@saibolla/ada 0.1.2

package/skills/consciousness-council/SKILL.md

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+---
+name: consciousness-council
+description: Run a multi-perspective Mind Council deliberation on any question, decision, or creative challenge. Use this skill whenever the user wants diverse viewpoints, needs help making a tough decision, asks for a council/panel/board discussion, wants to explore a problem from multiple angles, requests devil's advocate analysis, or says things like "what would different experts think about this", "help me think through this from all sides", "council mode", "mind council", or "deliberate on this". Also trigger when the user faces a dilemma, trade-off, or complex choice with no obvious answer.
+allowed-tools: Read Write
+license: MIT license
+metadata:
+  skill-author: AHK Strategies (ashrafkahoush-ux)
+---
+
+# Consciousness Council
+
+A structured multi-perspective deliberation system that generates genuine cognitive diversity on any question. Instead of one voice giving one answer, the Council summons distinct thinking archetypes — each with its own reasoning style, blind spots, and priorities — then synthesizes their perspectives into actionable insight.
+
+## Why This Exists
+
+Single-perspective thinking has a ceiling. When you ask one mind for an answer, you get one frame. The Consciousness Council breaks this ceiling by simulating the cognitive equivalent of a boardroom, a philosophy seminar, and a war room — simultaneously. It's not roleplay. It's structured epistemic diversity.
+
+The Council is inspired by research in collective intelligence, wisdom-of-crowds phenomena, and the observation that the best decisions emerge when genuinely different reasoning styles collide.
+
+## How It Works
+
+The Council has three phases:
+
+### Phase 1 — Summon the Council
+
+Based on the user's question, select 4-6 Council Members from the archetypes below. Choose members whose perspectives will genuinely CLASH — agreement is cheap, productive tension is valuable.
+
+**The 12 Archetypes:**
+
+| #   | Archetype          | Thinking Style                         | Asks                                         | Blind Spot                                |
+| --- | ------------------ | -------------------------------------- | -------------------------------------------- | ----------------------------------------- |
+| 1   | **The Architect**  | Systems thinking, structure-first      | "What's the underlying structure?"           | Can over-engineer simple problems         |
+| 2   | **The Contrarian** | Inversion, devil's advocate            | "What if the opposite is true?"              | Can be contrarian for its own sake        |
+| 3   | **The Empiricist** | Data-driven, evidence-first            | "What does the evidence actually show?"      | Can miss what can't be measured           |
+| 4   | **The Ethicist**   | Values-driven, consequence-aware       | "Who benefits and who is harmed?"            | Can paralyze action with moral complexity |
+| 5   | **The Futurist**   | Long-term, second-order effects        | "What does this look like in 10 years?"      | Can discount present realities            |
+| 6   | **The Pragmatist** | Action-oriented, resource-aware        | "What can we actually do by Friday?"         | Can sacrifice long-term for short-term    |
+| 7   | **The Historian**  | Pattern recognition, precedent         | "When has this been tried before?"           | Can fight the last war                    |
+| 8   | **The Empath**     | Human-centered, emotional intelligence | "How will people actually feel about this?"  | Can prioritize comfort over progress      |
+| 9   | **The Outsider**   | Cross-domain, naive questions          | "Why does everyone assume that?"             | Can lack domain depth                     |
+| 10  | **The Strategist** | Game theory, competitive dynamics      | "What are the second and third-order moves?" | Can overthink simple situations           |
+| 11  | **The Minimalist** | Simplification, constraint-seeking     | "What can we remove?"                        | Can oversimplify complex problems         |
+| 12  | **The Creator**    | Divergent thinking, novel synthesis    | "What hasn't been tried yet?"                | Can chase novelty over reliability        |
+
+**Selection heuristic:** Match the question type to the most productive tension:
+
+- **Business decisions** → Strategist + Pragmatist + Ethicist + Futurist + Contrarian
+- **Technical architecture** → Architect + Minimalist + Empiricist + Outsider
+- **Personal dilemmas** → Empath + Contrarian + Futurist + Pragmatist
+- **Creative challenges** → Creator + Outsider + Historian + Minimalist
+- **Ethical questions** → Ethicist + Contrarian + Empiricist + Empath + Historian
+- **Strategy/competition** → Strategist + Historian + Futurist + Contrarian + Pragmatist
+
+These are starting points — adapt based on the specific question. The goal is productive disagreement, not consensus.
