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Write technology transfer protocols. TRIGGERS - Use when user needs help with tech-transfer-protocol related tasks.
Access bioDBnet REST services for biological identifier conversion, pathway retrieval, and ortholog mapping. Use when you need to convert gene/protein IDs, find pathways, or retrieve biological annotations via bioDBnet.
Virtual gene knockout simulation using foundation models to predict transcriptional
Comprehensive scientific research toolkit with 139 specialized skills for biology, chemistry, medicine, data science, and computational research. Transforms Claude into an AI research assistant with access to scientific databases, analysis tools, and domain-specific workflows.
Compute pairwise r² between a lead variant and every variant in a window using the 1000 Genomes Phase 3 GRCh38 reference panel, ancestry-stratified. Use when an agent needs LD coloring for a regional plot or LD pruning around a candidate causal variant. Single client (on-demand region fetch from ...
Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetching GenBank/GenPept records, getting document summaries, parsing nested XML, navigating GI deprecation, choosing between rettype+retmode combinations, and parsing into Biopytho...
Reusable plotting functions for common omics visualizations. Custom ggplot2/matplotlib implementations of volcano, MA, PCA, enrichment dotplots, boxplots, and survival curves. Use when creating volcano, MA, or enrichment plots.
Query NCBI Gene Expression Omnibus (GEO) for expression datasets using Biopython Bio.Entrez. Use when finding microarray/RNA-seq datasets, downloading expression data, or linking GEO series to SRA runs.
Statistical testing for differentially abundant proteins between conditions. Covers limma and MSstats workflows with multiple testing correction. Use when identifying proteins with significant abundance changes between experimental groups.
Calculate translation efficiency (TE) as the ratio of ribosome occupancy to mRNA abundance. Use when comparing translational regulation between conditions or identifying genes with altered translation independent of transcription.
Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets, generating QC reports, or comparing assemblies.
Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data.
Annotate and filter VCF variants with SnpEff and SnpSift. SnpEff predicts functional effects (HIGH/MODERATE/LOW/MODIFIER), genes, transcripts, AA changes, HGVS; SnpSift filters and adds ClinVar/dbSNP. Java CLI with Python subprocess integration. Use ANNOVAR for multi-database annotation; Ensembl ...
Splice-aware RNA-seq aligner producing sorted BAM and splice junction tables. Builds genome index, runs two-pass alignment for better junctions. Outputs sorted BAM, junctions (SJ.out.tab), stats (Log.final.out), optional gene counts. Use Salmon for fast pseudoalignment; STAR when a BAM is needed ...
Generate alignment statistics using samtools flagstat, stats, depth, and coverage. Use when assessing alignment quality, calculating coverage, or generating QC reports.
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting exp...
Bridge layer connecting Vertex AI / Google Cloud to plurigrid/asi protein-scale biology skills. Wires AlphaFold, ESM, DiffDock, DeepChem, and TorchDrug into Vertex AI Pipelines, Endpoints, and BigQuery genomics for protein design-predict-validate loops.
Prepare IND applications. TRIGGERS - Use when user needs help with ind-application-prep related tasks.
Write validation master plans. TRIGGERS - Use when user needs help with validation-master-plan related tasks.
Design clinical data management systems and processes. TRIGGERS - Use when user needs help with clinical-data-management related tasks.
Build clinical trial budgets. TRIGGERS - Use when user needs help with clinical-trial-budget related tasks.
Conduct supplier audits. TRIGGERS - Use when user needs help with supplier-audit-biotech related tasks.
Plan drug formulation development programs. TRIGGERS - Use when user needs help with formulation-development related tasks.
Genome in a Bottle benchmark validation skill for pipeline accuracy assessment
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