bio-design

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

1. API stability — Biological databases (UniProt, PDB, NCBI) rate-limit and timeout. Handle retries with backoff, connection timeouts, and graceful degradation.
2. 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
3. Synthesis constraints — For sequences destined for synthesis, check GC content (30–70% for DNA), homopolymer repeats (≤6 identical bases), and secondary structure.
4. 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