+
+### Phase 2 — Deliberation
+
+Each Council Member delivers their perspective in this format:
+
+```
+🎭 [ARCHETYPE NAME]
+
+Position: [One-sentence stance]
+
+Reasoning: [2-4 sentences explaining their logic from their specific lens]
+
+Key Risk They See: [The danger others might miss]
+
+Surprising Insight: [Something non-obvious that emerges from their frame]
+```
+
+**Critical rules for deliberation:**
+
+- Each member MUST disagree with at least one other member on something substantive. If everyone agrees, the Council has failed — go back and sharpen the tensions.
+- Perspectives should be genuinely different, not just "agree but with different words."
+- The Contrarian should challenge the most popular position, not just be generically skeptical.
+- Keep each member's contribution focused and sharp. Depth over breadth.
+
+### Phase 3 — Synthesis
+
+After all members speak, deliver:
+
+```
+⚖️ COUNCIL SYNTHESIS
+
+Points of Convergence: [Where 3+ members agreed — these are high-confidence signals]
+
+Core Tension: [The central disagreement that won't resolve easily — this IS the insight]
+
+The Blind Spot: [What NO member addressed — the question behind the question]
+
+Recommended Path: [Actionable recommendation that respects the tension rather than ignoring it]
+
+Confidence Level: [High / Medium / Low — based on how much convergence vs. divergence emerged]
+
+One Question to Sit With: [The question the user should keep thinking about after this session]
+```
+
+## Council Configurations
+
+The user can customize the Council:
+
+- **"Quick council"** or **"fast deliberation"** → Use 3 members, shorter responses
+- **"Deep council"** or **"full deliberation"** → Use 6 members, extended reasoning
+- **"Add [archetype]"** → Include a specific archetype
+- **"Without [archetype]"** → Exclude a specific archetype
+- **"Custom council: [list]"** → User picks exact members
+- **"Anonymous council"** → Don't reveal which archetype is speaking until synthesis (reduces anchoring bias)
+- **"Devil's advocate mode"** → Every member must argue AGAINST whatever seems most intuitive
+- **"Rounds mode"** → After initial positions, members respond to each other for a second round
+
+## What Makes a Good Council Question
+
+The Council works best on questions where:
+
+- There's genuine uncertainty or trade-offs
+- Multiple valid perspectives exist
+- The user is stuck or going in circles
+- The stakes are high enough to warrant multi-angle thinking
+- The user's own bias might be limiting their view
+
+The Council adds less value on:
+
+- Pure factual questions with clear answers
+- Questions where the user has already decided and just wants validation
+- Trivial choices with low stakes
+
+If the question seems too simple for a full Council, say so — and offer a quick 2-perspective contrast instead.
+
+## Tone and Quality
+
+- Write each archetype's voice with enough distinctiveness that the user could identify them without labels.
+- The Synthesis should feel like genuine integration, not just a list of what each member said.
+- "Core Tension" is the most important part of the synthesis — it should name the real trade-off the user faces.
+- "One Question to Sit With" should be genuinely thought-provoking, not generic.
+- Never let the Council devolve into everyone agreeing politely. Productive friction is the point.
+
+## Example
+
+**User:** "Should I quit my stable corporate job to start a company?"
+
+**Council Selection:** Pragmatist, Futurist, Empath, Contrarian, Strategist (5 members — high-stakes life decision with financial, emotional, and strategic dimensions)
+
+Then run the full 3-phase deliberation.
+
+## Attribution
+
+Created by AHK Strategies — consciousness infrastructure for the age of AI.
+Learn more: https://ahkstrategies.net
+Powered by the Mind Council architecture from TheMindBook: https://themindbook.app

package/skills/consciousness-council/references/advanced-configurations.md

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+# Advanced Council Configurations
+
+Reference guide for specialized Council configurations beyond the defaults.
