factorforge-cds 3.3.0

FactorForge - open-source CDS design and pre-synthesis sequence review by Eijex.

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 profile-guided 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).

→ Full Documentation · Roadmap

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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	MCP-compatible agent access	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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⚠️ 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.

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Citing

FactorForge v3.3.0 (2026). Open-source constraint-based CDS design and sequence review.
Eijex. https://github.com/eijex/factorforge-cds

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Maintainer

Mun-Kyu Kim (@eijex)

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.

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Get in Touch

• 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 [e-mail] for private or sensitive summaries. See VALIDATION.md before submitting.
• GitHub Issues — bugs, features: github.com/eijex/factorforge-cds/issues
• Email — [e-mail]
• FactorForge — factorforge.eijex.com
• Eijex MCP — mcp.eijex.com
• Lab — www.eijex.com