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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).

License PyPI CI codecov DOI

FactorForge performs profile-guided CDS design with CAI/GC metrics, PolyA-signal screening, and Golden Gate/MoClo-aware checks. It supports reproducible in-silico CDS candidate generation and pre-synthesis sequence review for plant CDS workflows. Primary support: N. benthamiana (agroinfiltration). Experimental host context: Tobacco BY-2 (--host by2).

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
Web App No installation, demo & light use
CLI / Python Local use, batch processing, data privacy
Docker Full web interface locally, no data leaves your machine (docker pull ghcr.io/eijex/factorforge-cds:latest)
Eijex MCP MCP-compatible agent access

Engineering Benchmark

Benchmarked on N. benthamiana SGN CDS (v3.2.0, balanced profile, N=49,257 sequences, seed=320):

Metric Value Target
CAI (mean) 0.94 ≥ 0.75
GC in target range 98.2% 55–65%
AA identity 100% 100%
Validator pass rate 100% 100%

Note: The figures above are an engineering reference benchmark — a reproducible measurement against a specific version, profile, and dataset. A formal comparative benchmark against other CDS design tools is not yet available.

Reproduce the benchmark:

python scripts/benchmark.py --n 100  # quick validation (~30s)
python scripts/benchmark.py          # full benchmark (N. benthamiana SGN CDS)

Reproducible benchmark foundation: see benchmarks/README.md.

Supported Hosts

Host Status
Nicotiana benthamiana ✅ Supported (--host nbenthamiana, default)
Tobacco BY-2 (N. tabacum) ⚠️ Experimental (--host by2)
Wolffia globosa 🔶 Codon table available, coming soon
Other plant hosts 📋 Planned

Validation Status

FactorForge outputs are in-silico only and have not been experimentally validated in wet-lab conditions. They support reviewability and reproducibility, not guarantees of expression, yield, synthesis acceptance, folding, glycosylation, regulatory approval, or downstream biological performance. See Validation for details.

Paper-to-product journey

FactorForge's public roadmap keeps the paper/research-software track and product track connected but claim-bounded. The research track focuses on reproducible in-silico CDS candidate generation, documented benchmarks, and explicit limitations. The product track extends those artifacts toward a pre-synthesis review harness: assembly-relevant checks, host/profile maturity labels, quality-risk-aware annotations, and privacy-aware feedback records.

These extensions are future-facing review aids; they do not establish wet-lab performance, synthesis acceptance, biosecurity compliance, or regulatory approval.

Share Wet-lab Results

Used FactorForge in the lab? Share public-safe feedback to help improve the tool: