AlphaFold2 / AlphaFold-Multimer structure prediction for validation and confidence scoring. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer.
EnglishDesigns Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtures for external data…
EnglishBuild whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net…
EnglishSelects informative features for biomarker discovery using Boruta all-relevant selection, mRMR minimum redundancy, and LASSO regularization.
EnglishPLINK file formats, format conversion, and quality control filtering for population genetics.
EnglishView, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam.
EnglishCreate scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution.
EnglishFull reimplementation of DnaSP 6 for population genetics analysis of aligned DNA sequences. Covers nucleotide diversity, haplotype statistics, neutrality tests (Tajima's D, Fu & Li's D/F, R2), linkage disequilibrium (D, D', R2, ZnS, Za, ZZ), minimum recombination (Rm), mismatch distribution, InDel polymorphism, between-population divergence (Dxy, Da, fixed/shared sites), outgroup-based Fu & Li D/F tests (fuliout), the HKA multi-locus neutrality test (hka), the McDonald-Kreitman test (mk), Ka/Ks (dN/dS) via the Nei-Gojobori (1986) method (kaks), Fu's Fs test (fufs), the site frequency spectrum (sfs, folded and outgroup-unfolded), transition/transversion ratio (tstv), and codon usage bias - RSCU (Sharp & Li 1987) and ENC (Wright 1990) (codon). Accepts FASTA or NEXUS input; outputs DnaSP-compatible TSV and a Markdown report.
EnglishESM2 protein language model for sequence scoring, embeddings, and plausibility checks. Use this skill when: (1) Computing pseudo-log-likelihood (PLL) scores, (2) Getting protein embeddings for clustering, (3) Filtering designs by sequence plausibility, (4) Zero-shot variant effect prediction, (5) Analyzing sequence-function relationships.
EnglishUse this model doc whenever the user wants to run FM-APP for phenotype prediction using fMRI ROI features and optional sMRI features. This document provides model-level usage and delegates preprocessing to fmri-skill and smri-skill.
EnglishPersonalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) — interrogates…
EnglishAggregate public target-level evidence across omics and translational sources for research triage.
EnglishSkills for Open-ST spatial transcriptomics data processing, from raw BCL files to spatially-resolved single-cell h5ad objects.
EnglishQuery AlphaFold protein structure predictions. Use when user asks about protein structure, 3D structure, protein folding, or structure prediction. Triggers on "alphafold", "protein structure", "3D structure", "folding", "pLDDT", "structure prediction".
EnglishSkills for biological image analysis: cell/nucleus segmentation, image restoration, and spatial data processing.
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AGENT SKILLS ATLASIncludes Alphafold2 Multimer, Bio Clinical Biostatistics Bayesian Trials, Bio Comparative Genomics Whole Genome Alignment, and other workflows.
Claude Code
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GitHub Copilot
Gemini CLISupported by the Atlas install prompt. Skill-specific requirements vary.
Pack stats
What’s included
Alphafold2 Multimer
AlphaFold2 / AlphaFold-Multimer structure prediction for validation and confidence scoring. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer.
Bio Clinical Biostatistics Bayesian Trials
Designs Bayesian clinical trials including Phase I dose-finding (BOIN, CRM, EWOC, mTPI-2), meta-analytic-predictive (MAP) priors with robust mixtures for external data bo
Bio Comparative Genomics Whole Genome Alignment
Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (U
Bio Machine Learning Biomarker Discovery
Selects informative features for biomarker discovery using Boruta all-relevant selection, mRMR minimum redundancy, and LASSO regularization. Use when identifying biomarke
Bio Population Genetics Plink Basics
PLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/BIM/FAM, and PED/MAP formats, apply MAF, genotyping
Bio Sam Bam Basics
View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignmen
Bio Workflow Management Nextflow Pipelines
Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution. Use when building portable pipelines with
Dnasp
Full reimplementation of DnaSP 6 for population genetics analysis of aligned DNA sequences. Covers nucleotide diversity, haplotype statistics, neutrality tests (Tajima's D, Fu & Li's D/F, R2), linkage disequilibrium (D, D', R2, ZnS, Za, ZZ), minimum recombination (Rm), mismatch distribution, InDel polymorphism, between-population divergence (Dxy, Da, fixed/shared sites), outgroup-based Fu & Li D/F tests (fuliout), the HKA multi-locus neutrality test (hka), the McDonald-Kreitman test (mk), Ka/Ks (dN/dS) via the Nei-Gojobori (1986) method (kaks), Fu's Fs test (fufs), the site frequency spectrum (sfs, folded and outgroup-unfolded), transition/transversion ratio (tstv), and codon usage bias - RSCU (Sharp & Li 1987) and ENC (Wright 1990) (codon). Accepts FASTA or NEXUS input; outputs DnaSP-compatible TSV and a Markdown report.
Esm2 Sequence Scoring
ESM2 protein language model for sequence scoring, embeddings, and plausibility checks. Use this skill when: (1) Computing pseudo-log-likelihood (PLL) scores, (2) Getting protein embeddings for clustering, (3) Filtering designs by sequence plausibility, (4) Zero-shot variant effect prediction, (5) Analyzing sequence-function relationships.
Fm App
Use this model doc whenever the user wants to run FM-APP for phenotype prediction using fMRI ROI features and optional sMRI features. This document provides model-level usage and delegates preprocessing to fmri-skill and smri-skill.
Nutrigx Advisor
Personalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) — interrogates nutritionally-relevant
Omics Target Evidence Mapper
Aggregate public target-level evidence across omics and translational sources for research triage.
Open ST Skills Index
Skills for Open-ST spatial transcriptomics data processing, from raw BCL files to spatially-resolved single-cell h5ad objects.
Query Alphafold
Query AlphaFold protein structure predictions. Use when user asks about protein structure, 3D structure, protein folding, or structure prediction. Triggers on "alphafold", "protein structure", "3D structure", "folding", "pLDDT", "structure prediction".
Bio Image Processing Skills Index
Skills for biological image analysis: cell/nucleus segmentation, image restoration, and spatial data processing.
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