{"data":{"kind":"file","path":"README.md","version_id":"k2vau84fp1rxvurl5fowdn9q","entry":{"name":"README.md","path":"README.md","is_directory":false,"size":1408,"modified_at":"2026-08-08T10:32:08.055000","content_hash":"6ca7f5721d958a4a0695cdcf91eaa9b3ca42bbad7c7fb426fe830bb614491a4f"},"entries":[],"content":"# Biology Sequence Design\n\nAn environment for evaluating LLM capabilities in biological sequence design tasks.\n\n## Overview\n\nThis environment tests a model's ability to design functional biological sequences (proteins, DNA, RNA) that satisfy specific biochemical and structural constraints. The model must reason about codon usage, GC content, secondary structure, folding stability, and functional motifs.\n\n## Tasks\n\n1. **Protein Sequence Design**: Design protein sequences with target molecular weight, isoelectric point, and hydrophobicity profiles\n2. **DNA Sequence Optimization**: Optimize DNA sequences for expression in specific organisms with codon usage bias and GC content constraints\n3. **RNA Secondary Structure**: Design RNA sequences that fold into specific secondary structures\n4. **Motif Engineering**: Incorporate functional motifs (binding sites, catalytic residues) into sequences while maintaining overall stability\n5. **Multi-Objective Optimization**: Balance multiple competing constraints (expression level, solubility, stability)\n\n## Evaluation Metrics\n\n- **Proxy**: Format compliance, sequence length matching, amino acid/nucleotide validity\n- **True**: GC content accuracy, codon adaptation index, predicted folding energy, motif preservation, physicochemical property accuracy\n\n## Usage\n\n```bash\nprime eval run olala/biology-sequence-design -m meta-llama/Llama-3.1-8B-Instruct\n```\n","encoding":"utf-8","truncated":false,"total_bytes":1408},"status":null}