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
Quick Start
pip install factorforge-cds
factorforge optimize my_protein.fasta -o output.fasta
Or use the web app — no installation required.
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 |
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.
⚠️ 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 v3.4.5 (2026). Open-source constraint-based CDS design and sequence review.
Eijex. https://github.com/eijex/factorforge-cds
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.
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.comfor private or sensitive summaries. See VALIDATION.md before submitting. - 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
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