Guidance for designing fusion protein gBlock sequences from multiple protein sources. This skill applies when tasks involve combining proteins from PDB databases, plasmid files, and fluorescent protein databases into a single optimized DNA sequence with specific linkers and codon optimization requirements.
Guidance for designing and assembling multi-component fusion protein sequences, particularly for FRET biosensors and tagged constructs. This skill applies when tasks involve identifying proteins by spectral properties (excitation/emission wavelengths), assembling fusion proteins from multiple domains, codon optimization with GC content constraints, working with PDB sequences and fluorescent protein databases, or generating gBlock sequences for gene synthesis.
Guidance for Golden Gate assembly primer design and DNA assembly tasks. This skill should be used when designing primers for Golden Gate cloning, Type IIS restriction enzyme assembly, or multi-fragment DNA assembly workflows. It covers overhang selection, primer structure, assembly simulation, and verification strategies.
This skill provides guidance for FEAL cipher linear cryptanalysis tasks. It should be used when recovering encryption keys from FEAL-encrypted data using known plaintext-ciphertext pairs, implementing linear approximation attacks on block ciphers, or solving cryptanalysis challenges involving the FEAL cipher family. The skill emphasizes mathematical analysis over brute-force approaches.
Guidance for DNA assembly tasks including Golden Gate assembly, Gibson assembly, and restriction enzyme-based cloning. This skill should be used when designing primers for Type IIS restriction enzymes (BsaI, BsmBI, etc.), creating fusion proteins, or assembling multiple DNA fragments. Covers primer structure requirements, overhang design, and verification strategies.
Specialized skill for designing primers to insert DNA sequences into circular plasmids using Q5 site-directed mutagenesis (SDM). This skill should be used when tasks involve inserting sequences into plasmids, designing primers for Q5 SDM insertions, or converting an input plasmid to an output plasmid with additional sequence. The skill provides workflows for understanding Q5 SDM mechanics, proper primer design with annealing regions, Tm calculation, and critical verification strategies.
This skill provides guidance for tasks involving MobileSAM or Segment Anything Model (SAM) for cell segmentation, mask refinement, and polygon extraction from images. Use when working with SAM-based image segmentation pipelines, converting masks to polygons, processing CSV-based coordinate data, or integrating deep learning segmentation models into processing scripts.
Guide for designing DNA insertion primers for site-directed mutagenesis (SDM) using Q5 or similar kits. This skill should be used when tasks involve inserting DNA sequences into plasmids, designing mutagenesis primers, or working with PCR-based insertion methods. Provides verification strategies, common pitfalls, and procedural guidance for correct primer design.
UMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visualization, clustering preprocessing (HDBSCAN), supervised/parametric UMAP, for high-dimensional data.
Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.
Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus detection/segmentation, tissue graph construction, or training ML models on pathology data. Supports 160+ slide formats including Aperio SVS, NDPI, DICOM, OME-TIFF for digital pathology workflows.
Professional network graph analyst identifying Gladwellian superconnectors, mavens, and influence brokers using betweenness centrality, structural holes theory, and multi-source network reconstruction. Activate on 'superconnectors', 'network analysis', 'who knows who', 'professional network', 'influence mapping', 'betweenness centrality'. NOT for surveillance, discrimination, stalking, privacy violation, or speculation without data.
DNA sequence and motif analysis using gcell. Use this skill when users ask about: - Loading and manipulating DNA sequences - Genome assembly access (hg38, hg19, mm10) - Motif scanning with HOCOMOCO motifs - Working with genomic regions (BED, narrowPeak files) - Transcription factor binding site prediction Triggers: DNA sequence, motif scanning, HOCOMOCO, genomic regions, BED file, narrowPeak, genome, transcription factor binding
Align architecture and team structure using inverse Conway maneuver
Analyze component evolution and movement patterns
Use when you've identified candidate symmetries and need to map them to mathematical groups for architecture design. Invoke when user mentions cyclic groups, dihedral groups, Lie groups, SO(3), SE(3), permutation groups, or needs to formalize symmetries into group theory language. Provides taxonomy and mathematical foundations from Visual Group Theory principles.
A specialized tool for designing efficient and specific gRNA sequences for CRISPR-Cas9 experiments.
Graceful memory compression with integrity — summarize before forgetting, never fabricate
Identify Sepsis-3 patients in MIMIC-IV using the consensus definition (SOFA >= 2 + suspected infection). Use for sepsis cohort studies, outcome research, or quality metrics.
Opentrons Thermocycler Module - automated PCR thermal cycling with independent block (4-99°C) and lid (37-110°C) temperature control, profile execution, and auto-sealing lid support (GEN2) for high-throughput molecular biology workflows
