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Proto

Status: Planned. No public integration claim is made.

Proto is Evo Design's framework for biological design programs. It may fit after a GeneCluster campaign produces a reviewed candidate map. A later design stage could then rank sequences, constructs, promoters, or protein variants.

Relevant components

  • proto-language defines typed sequences, regions, constructs, generators, constraints, optimizers, and programs.
  • proto-tools provides common input, configuration, and output wrappers for biological tools.
  • The hosted MCP service provides tool discovery, schema inspection, runs, asset retrieval, program validation, and metrics.

Possible uses

  • Turn evidence gaps into ranked design candidates.
  • Give multiple design tools a consistent output contract.
  • Compare wrappers for search, alignment, annotation, protein-language models, structure prediction, scoring, and retrieval.
  • Reuse the program vocabulary when execution remains local or runs on external compute.

Proposed output contract

proto-design/
  proto-program.py
  proto-program-export/
  proto-design-candidates.tsv
  proto-constraint-scores.tsv
  proto-run-metadata.json
  validation-report.json

Record:

  • package or API version
  • local or hosted execution
  • tools and models used
  • input provenance
  • candidate identifiers, scores, thresholds, and ranks
  • artifact hashes

Evaluation procedure

  1. Use public or synthetic inputs.
  2. Keep runtime files and caches outside Git or under ignored .runtime/ storage.
  3. Export the result.
  4. Normalize the export to the proposed output contract.
  5. Confirm that credentials, model weights, raw inputs, and heavy outputs remain outside the repository.

Public sources