factorforge-cds 3.1.8

FactorForge - open-source constraint-based CDS design engine by Eijex.

FactorForge

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).

→ Full Documentation

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Quick Start

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

Or use the web app — no installation required.

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Access Options

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
Eijex MCP	AI agent access (Claude Code, Cursor)	mcp.eijex.com

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Repository Structure

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.

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Development History

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.

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⚠️ Validation Status

FactorForge predictions are in-silico only and have not been experimentally validated in wet-lab conditions. See Validation and VALIDATION.md.

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Citing

FactorForge v3.1.8 (2026). Open-source constraint-based CDS design engine.
Eijex. https://github.com/eijex/factorforge-cds

A citable publication is in preparation.

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Contributors

	Name	Role
👤	Mun-Kyu Kim (@eijex)	Author & maintainer
🤖	Claude (Anthropic)	Design, analysis, planning
🤖	Codex (OpenAI)	Implementation

License

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.

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Get in Touch

• 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 — [e-mail]
• Web — factorforge.eijex.com