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Sequence Policy Boundary

FactorForge does not define, approve, or validate a laboratory standard operating procedure (SOP). It provides a deterministic CDS-design engine, structured sequence findings, and a versioned mechanism for applying the sequence-review policy chosen by the user or laboratory.

The public product term is Sequence Policy Profile. The existing SopProfile name remains in the Python and API implementation for backward compatibility; it should not be interpreted as a claim that FactorForge covers or certifies a complete laboratory SOP.

Responsibility split

FactorForge invariants

These are software and CDS-integrity guarantees enforced by FactorForge rather than optional laboratory preferences:

  • the output is a valid CDS;
  • the translated amino-acid sequence is preserved;
  • no unintended internal stop codon is introduced;
  • reading-frame and schema requirements remain valid; and
  • deterministic findings and provenance are reported reproducibly.

User or laboratory policy

The treatment of advisory findings depends on the experimental and assembly workflow. The user or laboratory decides whether findings such as splice-like motifs, PolyA-like motifs, AU-rich regions, local-GC warnings, homopolymers, or specific restriction sites are required, advisory, or ignored.

FactorForge can express and apply that decision consistently. It does not claim that one setting is biologically correct for every laboratory, host, construct, or downstream process.

Bundled example

The bundled FactorForge policy is an illustrative example configuration. It reports supported advisory findings without treating an unvalidated predictor signal as biological ground truth. It is not:

  • a validated laboratory SOP;
  • a policy approved by PlantForm or any other laboratory;
  • regulatory or biosafety guidance;
  • wet-lab evidence; or
  • a guarantee of expression, yield, synthesis acceptance, or biological performance.

Users should adapt the example to their own reviewed workflow. A laboratory- specific profile remains the responsibility of that laboratory.

Provenance contract

When a Sequence Policy Profile is used, FactorForge records its version and digest with the computational result. This supports reproducibility; it does not validate the policy itself.

For prospective studies, preserve the generated design separately from the post-review built construct. Any expert-requested sequence change should be recorded as a remediation event rather than attributed silently to the design engine.

Privacy and contributions

Do not publish confidential laboratory policies, raw sequences, construct identifiers, or private process parameters. Public contributions must be sanitized, sequence-free suggestions. Laboratory-specific profiles should be shared only through an authorized private channel.