Documentation agent for METAINFORMANT's simulation module.
src/metainformant/simulation/— Synthetic data generators and simulation enginesdocs/simulation/— User-facing simulation documentationscripts/simulation/— Simulation workflow scripts
- Sequence simulation: Synthetic DNA/RNA/protein sequence generation
- RNA-seq simulation: Simulated count matrices with known DE genes
- Population genetics: Wright-Fisher, coalescent, and selection models
- Agent-based models: Ecosystem and colony simulation
- Benchmark generation: Reference datasets for method validation
- Real implementations only — NO_MOCKING_POLICY applies
- Package management:
uvfor all Python operations - I/O: Use
metainformant.core.iofor all file operations - Paths: Use
metainformant.core.pathsfor path handling - Environment variables: Prefix with
SIM_ - Output: Write to
output/simulation/