pi-skill-search 0.1.0

package/skills/scientific-schematics/SKILL.md

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+---
+name: scientific-schematics
+description: Create publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.1 Pro Preview for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.
+---
+
+# Scientific Schematics and Diagrams
+
+## Overview
+
+Scientific schematics and diagrams transform complex concepts into clear visual representations for publication. **This skill uses Nano Banana 2 AI for diagram generation with Gemini 3.1 Pro Preview quality review.**
+
+**How it works:**
+- Describe your diagram in natural language
+- Nano Banana 2 generates publication-quality images automatically
+- **Gemini 3.1 Pro Preview reviews quality** against document-type thresholds
+- **Smart iteration**: Only regenerates if quality is below threshold
+- Publication-ready output in minutes
+- No coding, templates, or manual drawing required
+
+**Quality Thresholds by Document Type:**
+| Document Type | Threshold | Description |
+|---------------|-----------|-------------|
+
+## Quick Start: Generate Any Diagram
+
+Create any scientific diagram by simply describing it. Nano Banana 2 handles everything automatically with **smart iteration**:
+
+```bash
+# Generate for journal paper (highest quality threshold: 8.5/10)
+python scripts/generate_schematic.py "CONSORT participant flow diagram with 500 screened, 150 excluded, 350 randomized" -o figures/consort.png --doc-type journal
+
+# Generate for presentation (lower threshold: 6.5/10 - faster)
+python scripts/generate_schematic.py "Transformer encoder-decoder architecture showing multi-head attention" -o figures/transformer.png --doc-type presentation
+
+# Generate for poster (moderate threshold: 7.0/10)
+python scripts/generate_schematic.py "MAPK signaling pathway from EGFR to gene transcription" -o figures/mapk_pathway.png --doc-type poster
+
+# Custom max iterations (max 2)
+python scripts/generate_schematic.py "Complex circuit diagram with op-amp, resistors, and capacitors" -o figures/circuit.png --iterations 2 --doc-type journal
+```
+
+**What happens behind the scenes:**
+1. **Generation 1**: Nano Banana 2 creates initial image following scientific diagram best practices
+2. **Review 1**: **Gemini 3.1 Pro Preview** evaluates quality against document-type threshold
+3. **Decision**: If quality >= threshold → **DONE** (no more iterations needed!)
+4. **If below threshold**: Improved prompt based on critique, regenerate
+5. **Repeat**: Until quality meets threshold OR max iterations reached
+
+**Smart Iteration Benefits:**
+- ✅ Saves API calls if first generation is good enough
+- ✅ Higher quality standards for journal papers
+- ✅ Faster turnaround for presentations/posters
+
+### Configuration
+
+Set your OpenRouter API key:
+```bash
+export OPENROUTER_API_KEY='your_api_key_here'
+```
+
+Get an API key at: https://openrouter.ai/keys
+
+### AI Generation Best Practices
+
+**Effective Prompts for Scientific Diagrams:**
+
+✓ **Good prompts** (specific, detailed):
+- "CONSORT flowchart showing participant flow from screening (n=500) through randomization to final analysis"
+- "Transformer neural network architecture with encoder stack on left, decoder stack on right, showing multi-head attention and cross-attention connections"
+- "Biological signaling cascade: EGFR receptor → RAS → RAF → MEK → ERK → nucleus, with phosphorylation steps labeled"
+- "Block diagram of IoT system: sensors → microcontroller → WiFi module → cloud server → mobile app"
+
+✗ **Avoid vague prompts**:
+- "Make a flowchart" (too generic)
+- "Neural network" (which type? what components?)
+- "Pathway diagram" (which pathway? what molecules?)
+
+
+## When to Use This Skill
+
+This skill should be used when:
+- Creating neural network architecture diagrams (Transformers, CNNs, RNNs, etc.)
