| name | bio-design |
| description | Computational biology guardrails: stable API retrieval from biological databases, biological validity constraints (amino acid / DNA alphabets), synthesis constraints (GC content, repeats), and data provenance. Use for protein design, DNA/RNA analysis, molecular dynamics.
|
Bio-Design
Leading word: alphabet — every biological sequence belongs to a constrained alphabet. Validate against it before any operation.
Rules
- API stability — Biological databases (UniProt, PDB, NCBI) rate-limit and timeout. Handle retries with backoff, connection timeouts, and graceful degradation.
- Alphabet validation — Every sequence must be validated against its biological alphabet before processing:
- Amino acids: standard 20-letter code only
- DNA:
A/T/G/C only
- RNA:
A/U/G/C only
- Synthesis constraints — For sequences destined for synthesis, check GC content (30–70% for DNA), homopolymer repeats (≤6 identical bases), and secondary structure.
- Provenance — Record source and version of every reference database used.
Setup
pip install biopython requests
Detailed constraints: see references/synthesis-constraints.md
Pseudocode
SKILL bio-design
INPUTS:
moleculeType: string // protein, dna, rna, small_molecule
sourceDatabase: string // uniprot, pdb, ncbi, custom
designGoal: string // synthesis, analysis, prediction
sequence?: string // Optional input sequence
OUTPUTS:
validatedSequence: string // Biologically validated sequence
provenanceLog: object // Database sources and versions
PRECONDITIONS:
- API rate limits respected for external databases
- Biological alphabet constraints checked (20aa / ATGC)
- Sequence length within synthesis constraints
POSTCONDITIONS:
- Sequence uses only standard biological alphabet
- GC content within 30–70% for synthetic DNA
- No homopolymer repeats >6 identical bases
- All data sources recorded with version
ERROR_HANDLING:
- API rate limited → exponential backoff with jitter
- Invalid characters → reject with character-level details
- GC content out of bounds → flag for synthesis review