+
+## Domain-Specific Councils
+
+### Startup Decisions
+**Members:** Strategist, Pragmatist, Contrarian, Futurist, Empiricist
+**Why this mix:** Startups need vision (Futurist) grounded in reality (Pragmatist), challenged by skepticism (Contrarian), backed by data (Empiricist), with competitive awareness (Strategist).
+**Key tension to watch:** Futurist vs. Pragmatist — ambition vs. execution capacity.
+
+### Technical Architecture
+**Members:** Architect, Minimalist, Empiricist, Outsider, Pragmatist
+**Why this mix:** Architecture needs structure (Architect) that's not over-engineered (Minimalist), validated by evidence (Empiricist), challenged by fresh eyes (Outsider), and actually buildable (Pragmatist).
+**Key tension to watch:** Architect vs. Minimalist — elegance vs. simplicity.
+
+### Hiring / People Decisions
+**Members:** Empath, Strategist, Pragmatist, Ethicist, Historian
+**Why this mix:** People decisions need emotional intelligence (Empath), strategic fit (Strategist), practical constraints (Pragmatist), fairness (Ethicist), and pattern recognition (Historian).
+**Key tension to watch:** Empath vs. Strategist — caring for the person vs. optimizing for the team.
+
+### Creative Direction
+**Members:** Creator, Outsider, Historian, Empiricist, Minimalist
+**Why this mix:** Creativity needs divergent thinking (Creator), fresh perspective (Outsider), awareness of what's been done (Historian), audience validation (Empiricist), and restraint (Minimalist).
+**Key tension to watch:** Creator vs. Historian — novelty vs. proven patterns.
+
+### Crisis Management
+**Members:** Pragmatist, Strategist, Empath, Contrarian, Architect
+**Why this mix:** Crisis needs immediate action (Pragmatist), long-term thinking (Strategist), human awareness (Empath), challenge to groupthink (Contrarian), and systemic fix (Architect).
+**Key tension to watch:** Pragmatist vs. Architect — quick fix vs. root cause.
+
+### Ethical Dilemmas
+**Members:** Ethicist, Contrarian, Empath, Historian, Futurist, Empiricist
+**Why this mix (6 members):** Ethical questions deserve more voices. Values framework (Ethicist), challenge to moral certainty (Contrarian), human impact (Empath), precedent (Historian), long-term consequences (Futurist), and evidence (Empiricist).
+**Key tension to watch:** Ethicist vs. Pragmatist (if added) — doing right vs. doing what's possible.
+
+### Investment / Financial Decisions
+**Members:** Empiricist, Strategist, Contrarian, Futurist, Pragmatist
+**Why this mix:** Money decisions need data (Empiricist), game theory (Strategist), skepticism of hype (Contrarian), trend awareness (Futurist), and execution reality (Pragmatist).
+**Key tension to watch:** Futurist vs. Empiricist — future potential vs. present evidence.
+
+## Custom Archetype Creation
+
+Users can define custom archetypes for domain-specific councils. When a user defines a custom member, capture:
+
+1. **Name:** What this archetype is called
+2. **Lens:** The primary frame through which they see everything
+3. **Signature question:** The one question they always ask
+4. **Blind spot:** What they consistently miss
+5. **Disagrees with:** Which other archetype they most often clash with
+
+**Example custom archetype:**
+```
+Name: The Regulator
+Lens: Compliance and risk management
+Signature question: "What could go wrong legally?"
+Blind spot: Can kill innovation with caution
+Disagrees with: Creator, Futurist
+```
+
+## Scoring the Deliberation
+
+After synthesis, the Council can optionally score the deliberation quality:
+
+| Metric | Scale | What It Measures |
+|--------|-------|-----------------|
+| Diversity Score | 1-5 | How different were the perspectives? (1 = everyone agreed, 5 = genuine disagreement) |
+| Tension Quality | 1-5 | How productive was the central disagreement? (1 = trivial, 5 = illuminating) |
+| Blind Spot Discovery | 1-5 | Did the synthesis reveal something no individual member saw? |
+| Actionability | 1-5 | How concrete and useful is the recommended path? |
+| Overall CQS | 1-5 | Council Quality Score — weighted average |
+
+**CQS Formula:** (Diversity × 0.25) + (Tension × 0.30) + (Blind Spot × 0.25) + (Actionability × 0.20)
+
+A good deliberation scores 3.5+ overall. Below 3.0, consider re-running with different members or a reframed question.
