Open-source constraint-based CDS design engine for plant expression workflows, with initial focus on Nicotiana benthamiana and Tobacco BY-2.
FactorForge optimizes protein sequences into host-compatible CDS by maximizing CAI, controlling GC content, eliminating PolyA signals, and producing MoClo/Golden Gate-ready constructs. Supports N. benthamiana (agroinfiltration) and Tobacco BY-2 (--host by2, bioreactor/cGMP workflows).
pip install factorforge-cds
factorforge optimize my_protein.fasta -o output.fastaOr use the web app — no installation required.
| Method | Description | Link |
|---|---|---|
| Web App | No installation, demo & light use | factorforge.eijex.com |
| CLI / Python | Local use, batch processing, data privacy | pip install factorforge-cds |
| Docker | Full web interface locally | docker pull ghcr.io/eijex/factorforge-cds:latest |
The supported production engine is the deterministic profile engine under:
src/factorforge/engines/profile/
Historical implementation tracks are preserved under archive/ for provenance
and are not imported by the installed package or exposed as supported engines.
FactorForge has gone through several implementation generations before the current public release:
| Generation | Status | Description |
|---|---|---|
| v1 — NBent_OptiCodon | Internal | Thesis-derived codon optimization baseline for N. benthamiana |
| v2 — Rule-Based Engine | Internal → Production | Deterministic, constraint-aware design engine; became the foundation for the public release |
| v3-alpha — ML Prototype | Archived | ML-based design attempt; performance was insufficient for production use; preserved under archive/v3-ml-prototype/ |
| v3.0+ — Current release | Public | Open-source release of the matured v2 engine under factorforge.engines.profile |
| v3.7+ — ML Engine | Planned | ML-based design as --engine ml; added once sufficient wet-lab data is available |
The archive/ directory preserves all three earlier tracks for provenance. None are installed or exposed by the current package.
FactorForge predictions are in-silico only and have not been experimentally validated in wet-lab conditions. See Validation and VALIDATION.md.
FactorForge v3.1.6 (2026). Open-source constraint-based CDS design engine.
Eijex. https://github.com/eijex/factorforge-cds
A citable publication is in preparation.
| Name | Role | |
|---|---|---|
| 👤 | Mun-Kyu Kim (@eijex) | Author & maintainer |
| 🤖 | Claude (Anthropic) | Design, analysis, planning |
| 🤖 | Codex (OpenAI) | Implementation |
GNU Affero General Public License v3.0 — see LICENSE.
Disclaimer: FactorForge is provided for research purposes only. Predictions are computational and have not been experimentally validated.
- Docs — eijex.github.io/factorforge-cds
- Wet-lab Results — Submit via Google Form (recommended) or GitHub Issue
- GitHub Issues — bugs, features: github.com/eijex/factorforge-cds/issues
- Email — eijex.lab@gmail.com
- Web — factorforge.eijex.com