+- Illustrating system architectures and data flow diagrams
+- Drawing methodology flowcharts for study design (CONSORT, PRISMA)
+- Visualizing algorithm workflows and processing pipelines
+- Creating circuit diagrams and electrical schematics
+- Depicting biological pathways and molecular interactions
+- Generating network topologies and hierarchical structures
+- Illustrating conceptual frameworks and theoretical models
+- Designing block diagrams for technical papers
+
+## How to Use This Skill
+
+**Simply describe your diagram in natural language.** Nano Banana 2 generates it automatically:
+
+```bash
+python scripts/generate_schematic.py "your diagram description" -o output.png
+```
+
+**That's it!** The AI handles:
+- ✓ Layout and composition
+- ✓ Labels and annotations
+- ✓ Colors and styling
+- ✓ Quality review and refinement
+- ✓ Publication-ready output
+
+
+# AI Generation Mode (Nano Banana 2 + Gemini 3.1 Pro Preview Review)
+
+## Smart Iterative Refinement Workflow
+
+The AI generation system uses **smart iteration** - it only regenerates if quality is below the threshold for your document type:
+
+### How Smart Iteration Works
+
+

package/skills/scientific-slides/SKILL.md

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+---
+name: scientific-slides
+description: Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.
+---
+
+# Scientific Slides
+
+## Overview
+
+Scientific presentations are a critical medium for communicating research, sharing findings, and engaging with academic and professional audiences. This skill provides comprehensive guidance for creating effective scientific presentations, from structure and content development to visual design and delivery preparation.
+
+**Key Focus**: Oral presentations for conferences, seminars, defenses, and professional talks.
+
+**CRITICAL DESIGN PHILOSOPHY**: Scientific presentations should be VISUALLY ENGAGING and RESEARCH-BACKED. Avoid dry, text-heavy slides at all costs. Great scientific presentations combine:
+- **Compelling visuals**: High-quality figures, images, diagrams (not just bullet points)
+- **Research context**: Proper citations from research-lookup establishing credibility
+- **Minimal text**: Bullet points as prompts, YOU provide the explanation verbally
+- **Professional design**: Modern color schemes, strong visual hierarchy, generous white space
+- **Story-driven**: Clear narrative arc, not just data dumps
+
+**Remember**: Boring presentations = forgotten science. Make your slides visually memorable while maintaining scientific rigor through proper citations.
+
+## When to Use This Skill
+
+This skill should be used when:
+- Preparing conference presentations (5-20 minutes)
+- Developing academic seminars (45-60 minutes)
+- Creating thesis or dissertation defense presentations
+- Designing grant pitch presentations
+- Preparing journal club presentations
+- Giving research talks at institutions or companies
+- Teaching or tutorial presentations on scientific topics
+
+## Slide Generation with Nano Banana Pro
+
+**This skill uses Nano Banana Pro AI to generate stunning presentation slides automatically.**
+
+There are two workflows depending on output format:
+
+### Default Workflow: PDF Slides (Recommended)
+
+Generate each slide as a complete image using Nano Banana Pro, then combine into a PDF. This produces the most visually stunning results.
+
+**How it works:**
+1. **Plan the deck**: Create a detailed plan for each slide (title, key points, visual elements)
+2. **Generate slides**: Call Nano Banana Pro for each slide to create complete slide images
+3. **Combine to PDF**: Assemble slide images into a single PDF presentation
+
+**Step 1: Plan Each Slide**
+
+Before generating, create a detailed plan for your presentation:
+
+```markdown
+# Presentation Plan: Introduction to Machine Learning
+
+## Slide 1: Title Slide
+- Title: "Machine Learning: From Theory to Practice"
+- Subtitle: "AI Conference 2025"
+- Speaker: Dr. Jane Smith, University of XYZ
+- Visual: Modern abstract neural network background
+
+## Slide 2: Introduction
+- Title: "Why Machine Learning Matters"
+- Key points: Industry adoption, breakthrough applications, future potential
+- Visual: Icons showing different ML applications (healthcare, finance, robotics)
+
+## Slide 3: Core Concepts
+- Title: "The Three Types of Learning"
+- Content: Supervised, Unsupervised, Reinforcement
+- Visual: Three-part diagram showing each type with examples
+
+... (continue for all slides)
+```
+
+**Step 2: Generate Each Slide**
+
+Use the `generate_slide_image.py` script to create each slide.
+
+**CRITICAL: Formatting Consistency Protocol**
+
+To ensure unified formatting across all slides in a presentation:
+
+# Title slide (first slide - establishes the style)
+python scripts/generate_slide_image.py "Title slide for presentation: 'Machine Learning: From Theory to Practice'. Subtitle: 'AI Conference 2025'. Speaker: K-Dense. FORMATTING GOAL: Dark blue background (#1a237e), white text, gold accents (#ffc107), minimal design, sans-serif fonts, generous margins, no decorative elements." -o slides/01_title.png
+
+# Content slide with citations (attach previous slide for consistency)
+python scripts/generate_slide_image.py "Presentation slide titled 'Why Machine Learning Matters'. Three key points with simple icons: 1) Industry adoption, 2) Breakthrough applications, 3) Future potential. CITATIONS: Include at bottom in small text: (LeCun et al., 2015; Goodfellow et al., 2016). FORMATTING GOAL: Match attached slide style - dark blue background, white text, gold accents, minimal professional design, no visual clutter." -o slides/02_intro.png --attach slides/01_title.png
+
+# Background slide with multiple citations
+python scripts/generate_slide_image.py "Presentation slide titled 'Deep Learning Revolution'. Key milestones: ImageNet breakthrough (2012), transformer architecture (2017), GPT models (2018-present). CITATIONS: Show references at bottom: (Krizhevsky et al., 2012; Vaswani et al., 2017; Brown et al., 2020). FORMATTING GOAL: Match attached slide style exactly - same colors, fonts, minimal design." -o slides/03_background.png --attach slides/02_intro.png
+
+# RESULTS SLIDE - Attach actual data figure from working directory
+# First, check what figures exist: ls figures/ or ls results/
+python scripts/generate_slide_image.py "Presentation slide titled 'Model Performance Results'. Create a slide presenting the attached accuracy chart. Key findings to highlight: 1) 95% accuracy achieved, 2) Outperforms baseline by 12%, 3) Consistent across test sets. CITATIONS: Include at bottom: (Our results, 2025). FORMATTING GOAL: Match attached slide style exactly." -o slides/04_results.png --attach slides/03_background.png --attach figures/accuracy_chart.png
+
+# RESULTS SLIDE - Multiple figures comparison
+python scripts/generate_slide_image.py "Presentation slide titled 'Before vs After Comparison'. Build a side-by-side comparison slide using the two attached figures. Left: baseline results, Right: our improved results. Add brief labels explaining the improvement. FORMATTING GOAL: Match attached slide style exactly." -o slides/05_comparison.png --attach slides/04_results.png --attach figures/baseline.png --attach figures/improved.png
+
+# METHODOLOGY SLIDE - Attach existing diagram
+python scripts/generate_slide_image.py "Presentation slide titled 'System Architecture'. Present the attached architecture diagram with brief explanatory bullet points: 1) Input processing, 2) Model inference, 3) Output generation. FORMATTING GOAL: Match attached slide style exactly." -o slides/06_architecture.png --attach slides/05_comparison.png --attach diagrams/system_architecture.png
+```
+
+**IMPORTANT: Before creating results slides, always:**
+1. List files in working directory: `ls -la figures/` or `ls -la results/`
+2. Check user-provided directories for relevant figures
+3. Attach ALL relevant figures that should appear on the slide
+4. Describe how Nano Banana Pro should incorporate the attached figures
+
+**Prompt Template:**
+
+Include these elements in every prompt (customize as needed):
+```
+[Slide content description]
+
+# Combine all slides into a PDF presentation
+
+

package/skills/scientific-visualization/SKILL.md

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+---
+name: scientific-visualization
+description: Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates matplotlib/seaborn/plotly with publication styles. For quick exploration use seaborn or plotly directly.
+---
+
+# Scientific Visualization
+
+## Overview
+
+Scientific visualization transforms data into clear, accurate figures for publication. Create journal-ready plots with multi-panel layouts, error bars, significance markers, and colorblind-safe palettes. Export as PDF/EPS/TIFF using matplotlib, seaborn, and plotly for manuscripts.
+
+## When to Use This Skill
+
+This skill should be used when:
+- Creating plots or visualizations for scientific manuscripts
+- Preparing figures for journal submission (Nature, Science, Cell, PLOS, etc.)
+- Ensuring figures are colorblind-friendly and accessible
+- Making multi-panel figures with consistent styling
+- Exporting figures at correct resolution and format
+- Following specific publication guidelines
+- Improving existing figures to meet publication standards
+- Creating figures that need to work in both color and grayscale
+
+## Quick Start Guide
+
+### Basic Publication-Quality Figure
+
+```python
+import matplotlib.pyplot as plt
+import numpy as np
+
+# Apply publication style (from scripts/style_presets.py)
+from style_presets import apply_publication_style
+apply_publication_style('default')
+
+# Create figure with appropriate size (single column = 3.5 inches)
+fig, ax = plt.subplots(figsize=(3.5, 2.5))
+
+# Plot data
+x = np.linspace(0, 10, 100)
+ax.plot(x, np.sin(x), label='sin(x)')
+ax.plot(x, np.cos(x), label='cos(x)')
+
+# Proper labeling with units
+ax.set_xlabel('Time (seconds)')
+ax.set_ylabel('Amplitude (mV)')
+ax.legend(frameon=False)
+
+# Remove unnecessary spines
+ax.spines['top'].set_visible(False)
+ax.spines['right'].set_visible(False)
+
+### Using Pre-configured Styles
+
+Apply journal-specific styles using the matplotlib style files in `assets/`:
+
+```python
+import matplotlib.pyplot as plt
+
+# Option 1: Use style file directly
+plt.style.use('assets/nature.mplstyle')
+
+# Option 2: Use style_presets.py helper
+from style_presets import configure_for_journal
+configure_for_journal('nature', figure_width='single')
+
+# Now create figures - they'll automatically match Nature specifications
+fig, ax = plt.subplots()
+# ... your plotting code ...
+```
+
+### Quick Start with Seaborn
+
+For statistical plots, use seaborn with publication styling:
+
+```python
+import seaborn as sns
+import matplotlib.pyplot as plt
+from style_presets import apply_publication_style
+
+# Apply publication style
+apply_publication_style('default')
+sns.set_theme(style='ticks', context='paper', font_scale=1.1)
+sns.set_palette('colorblind')
+
+# Create statistical comparison figure
+fig, ax = plt.subplots(figsize=(3.5, 3))
+sns.boxplot(data=df, x='treatment', y='response', 
+            order=['Control', 'Low', 'High'], palette='Set2', ax=ax)
+sns.stripplot(data=df, x='treatment', y='response',
+              order=['Control', 'Low', 'High'], 
+              color='black', alpha=0.3, size=3, ax=ax)
+ax.set_ylabel('Response (μM)')
+sns.despine()
+
+# Save figure
+from figure_export import save_publication_figure
+save_publication_figure(fig, 'treatment_comparison', formats=['pdf', 'png'], dpi=300)
+```
+
+## Core Principles and Best Practices
+
+# Use the figure_export.py script for correct settings
+from figure_export import save_publication_figure
+
+# Or save for specific journal requirements
+from figure_export import save_for_journal
+save_for_journal(fig, 'figure1', journal='nature', figure_type='combination')
+```

package/skills/scientific-writing/SKILL.md

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+---
+name: scientific-writing
+description: Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.
+---
+
+# Scientific Writing
+
+## Overview
+
+**This is the core skill for the deep research and writing tool**—combining AI-driven deep research with well-formatted written outputs. Every document produced is backed by comprehensive literature search and verified citations through the research-lookup skill.
+
+Scientific writing is a process for communicating research with precision and clarity. Write manuscripts using IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, and reporting guidelines (CONSORT/STROBE/PRISMA). Apply this skill for research papers and journal submissions.
+
+**Critical Principle: Always write in full paragraphs with flowing prose. Never submit bullet points in the final manuscript.** Use a two-stage process: first create section outlines with key points using research-lookup, then convert those outlines into complete paragraphs.
+
+## When to Use This Skill
+
+This skill should be used when:
+- Writing or revising any section of a scientific manuscript (abstract, introduction, methods, results, discussion)
+- Structuring a research paper using IMRAD or other standard formats
+- Formatting citations and references in specific styles (APA, AMA, Vancouver, Chicago, IEEE)
+- Creating, formatting, or improving figures, tables, and data visualizations
+- Applying study-specific reporting guidelines (CONSORT for trials, STROBE for observational studies, PRISMA for reviews)
+- Drafting abstracts that meet journal requirements (structured or unstructured)
+- Preparing manuscripts for submission to specific journals
+- Improving writing clarity, conciseness, and precision
+- Ensuring proper use of field-specific terminology and nomenclature
+- Addressing reviewer comments and revising manuscripts
+
+## Visual Enhancement with Scientific Schematics
+
+**⚠️ MANDATORY: Every scientific paper MUST include a graphical abstract plus 1-2 additional AI-generated figures using the scientific-schematics skill.**
+
+This is not optional. Scientific papers without visual elements are incomplete. Before finalizing any document:
+1. **ALWAYS generate a graphical abstract** as the first visual element
+2. Generate at minimum ONE additional schematic or diagram using scientific-schematics
+3. Prefer 3-4 total figures for comprehensive papers (graphical abstract + methods flowchart + results visualization + conceptual diagram)
+
+### Graphical Abstract (REQUIRED)
+
+**Every scientific writeup MUST include a graphical abstract.** This is a visual summary of your paper that:
+- Appears before or immediately after the text abstract
+- Captures the entire paper's key message in one image
+- Is suitable for journal table of contents display
+- Uses landscape orientation (typically 1200x600px)
+
+**Generate the graphical abstract FIRST:**
+```bash
+python scripts/generate_schematic.py "Graphical abstract for [paper title]: [brief description showing workflow from input → methods → key findings → conclusions]" -o figures/graphical_abstract.png
+```
+
+**Graphical Abstract Requirements:**
+- **Content**: Visual summary showing workflow, key methods, main findings, and conclusions
+
+### Additional Figures (GENERATE EXTENSIVELY)
+
+**⚠️ CRITICAL: Use BOTH scientific-schematics AND generate-image EXTENSIVELY throughout all documents.**
+
+Every document should be richly illustrated. Generate figures liberally - when in doubt, add a visual.
+
+**MINIMUM Figure Requirements:**
+
+| Document Type | Minimum | Recommended |
+|--------------|---------|-------------|
+| Research Papers | 5 | 6-8 |
+| Literature Reviews | 4 | 5-7 |
+| Market Research | 20 | 25-30 |
+| Presentations | 1/slide | 1-2/slide |
+| Posters | 6 | 8-10 |
+
+## Core Capabilities
+
+### 1. Manuscript Structure and Organization
+
+**IMRAD Format**: Guide papers through the standard Introduction, Methods, Results, And Discussion structure used across most scientific disciplines. This includes:
+- **Introduction**: Establish research context, identify gaps, state objectives
+- **Methods**: Detail study design, populations, procedures, and analysis approaches
+- **Results**: Present findings objectively without interpretation
+- **Discussion**: Interpret results, acknowledge limitations, propose future directions
+
+For detailed guidance on IMRAD structure, refer to `(see docs)`.
+
+**Alternative Structures**: Support discipline-specific formats including:
+- Review articles (narrative, systematic, scoping)
+- Case reports and case series
+- Meta-analyses and pooled analyses
+- Theoretical/modeling papers
+- Methods papers and protocols
+
+### 2. Section-Specific Writing Guidance
+
+**Abstract Composition**: Craft concise, standalone summaries (100-250 words) that capture the paper's purpose, methods, results, and conclusions. Support both structured abstracts (with labeled sections) and unstructured single-paragraph formats.
+
+**Introduction Development**: Build compelling introductions that:
+- Establish the research problem's importance
+- Review relevant literature systematically
+- Identify knowledge gaps or controversies
+- State clear research questions or hypotheses
+- Explain the study's novelty and significance
+
+**Methods Documentation**: Ensure reproducibility through:
+- Detailed participant/sample descriptions
+- Clear procedural documentation
+- Statistical methods with justification
+
+### 3. Citation and Reference Management
+
+Apply citation styles correctly across disciplines. For comprehensive style guides, refer to `(see docs)`.
+
+**Major Citation Styles:**
+- **AMA (American Medical Association)**: Numbered superscript citations, common in medicine
+- **Vancouver**: Numbered citations in square brackets, biomedical standard
+- **APA (American Psychological Association)**: Author-date in-text citations, common in social sciences
+- **Chicago**: Notes-bibliography or author-date, humanities and sciences
+- **IEEE**: Numbered square brackets, engineering and computer science
+
+**Best Practices:**
+
+

package/skills/scikit-bio/SKILL.md

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+---
+name: scikit-bio
+description: Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
+---
+
+# scikit-bio
+
+## Overview
+
+scikit-bio is a comprehensive Python library for working with biological data. Apply this skill for bioinformatics analyses spanning sequence manipulation, alignment, phylogenetics, microbial ecology, and multivariate statistics.
+
+## When to Use This Skill
+
+This skill should be used when the user:
+- Works with biological sequences (DNA, RNA, protein)
+- Needs to read/write biological file formats (FASTA, FASTQ, GenBank, Newick, BIOM, etc.)
+- Performs sequence alignments or searches for motifs
+- Constructs or analyzes phylogenetic trees
+- Calculates diversity metrics (alpha/beta diversity, UniFrac distances)
+- Performs ordination analysis (PCoA, CCA, RDA)
+- Runs statistical tests on biological/ecological data (PERMANOVA, ANOSIM, Mantel)
+- Analyzes microbiome or community ecology data
+- Works with protein embeddings from language models
+- Needs to manipulate biological data tables
+
+## Core Capabilities
+
+### 1. Sequence Manipulation
+
+Work with biological sequences using specialized classes for DNA, RNA, and protein data.
+
+**Key operations:**
+- Read/write sequences from FASTA, FASTQ, GenBank, EMBL formats
+- Sequence slicing, concatenation, and searching
+- Reverse complement, transcription (DNA→RNA), and translation (RNA→protein)
+- Find motifs and patterns using regex
+- Calculate distances (Hamming, k-mer based)
+- Handle sequence quality scores and metadata
+
+**Common patterns:**
+```python
+import skbio
+
+# Read sequences from file
+seq = skbio.DNA.read('input.fasta')
+
+# Sequence operations
+rc = seq.reverse_complement()
+rna = seq.transcribe()
+protein = rna.translate()
+
+# Find motifs
+motif_positions = seq.find_with_regex('ATG[ACGT]{3}')
+
+# Check for properties
+has_degens = seq.has_degenerates()
+seq_no_gaps = seq.degap()
+```
+
+**Important notes:**
+- Use `DNA`, `RNA`, `Protein` classes for grammared sequences with validation
+- Use `Sequence` class for generic sequences without alphabet restrictions
+- Quality scores automatically loaded from FASTQ files into positional metadata
+- Metadata types: sequence-level (ID, description), positional (per-base), interval (regions/features)
+
+### 2. Sequence Alignment
+
+Perform pairwise and multiple sequence alignments using dynamic programming algorithms.