+
+## Multi-Round Deliberation
+
+For complex questions, enable "Rounds Mode":
+
+**Round 1:** Initial positions (standard deliberation)
+**Round 2:** Each member responds to the member they most disagree with
+**Round 3:** Revised positions after hearing counterarguments
+**Final Synthesis:** Incorporates all rounds
+
+Multi-round deliberation produces deeper insight but takes longer. Use for high-stakes decisions where the extra depth is worth it.
+
+## Silent Council Mode
+
+Sometimes the user doesn't need the full deliberation output — they just need the synthesis. In "Silent Council" mode:
+
+1. Run the full deliberation internally
+2. Only output the Synthesis section
+3. Offer to "show the full deliberation" if the user wants the reasoning
+
+This is faster and less overwhelming for quick decisions.

package/skills/cosmic-database/SKILL.md

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+---
+name: cosmic-database
+description: Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
+license: Unknown
+metadata:
+    skill-author: K-Dense Inc.
+---
+
+# COSMIC Database
+
+## Overview
+
+COSMIC (Catalogue of Somatic Mutations in Cancer) is the world's largest and most comprehensive database for exploring somatic mutations in human cancer. Access COSMIC's extensive collection of cancer genomics data, including millions of mutations across thousands of cancer types, curated gene lists, mutational signatures, and clinical annotations programmatically.
+
+## When to Use This Skill
+
+This skill should be used when:
+- Downloading cancer mutation data from COSMIC
+- Accessing the Cancer Gene Census for curated cancer gene lists
+- Retrieving mutational signature profiles
+- Querying structural variants, copy number alterations, or gene fusions
+- Analyzing drug resistance mutations
+- Working with cancer cell line genomics data
+- Integrating cancer mutation data into bioinformatics pipelines
+- Researching specific genes or mutations in cancer contexts
+
+## Prerequisites
+
+### Account Registration
+COSMIC requires authentication for data downloads:
+- **Academic users**: Free access with registration at https://cancer.sanger.ac.uk/cosmic/register
+- **Commercial users**: License required (contact QIAGEN)
+
+### Python Requirements
+```bash
+uv pip install requests pandas
+```
+
+## Quick Start
+
+### 1. Basic File Download
+
+Use the `scripts/download_cosmic.py` script to download COSMIC data files:
+
+```python
+from scripts.download_cosmic import download_cosmic_file
+
+# Download mutation data
+download_cosmic_file(
+    email="your_email@institution.edu",
+    password="your_password",
+    filepath="GRCh38/cosmic/latest/CosmicMutantExport.tsv.gz",
+    output_filename="cosmic_mutations.tsv.gz"
+)
+```
+
+### 2. Command-Line Usage
+
+```bash
+# Download using shorthand data type
+python scripts/download_cosmic.py user@email.com --data-type mutations
+
+# Download specific file
+python scripts/download_cosmic.py user@email.com \
+    --filepath GRCh38/cosmic/latest/cancer_gene_census.csv
+
+# Download for specific genome assembly
+python scripts/download_cosmic.py user@email.com \
+    --data-type gene_census --assembly GRCh37 -o cancer_genes.csv
+```
+
+### 3. Working with Downloaded Data
+
+```python
+import pandas as pd
+
+# Read mutation data
+mutations = pd.read_csv('cosmic_mutations.tsv.gz', sep='\t', compression='gzip')
+
+# Read Cancer Gene Census
+gene_census = pd.read_csv('cancer_gene_census.csv')
+
+# Read VCF format
+import pysam
+vcf = pysam.VariantFile('CosmicCodingMuts.vcf.gz')
+```
+
+## Available Data Types
+
+### Core Mutations
+Download comprehensive mutation data including point mutations, indels, and genomic annotations.
