseline masking strategies and other considerations for gene-level burden tests"
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"Empirically determined baseline masking strategies and other considerations for gene-level burden tests"
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"Empirically determined baseline masking strategies and other considerations for gene-level burden tests"
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"Empirically determined baseline masking strategies and other considerations for gene-level burden tests"
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"Empirically determined baseline masking strategies and other considerations for gene-level burden tests"
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RE: https://mastodon.social/@killercup/116538545269011416
Extremely cool stuff coming from the team here: a performance-focused, compile-time type checked alternative to htslib. #nerdcore #bioinformatics #ngs
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RE: https://mastodon.social/@killercup/116538545269011416
Extremely cool stuff coming from the team here: a performance-focused, compile-time type checked alternative to htslib. #nerdcore #bioinformatics #ngs
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RE: https://mastodon.social/@killercup/116538545269011416
Extremely cool stuff coming from the team here: a performance-focused, compile-time type checked alternative to htslib. #nerdcore #bioinformatics #ngs
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RE: https://mastodon.social/@killercup/116538545269011416
Extremely cool stuff coming from the team here: a performance-focused, compile-time type checked alternative to htslib. #nerdcore #bioinformatics #ngs
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RE: https://mastodon.social/@killercup/116538545269011416
Extremely cool stuff coming from the team here: a performance-focused, compile-time type checked alternative to htslib. #nerdcore #bioinformatics #ngs
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Just shipped v0.1.0 of CellSeg — an open-source Android app that runs Cellpose cell segmentation on-device
Free, MIT-licensed, no ads, no tracking. ~14 MB cyto3 ONNX model, runs fully offline after first download. Optional Cellpose-SAM cloud fallback via Hugging Face for harder cases
Written up the launch with the architecture, the licensing chapter, and an honest list of what v0.1.0 isn't yet:
https://kemal.yaylali.uk/cellseg-v0-1-0-is-out/
#bioinformatics #microscopy #cellpose #android #buildinpublic #opensource
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Just shipped v0.1.0 of CellSeg — an open-source Android app that runs Cellpose cell segmentation on-device
Free, MIT-licensed, no ads, no tracking. ~14 MB cyto3 ONNX model, runs fully offline after first download. Optional Cellpose-SAM cloud fallback via Hugging Face for harder cases
Written up the launch with the architecture, the licensing chapter, and an honest list of what v0.1.0 isn't yet:
https://kemal.yaylali.uk/cellseg-v0-1-0-is-out/
#bioinformatics #microscopy #cellpose #android #buildinpublic #opensource
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Just shipped v0.1.0 of CellSeg — an open-source Android app that runs Cellpose cell segmentation on-device
Free, MIT-licensed, no ads, no tracking. ~14 MB cyto3 ONNX model, runs fully offline after first download. Optional Cellpose-SAM cloud fallback via Hugging Face for harder cases
Written up the launch with the architecture, the licensing chapter, and an honest list of what v0.1.0 isn't yet:
https://kemal.yaylali.uk/cellseg-v0-1-0-is-out/
#bioinformatics #microscopy #cellpose #android #buildinpublic #opensource
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Just shipped v0.1.0 of CellSeg — an open-source Android app that runs Cellpose cell segmentation on-device
Free, MIT-licensed, no ads, no tracking. ~14 MB cyto3 ONNX model, runs fully offline after first download. Optional Cellpose-SAM cloud fallback via Hugging Face for harder cases
Written up the launch with the architecture, the licensing chapter, and an honest list of what v0.1.0 isn't yet:
https://kemal.yaylali.uk/cellseg-v0-1-0-is-out/
#bioinformatics #microscopy #cellpose #android #buildinpublic #opensource
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Just shipped v0.1.0 of CellSeg — an open-source Android app that runs Cellpose cell segmentation on-device
Free, MIT-licensed, no ads, no tracking. ~14 MB cyto3 ONNX model, runs fully offline after first download. Optional Cellpose-SAM cloud fallback via Hugging Face for harder cases
Written up the launch with the architecture, the licensing chapter, and an honest list of what v0.1.0 isn't yet:
https://kemal.yaylali.uk/cellseg-v0-1-0-is-out/
#bioinformatics #microscopy #cellpose #android #buildinpublic #opensource
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Working with data from Metabolomics Workbench again, and it always feels like the data is yelling at me with the fields in all caps.
Now that I've double checked, the Protein Data Bank file format was like this too, all caps everywhere (even more so).
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Pipeline release! nf-core/rnaseq v3.26.0 - nf-core/rnaseq v3.26.0 - Chromium Cuttlefish!
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.26.0 -
Pipeline release! nf-core/rnaseq v3.26.0 - nf-core/rnaseq v3.26.0 - Chromium Cuttlefish!
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.26.0 -
Pipeline release! nf-core/rnaseq v3.26.0 - nf-core/rnaseq v3.26.0 - Chromium Cuttlefish!
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.26.0 -
Pipeline release! nf-core/rnaseq v3.26.0 - nf-core/rnaseq v3.26.0 - Chromium Cuttlefish!
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.26.0 -
Pipeline release! nf-core/rnaseq v3.26.0 - nf-core/rnaseq v3.26.0 - Chromium Cuttlefish!
