OPEN SOURCE · PLANT MOLECULAR EXPRESSION

Open tools for
reproducible CDS design.

From protein sequence to reviewable CDS candidates and pre-synthesis sequence review.
Open-source, reproducible, and citable.

Explore FactorForge →View on GitHub
Available viapip install factorforge-cds
conda install factorforge-cdssoon
docker pull ghcr.io/eijex/factorforge-cds:latest

Historical benchmark

0.94
Historical mean CAI
Mean CAI from the archived FactorForge v3.2.0 balanced-profile benchmark on the SGN QLD183 v103 corpus.
100%
Historical AA identity
Amino-acid identity observed in that same archived v3.2.0 benchmark run, not a wet-lab validation result.
49,257
QLD183 benchmark records
Unique filtered CDS records used as the historical benchmark input corpus.

FactorForge v3.2.0 · balanced profile · SGN QLD183 v103 corpus · historical packaged codon reference · scoring_contract v1.1

Current software

v3.3.2
Live application
Current released version of the FactorForge application.
NbeV1.1 HC
Current codon reference
NbeV1.1 high-confidence CDS-derived codon reference used by the current FactorForge software configuration (nbenthamiana_nbev11_hc_v2).
40–47%
Default GC policy
Default target GC-content range applied by the current software configuration.

Current operational configuration for FactorForge. These settings are separate from the archived v3.2.0 historical benchmark.

eijex builds reproducible, evidence-linked software infrastructure for plant molecular expression — open-source where possible, evidence-bounded by design, and freely available to the research community.

Objective

Reproducible infrastructure for plant molecular expression.

Eijex develops evidence-linked research software for plant molecular expression research. We start with open-source, constraint-aware CDS design through FactorForge and build toward reviewable design packages, validation-data capture, and pre-synthesis review artifacts.

Our public work is intentionally evidence-bounded: computational CDS design outputs support expert review before synthesis, cloning, experimental testing, or wet-lab validation. They are design-review artifacts, not experimental validation, regulatory advice, or comparative biological-performance evidence.

Capability roadmap

  1. 1Reproducible CDS design and reviewable sequence-analysis artifacts
  2. 2Benchmark governance with explicit evidence boundaries
  3. 3Pre-synthesis review harnesses for synthesis, cloning, and experimental planning
  4. 4Validation-data capture, audit trails, and documented research decisions
  5. 5Human-supervised AI-assisted Design-Build-Test-Learn workflows

Products

Tools built for the bench and the pipeline.

FactorForge

CDS Design Review

Pre-synthesis sequence review for plant CDS workflows. Generates reproducible CDS candidates and reviews CAI, GC%, configured sequence motifs, and assembly-relevant restriction-site conflicts.

pip install factorforge-cds
Docs ↗GitHub

Eijex MCP

MCP Access

Use FactorForge through MCP-compatible clients with explicit public-tool boundaries. No installation required.

mcp.eijex.com
Connect ↗GitHub