+
+**Key capabilities:**
+- Global alignment (Needleman-Wunsch with semi-global variant)
+- Local alignment (Smith-Waterman)
+- Configurable scoring schemes (match/mismatch, gap penalties, substitution matrices)
+- CIGAR string conversion
+- Multiple sequence alignment storage and manipulation with `TabularMSA`
+
+**Common patterns:**
+```python
+from skbio.alignment import local_pairwise_align_ssw, TabularMSA
+
+# Pairwise alignment
+alignment = local_pairwise_align_ssw(seq1, seq2)
+
+# Access aligned sequences
+msa = alignment.aligned_sequences
+
+# Read multiple alignment from file
+msa = TabularMSA.read('alignment.fasta', constructor=skbio.DNA)
+
+# Calculate consensus
+consensus = msa.consensus()
+```

package/skills/scikit-learn/SKILL.md

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+---
+name: scikit-learn
+description: Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.
+---
+
+# Scikit-learn
+
+## Overview
+
+This skill provides comprehensive guidance for machine learning tasks using scikit-learn, the industry-standard Python library for classical machine learning. Use this skill for classification, regression, clustering, dimensionality reduction, preprocessing, model evaluation, and building production-ready ML pipelines.
+
+# Commonly used with
+uv pip install pandas numpy
+```
+
+## When to Use This Skill
+
+Use the scikit-learn skill when:
+
+- Building classification or regression models
+- Performing clustering or dimensionality reduction
+- Preprocessing and transforming data for machine learning
+- Evaluating model performance with cross-validation
+- Tuning hyperparameters with grid or random search
+- Creating ML pipelines for production workflows
+- Comparing different algorithms for a task
+- Working with both structured (tabular) and text data
+- Need interpretable, classical machine learning approaches
+
+## Quick Start
+
+### Classification Example
+
+```python
+from sklearn.model_selection import train_test_split
+from sklearn.preprocessing import StandardScaler
+from sklearn.ensemble import RandomForestClassifier
+from sklearn.metrics import classification_report
+
+# Split data
+X_train, X_test, y_train, y_test = train_test_split(
+    X, y, test_size=0.2, stratify=y, random_state=42
+)
+
+# Preprocess
+scaler = StandardScaler()
+X_train_scaled = scaler.fit_transform(X_train)
+X_test_scaled = scaler.transform(X_test)
+
+# Train model
+model = RandomForestClassifier(n_estimators=100, random_state=42)
+model.fit(X_train_scaled, y_train)
+
+# Evaluate
+y_pred = model.predict(X_test_scaled)
+print(classification_report(y_test, y_pred))
+```
+
+### Complete Pipeline with Mixed Data
+
+```python
+from sklearn.pipeline import Pipeline
+from sklearn.compose import ColumnTransformer
+from sklearn.preprocessing import StandardScaler, OneHotEncoder
+from sklearn.impute import SimpleImputer
+from sklearn.ensemble import GradientBoostingClassifier
+
+# Define feature types
+numeric_features = ['age', 'income']
+categorical_features = ['gender', 'occupation']
+
+# Create preprocessing pipelines
+numeric_transformer = Pipeline([
+    ('imputer', SimpleImputer(strategy='median')),
+    ('scaler', StandardScaler())
+])
+
+categorical_transformer = Pipeline([
+    ('imputer', SimpleImputer(strategy='most_frequent')),
+    ('onehot', OneHotEncoder(handle_unknown='ignore'))
+])
+
+# Combine transformers
+preprocessor = ColumnTransformer([
+    ('num', numeric_transformer, numeric_features),
+    ('cat', categorical_transformer, categorical_features)
+])
+
+# Full pipeline
+model = Pipeline([
+    ('preprocessor', preprocessor),
+    ('classifier', GradientBoostingClassifier(random_state=42))
+])
+
+# Fit and predict
+model.fit(X_train, y_train)
+y_pred = model.predict(X_test)
+
+