FactorForge | Plant CDS Design — N. benthamiana & Tobacco BY-2

Metric	Original	Optimized
Sequence Length	-	-
GC Content	-	-
CAI Score	-	-
Codon Changes	N/A	-
AA Preserved	—	✅ 100%

Current

v3.1.6

2026-05-30

BY-2 Host (Experimental): --host by2 for Tobacco BY-2 suspension culture cells; N. tabacum codon table.
Profile Comparison: --compare-profiles balanced,high_cai,gc_target side-by-side table. API: POST /api/optimize/compare.
Batch API: POST /api/optimize/batch — up to 20 sequences per request.
Structure Links: AlphaFold DB + ESM Atlas links in result panel.
SynCodonLM Scoring: Optional 5th scoring dimension (pip install factorforge-cds[ml]).
GFP Tutorial: End-to-end worked example added to documentation.

v3.1.5

2026-05-28

Data File Packaging: JSON data files now correctly included in PyPI wheel; resolved path error after pip install.
Path Resolution: Replaced hardcoded parents[N] with get_data_path() across all engine files.
CI Matrix: Python 3.13 + Windows added.

v3.1.4

2026-05-27

Citation & Release Infrastructure: CITATION.cff, SECURITY.md, ROADMAP.md, bump_version.py added.
Development History: v1→v2→v3-alpha→v3.x→v3.7+(ML) lineage documented across README and CHANGELOG.
Benchmark Corrected: CAI 0.76, GC% 59.77%, target 55–65% (N=3,876 SGN CDS, balanced profile).

v3.1.3

2026-05-26

Profile Cards: Tooltips now accessible on hover for Coming Soon profiles; added "Pending wet-lab validation" notice.
Viral Delivery Tooltip: Corrected citation reference; updated to Peccoud et al. 2024.
Analytics Notice: Clarified — "Submitted sequences are not logged or stored".

v3.1.2

2026-05-26

Viral Delivery: Corrected citation reference; MFE weight 0.40→0.30 per PMC11718241 (Peccoud et al. 2024).
5' Ramp: N-terminal deoptimization strength reduced from bottom 50%→25% (mild deoptimization per PMC11718241).
Release Notes: Public documentation aligned with the v3.1.x stable CDS design workflow.

v3.1.1

2026-05-24

Wet-lab Feedback: Submit result button opens an embedded Google Form with version and profile pre-filled.
JSON Copy: One-click copy of the full optimization JSON output.
Design Objective Order: Reordered to match recommended wet-lab testing sequence.
Validation Fields: Issue template updated with promoter, subcellular targeting, harvest timepoint, and native control.
Deployment Fix: Resolved Vercel /api/optimize 404 caused by incorrect Root Directory setting.

v3.1.0

2026-05-24

Custom Restriction Sites: Synonymous substitution of user-specified restriction sites.
Rare Codon Run Detection: Detects consecutive rare codons for ribosome stalling risk.
Dinucleotide Reduction: CAI-budgeted CpG/TpA reduction (aggressive / balanced / cai_preserving modes).
Pipeline Metric Fix: CAI/GC/score now re-measured from final sequence after dinucleotide fix.
CAI Guard Fix: Guard weights updated to Sharp & Li 1987 golden set reference.

v3.0.0 - First Official Release

2026-05-23

DP Feasibility Engine: Constraint-based dynamic programming for CAI/GC co-optimization.
CLI: factorforge optimize command with FASTA and GenBank output.
Validator: Hard-fail contract — AA identity, stops, invalid codons, GC, length.
Open Source: AGPL-3.0, available at github.com/eijex/factorforge-cds.

v3.x pre-release - Profile Accuracy Fix

2026-04-05

High CAI Fix: Fixed codon selection to use Golden Set weights — CAI improved from 0.757 to 1.000.
GC Target Fix: Corrected default GC target from 50% to 42.5% ±2% matching N. benthamiana spec.
Viral Delivery UI: Added viral_delivery profile card and DNA input warning banner.

v3.x pre-release - Engine Throughput Optimization

2026-02-14

Pipeline Scan Reduction: Limited expensive full rescans by applying bounded windows after local sequence edits.
Scanner Speedup: Improved PolyA/GC traversal path to cut redundant operations on long CDS inputs.
Candidate Fast Path: Reduced mutation proposal overhead in synonymous candidate filtering.

v3.x pre-release - Engine Reliability Fix

2026-02-12

GC Pipeline Fix: Corrected key mismatch and added client-side calculation failover.
Enhanced Validation: New distinct states for "N/A" vs "Out of Range" GC content.
UX Refinement: Expanded real-time preview to 150bp for better terminal scrutiny.

v3.x pre-release - Production Dashboard

2026-02-11

Advanced UI: Full premium dashboard with glassmorphism and dark mode.
Real-time Stats: Live sequence length and GC% tracking.
Graphical Analysis: Dynamic GC distribution chart integration.
Privacy-First: Local session history stored securely in browser.

v3.x pre-release - Scientific Precision II

2026-02-09

Kozak Optimization: 5' translation initiation context scrutiny (AACAATG**GC**).
Dinucleotide Scrutiny: CpG and TpA density scanning to avoid silencing.

v3.x pre-release - Scientific Precision I

2026-02-05

Golden Set Table: Scientific baseline from high-expression gene data.
RAMP Optimization: N-terminal deoptimization for folding.
MoClo Check: Level 0 overhang validation and collision detection.

v3.x pre-release - Stability & Logging

2026-02-04

Centralized Data: Improved path management for codon tables and weights.
Robust Logging: Standardized logging framework across all design modules.
Hardened Security: Path traversal protection for template loading.

v3.x pre-release - Workflow Optimization

2026-01-30

Construct Builder: Automated sequence assembly logic.
GenBank Export: Full support for annotated feature files.

v3.x pre-release - Rule-based Design

2026-01-22

RuleEngine: 7 new scanners (PolyA, ARE, Splice-sites, etc.).
Domesticator: Automated Golden Gate restriction site removal.
Validation: Auto-detect protein/DNA/FASTA inputs.

Pre-release - Inference Harness

2026-01-28

Inference Harness: Baseline deployment path for sequence-design experiments.

Pre-release - Workflow Automation

2026-01-24

Workflow: Initial sequence-design workflow automation.

Pre-release - Foundation

2026-01-21

Initial CDS Design: Rule-oriented codon optimization foundation.
Initial Release: Foundation of N. benthamiana optimization.

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