+
+**Common data types**:
+- `mutations` - Complete coding mutations (TSV format)
+- `mutations_vcf` - Coding mutations in VCF format
+- `sample_info` - Sample metadata and tumor information
+
+```python
+# Download all coding mutations
+download_cosmic_file(
+    email="user@email.com",
+    password="password",
+    filepath="GRCh38/cosmic/latest/CosmicMutantExport.tsv.gz"
+)
+```
+
+### Cancer Gene Census
+Access the expert-curated list of ~700+ cancer genes with substantial evidence of cancer involvement.
+
+```python
+# Download Cancer Gene Census
+download_cosmic_file(
+    email="user@email.com",
+    password="password",
+    filepath="GRCh38/cosmic/latest/cancer_gene_census.csv"
+)
+```
+
+**Use cases**:
+- Identifying known cancer genes
+- Filtering variants by cancer relevance
+- Understanding gene roles (oncogene vs tumor suppressor)
+- Target gene selection for research
+
+### Mutational Signatures
+Download signature profiles for mutational signature analysis.
+
+```python
+# Download signature definitions
+download_cosmic_file(
+    email="user@email.com",
+    password="password",
+    filepath="signatures/signatures.tsv"
+)
+```
+
+**Signature types**:
+- Single Base Substitution (SBS) signatures
+- Doublet Base Substitution (DBS) signatures
+- Insertion/Deletion (ID) signatures
+
+### Structural Variants and Fusions
+Access gene fusion data and structural rearrangements.
+
+**Available data types**:
+- `structural_variants` - Structural breakpoints
+- `fusion_genes` - Gene fusion events
+
+```python
+# Download gene fusions
+download_cosmic_file(
+    email="user@email.com",
+    password="password",
+    filepath="GRCh38/cosmic/latest/CosmicFusionExport.tsv.gz"
+)
+```
+
+### Copy Number and Expression
+Retrieve copy number alterations and gene expression data.
+
+**Available data types**:
+- `copy_number` - Copy number gains/losses
+- `gene_expression` - Over/under-expression data
+
+```python
+# Download copy number data
+download_cosmic_file(
+    email="user@email.com",
+    password="password",
+    filepath="GRCh38/cosmic/latest/CosmicCompleteCNA.tsv.gz"
+)
+```
+
+### Resistance Mutations
+Access drug resistance mutation data with clinical annotations.
+
+```python
+# Download resistance mutations
+download_cosmic_file(
+    email="user@email.com",
+    password="password",
+    filepath="GRCh38/cosmic/latest/CosmicResistanceMutations.tsv.gz"
+)
+```
+
+## Working with COSMIC Data
+
+### Genome Assemblies
+COSMIC provides data for two reference genomes:
+- **GRCh38** (recommended, current standard)
+- **GRCh37** (legacy, for older pipelines)
+
+Specify the assembly in file paths:
+```python
+# GRCh38 (recommended)
+filepath="GRCh38/cosmic/latest/CosmicMutantExport.tsv.gz"
+
+# GRCh37 (legacy)
+filepath="GRCh37/cosmic/latest/CosmicMutantExport.tsv.gz"
+```
+
+### Versioning
+- Use `latest` in file paths to always get the most recent release
+- COSMIC is updated quarterly (current version: v102, May 2025)
+- Specific versions can be used for reproducibility: `v102`, `v101`, etc.
+
+### File Formats
+- **TSV/CSV**: Tab/comma-separated, gzip compressed, read with pandas
+- **VCF**: Standard variant format, use with pysam, bcftools, or GATK
+- All files include headers describing column contents
+
+### Common Analysis Patterns
+
+**Filter mutations by gene**:
+```python
+import pandas as pd
+
+mutations = pd.read_csv('cosmic_mutations.tsv.gz', sep='\t', compression='gzip')
+tp53_mutations = mutations[mutations['Gene name'] == 'TP53']
+```
+
+**Identify cancer genes by role**:
+```python
+gene_census = pd.read_csv('cancer_gene_census.csv')
+oncogenes = gene_census[gene_census['Role in Cancer'].str.contains('oncogene', na=False)]
+tumor_suppressors = gene_census[gene_census['Role in Cancer'].str.contains('TSG', na=False)]
+```
+
+**Extract mutations by cancer type**:
+```python
+mutations = pd.read_csv('cosmic_mutations.tsv.gz', sep='\t', compression='gzip')
+lung_mutations = mutations[mutations['Primary site'] == 'lung']
+```
+
+**Work with VCF files**:
+```python
+import pysam
+
+vcf = pysam.VariantFile('CosmicCodingMuts.vcf.gz')
+for record in vcf.fetch('17', 7577000, 7579000):  # TP53 region
+    print(record.id, record.ref, record.alts, record.info)
+```
+
+## Data Reference
+
+For comprehensive information about COSMIC data structure, available files, and field descriptions, see `references/cosmic_data_reference.md`. This reference includes:
+
+- Complete list of available data types and files
+- Detailed field descriptions for each file type
+- File format specifications
+- Common file paths and naming conventions
+- Data update schedule and versioning
+- Citation information
+
+Use this reference when:
+- Exploring what data is available in COSMIC
+- Understanding specific field meanings
+- Determining the correct file path for a data type
+- Planning analysis workflows with COSMIC data
+
+## Helper Functions
+
+The download script includes helper functions for common operations:
+
+### Get Common File Paths
+```python
+from scripts.download_cosmic import get_common_file_path
+
+# Get path for mutations file
+path = get_common_file_path('mutations', genome_assembly='GRCh38')
+# Returns: 'GRCh38/cosmic/latest/CosmicMutantExport.tsv.gz'
+
+# Get path for gene census
+path = get_common_file_path('gene_census')
+# Returns: 'GRCh38/cosmic/latest/cancer_gene_census.csv'
+```
+
+**Available shortcuts**:
+- `mutations` - Core coding mutations
+- `mutations_vcf` - VCF format mutations
+- `gene_census` - Cancer Gene Census
+- `resistance_mutations` - Drug resistance data
+- `structural_variants` - Structural variants
+- `gene_expression` - Expression data
+- `copy_number` - Copy number alterations
+- `fusion_genes` - Gene fusions
+- `signatures` - Mutational signatures
+- `sample_info` - Sample metadata
+
+## Troubleshooting
+
+### Authentication Errors
+- Verify email and password are correct
+- Ensure account is registered at cancer.sanger.ac.uk/cosmic
+- Check if commercial license is required for your use case
+
+### File Not Found
+- Verify the filepath is correct
+- Check that the requested version exists
+- Use `latest` for the most recent version
+- Confirm genome assembly (GRCh37 vs GRCh38) is correct
+
+### Large File Downloads
+- COSMIC files can be several GB in size
+- Ensure sufficient disk space
+- Download may take several minutes depending on connection
+- The script shows download progress for large files
+
+### Commercial Use
+- Commercial users must license COSMIC through QIAGEN
+- Contact: cosmic-translation@sanger.ac.uk
+- Academic access is free but requires registration
+
+## Integration with Other Tools
+
+COSMIC data integrates well with:
+- **Variant annotation**: VEP, ANNOVAR, SnpEff
+- **Signature analysis**: SigProfiler, deconstructSigs, MuSiCa
+- **Cancer genomics**: cBioPortal, OncoKB, CIViC
+- **Bioinformatics**: Bioconductor, TCGA analysis tools
+- **Data science**: pandas, scikit-learn, PyTorch
+
+## Additional Resources
+
+- **COSMIC Website**: https://cancer.sanger.ac.uk/cosmic
+- **Documentation**: https://cancer.sanger.ac.uk/cosmic/help
+- **Release Notes**: https://cancer.sanger.ac.uk/cosmic/release_notes
+- **Contact**: cosmic@sanger.ac.uk
+
+## Citation
+
+When using COSMIC data, cite:
+Tate JG, Bamford S, Jubb HC, et al. COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Research. 2019;47(D1):D941-D947.
+