FactorForge

Open-source constraint-based CDS design and pre-synthesis sequence review for plant CDS workflows, with primary support for Nicotiana benthamiana (Tobacco BY-2: experimental).

FactorForge performs deterministic CDS design with CAI/GC metrics, PolyA-signal screening, and Golden Gate/MoClo-aware checks. It is positioned as a pre-synthesis review harness: it helps teams generate reproducible CDS candidates, inspect assembly-relevant sequence constraints, and package design metadata before downstream synthesis, cloning, or experimental review. Primary support: N. benthamiana (agroinfiltration). Experimental host context: Tobacco BY-2 (--host by2).

FactorForge v3.5.1 uses independently versioned engines:

→ Full Documentation · Roadmap

Quick Start

pip install factorforge-cds
factorforge optimize my_protein.fasta -o output.fasta

Or use the web app — no installation required.

Access Options

Repository Structure

The supported deterministic engines are the profile engine, stable DP v2, and the explicit DP v2.1.1 development candidate under:

src/factorforge/engines/profile/
src/factorforge/engines/dp_v2.py
src/factorforge/engines/dp_v2_1_1.py
src/factorforge/engines/sllm/
src/factorforge/discovery/

DP v2.1.1 adds an exact active-layer 5′ GC guard and Aho-Corasick rejection of homopolymers of 6 nt or longer to the v2.1 initiation-aware objective. It emits local-composition metrics and, when ViennaRNA and sufficient transcript context are available, a separately evaluated 5′ MFE value. It is not the default; its single-target calibration does not establish holdout generalization or biological performance.

The v3.5.1 discovery-slate surface generates versioned Top-K research candidates, applies a shared deterministic hard-constraint filter, and records generator and fallback lineage. The sLLM path is disabled by default. A partial-DP rescue solves an exact suffix conditioned on the retained prefix; it is not a claim of global optimality and does not establish biological performance.

Historical implementation tracks are preserved under archive/ for provenance and are not imported by the installed package or exposed as supported engines.

⚠️ Validation Status

FactorForge outputs are in-silico only and have not been experimentally validated in wet-lab conditions. These checks support reviewability and reproducibility; they do not guarantee expression, yield, synthesis acceptance, folding, glycosylation, regulatory approval, or downstream biological performance. See Validation and VALIDATION.md.

Citing

FactorForge v3.5.3 (2026). Open-source constraint-based CDS design and sequence review.
Eijex. https://github.com/eijex/factorforge-cds

Maintainer

Mun-Kyu Kim (@eijex)

Optional PostgreSQL support

Install pip install "factorforge-cds[postgres]" only when using the PostgreSQL connector. Explicit local SQLite checkpoints do not require a PostgreSQL driver. Database integration tests require an explicitly configured DATABASE_URL.

License

GNU Affero General Public License v3.0 — see LICENSE.

Disclaimer: FactorForge is provided for research purposes only. Outputs are computational and have not been experimentally validated.

Get in Touch

• Sponsor — Support our research via GitHub Sponsors or PayPal
• Docs — eijex.github.io/factorforge-cds
• Wet-lab Feedback — Public-safe feedback summaries are welcome via Share Wet-lab Feedback (GitHub). Do not submit raw sequences, confidential construct details, internal batch IDs, patient data, private contact information, exact process parameters, or confidential partner/customer data. Email eijex.lab@gmail.com for private or sensitive summaries. See VALIDATION.md before submitting.
• Sequence Policy Profiles — FactorForge applies the sequence-review policy chosen by the user; it does not define or approve a laboratory SOP. The web app provides an illustrative YAML example and active-profile export. Sequence-free, non-confidential suggestions can be submitted through the public policy-template form; use eijex.lab@gmail.com for private or laboratory-specific profiles. See the sequence policy boundary.
• GitHub Issues — bugs, features: github.com/eijex/factorforge-cds/issues
• Email — eijex.lab@gmail.com
• FactorForge — factorforge.eijex.com
• Eijex MCP — mcp.eijex.com
• Lab — www.eijex.com