Soul2dna

Skill BioTender-max/awesome-bio-agent-skills/skills/clawbio/soul2dna

Compile SOUL.md character profiles into synthetic diploid genomes (.genome.json) via trait-to-allele mappingFrom its SKILL.md

Install

npx -y skills add BioTender-max/awesome-bio-agent-skills --skill soul2dna

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SKILL.md

2.3 KB, 543 tokens by cl100k_base, as published. Nobody here has run it

🧬 Soul2DNA Compiler

Purpose

Compile SOUL.md character profiles into synthetic diploid genomes. Each soul file describes a historical or fictional figure with trait scores (0.0 to 1.0). The compiler maps these scores to alleles at defined loci using additive, dominant, or recessive inheritance models, producing a .genome.json file per character.

How It Works

Parse SOUL.md files from GENOMEBOOK/DATA/SOULS/ extracting identity metadata (name, sex, ancestry, domain, era) and trait scores.
Load trait registry (GENOMEBOOK/DATA/trait_registry.json) which defines loci, alleles, chromosomal positions, dominance models, and effect sizes for each trait.
Assign genotypes at each locus based on trait score thresholds:
- Additive: <0.33 ref/ref, 0.33-0.66 ref/alt, >0.66 alt/alt
- Dominant: <0.40 ref/ref, 0.40-0.75 ref/alt, >0.75 alt/alt
- Recessive: <0.50 ref/ref, 0.50-0.80 ref/alt, >0.80 alt/alt
Write genome as JSON with full locus detail, trait scores, and metadata.

Input

GENOMEBOOK/DATA/SOULS/*.soul.md (20 historical figures)
GENOMEBOOK/DATA/trait_registry.json

Output

GENOMEBOOK/DATA/GENOMES/<name>-g0.genome.json per character

CLI Usage

# Compile all souls to genomes
python skills/soul2dna/soul2dna.py

# Demo mode (shows summary without writing files)
python skills/soul2dna/soul2dna.py --demo

Output Format

Each .genome.json contains:

{
  "id": "einstein-g0",
  "name": "Albert Einstein",
  "sex": "Male",
  "sex_chromosomes": "XY",
  "ancestry": "...",
  "generation": 0,
  "parents": [null, null],
  "loci": { "<locus_id>": { "chromosome": "...", "alleles": ["A","G"], ... } },
  "trait_scores": { "curiosity": 0.95, ... }
}

What ships with it: 1 file

3.0 KB alongside SKILL.md, 1 of them executable

soul2dna.pyruns3.0 KB