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.26.0 -
https://primateai3d.basespace.illumina.com/
PrimateAI scores measures the pathogenicity of protein coding missense variants. When the score is close to one, it means the variant is highly likely deleterious; whereas when it is close to 0, it is generally considered benign. It is recommended to use PrimateAI score cutoff of 0.8 to distinguish benign variants from deleterious variants.
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https://primateai3d.basespace.illumina.com/
PrimateAI scores measures the pathogenicity of protein coding missense variants. When the score is close to one, it means the variant is highly likely deleterious; whereas when it is close to 0, it is generally considered benign. It is recommended to use PrimateAI score cutoff of 0.8 to distinguish benign variants from deleterious variants.
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https://primateai3d.basespace.illumina.com/
PrimateAI scores measures the pathogenicity of protein coding missense variants. When the score is close to one, it means the variant is highly likely deleterious; whereas when it is close to 0, it is generally considered benign. It is recommended to use PrimateAI score cutoff of 0.8 to distinguish benign variants from deleterious variants.
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https://primateai3d.basespace.illumina.com/
PrimateAI scores measures the pathogenicity of protein coding missense variants. When the score is close to one, it means the variant is highly likely deleterious; whereas when it is close to 0, it is generally considered benign. It is recommended to use PrimateAI score cutoff of 0.8 to distinguish benign variants from deleterious variants.
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https://primateai3d.basespace.illumina.com/
PrimateAI scores measures the pathogenicity of protein coding missense variants. When the score is close to one, it means the variant is highly likely deleterious; whereas when it is close to 0, it is generally considered benign. It is recommended to use PrimateAI score cutoff of 0.8 to distinguish benign variants from deleterious variants.
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Pipeline release! nf-core/bacass v2.6.0 - nf-core/bacass v2.6.0 - Crimson Titanium Seahorse!
Simple bacterial assembly and annotation pipeline
Please see the changelog: https://github.com/nf-core/bacass/releases/tag/2.6.0#assembly #bacterialgenomes #denovo #denovoassembly #genomeassembly #hybridassembly #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics
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Pipeline release! nf-core/bacass v2.6.0 - nf-core/bacass v2.6.0 - Crimson Titanium Seahorse!
Simple bacterial assembly and annotation pipeline
Please see the changelog: https://github.com/nf-core/bacass/releases/tag/2.6.0#assembly #bacterialgenomes #denovo #denovoassembly #genomeassembly #hybridassembly #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics
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Pipeline release! nf-core/bacass v2.6.0 - nf-core/bacass v2.6.0 - Crimson Titanium Seahorse!
Simple bacterial assembly and annotation pipeline
Please see the changelog: https://github.com/nf-core/bacass/releases/tag/2.6.0#assembly #bacterialgenomes #denovo #denovoassembly #genomeassembly #hybridassembly #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics
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Pipeline release! nf-core/bacass v2.6.0 - nf-core/bacass v2.6.0 - Crimson Titanium Seahorse!
Simple bacterial assembly and annotation pipeline
Please see the changelog: https://github.com/nf-core/bacass/releases/tag/2.6.0#assembly #bacterialgenomes #denovo #denovoassembly #genomeassembly #hybridassembly #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics
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Pipeline release! nf-core/bacass v2.6.0 - nf-core/bacass v2.6.0 - Crimson Titanium Seahorse!
Simple bacterial assembly and annotation pipeline
Please see the changelog: https://github.com/nf-core/bacass/releases/tag/2.6.0#assembly #bacterialgenomes #denovo #denovoassembly #genomeassembly #hybridassembly #nanopore #nanoporesequencing #nfcore #openscience #nextflow #bioinformatics
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🧬 Could a single metric decode how genes are regulated across cells?
🔗 Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0044
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#GeneRegulation #Genomics #MultiOmics #SystemsBiology #Bioinformatics #ComputationalBiology #MolecularBiology #RNA #GeneExpression #Epigenetics #Transcriptomics
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🧬 Could a single metric decode how genes are regulated across cells?
🔗 Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0044
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#GeneRegulation #Genomics #MultiOmics #SystemsBiology #Bioinformatics #ComputationalBiology #MolecularBiology #RNA #GeneExpression #Epigenetics #Transcriptomics
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🧬 Could a single metric decode how genes are regulated across cells?
🔗 Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0044
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#GeneRegulation #Genomics #MultiOmics #SystemsBiology #Bioinformatics #ComputationalBiology #MolecularBiology #RNA #GeneExpression #Epigenetics #Transcriptomics
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🧬 Could a single metric decode how genes are regulated across cells?
🔗 Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0044
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#GeneRegulation #Genomics #MultiOmics #SystemsBiology #Bioinformatics #ComputationalBiology #MolecularBiology #RNA #GeneExpression #Epigenetics #Transcriptomics
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🧬 Could a single metric decode how genes are regulated across cells?
🔗 Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms. Computational and Structural Biotechnology Journal (CSBJ). DOI: https://doi.org/10.34133/csbj.0044
📚 CSBJ - A Science Partner Journal: https://spj.science.org/journal/csbj
#GeneRegulation #Genomics #MultiOmics #SystemsBiology #Bioinformatics #ComputationalBiology #MolecularBiology #RNA #GeneExpression #Epigenetics #Transcriptomics
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Performance test of QNome nanopore sequencer. Looks very interesting - I'm always on the lookout for alternate platforms for Binomica. More reason for us to build platform agnostic squiggle/QC tools for the future!
https://www.biorxiv.org/content/10.64898/2026.04.29.721586v1
