What's New This is a major release. The core pipeline scripts were substantially rewritten and extended, a complete plasmid design module was added, six feedback loops were implemented, a Python master orchestrator was introduced, and a native Electron desktop GUI was built on top of it all. Pipeline scripts (Phase 1 - genome_to_design.sh) Added dynamic genome_fetch.sh resolution - finds the script via PATH or relative to genome_to_design.sh, with TTY simulation fallback using script Added Step 1b: FASTA header sanitization (spaces and pipes → underscores) Added Step 2b: repeat masking via RepeatModeler + RepeatMasker; auto-skips for genomes under 1 Mbp; critical for eukaryotes Auto-detection of available CPU threads via nproc; GNU parallel used throughout if available BRAKER integration now auto-selects OrthoDB partition by querying Entrez taxonomy, downloads and sanitizes the partition FASTA, and repairs GTF transcript_id fields before gffread --auto_rnaseq mode: queries SRA, downloads with prefetch + fasterq-dump, aligns with STAR, merges BAMs with samtools BRAKER automatically retries in --esmode when fewer than 1000 introns are detected Added progress bars and ETA estimates for long-running loops RepeatModeler output filtered to suppress per-second countdown noise; full output preserved in logs/repeatmodeler_detail.log --force now clears both .done and .failed sentinels Organism-change detection: starting a new run automatically if the organism name changes between runs Auto-generated README.md run report written at pipeline completion Phase 2 - plasmid_design_moclo_v3.py (new) Complete MoClo Golden Gate plasmid design module: CDS domestication via DNA Chisel (if installed) with heuristic codon-frequency fallback Supports Marillonnet, CIDAR, and JUMP overhang standards with configurable enzyme pairs (BsaI-HFv2 / BpiI defaults) Dynamic path resolution: follows latest/ symlink, env vars, or auto-discovers the newest run directory Outputs GenBank (.gb) and FASTA files for SnapGene and synthesis ordering Phase 3 - Six feedback loops (all new) FB1 (feedback1_colabfold_to_rfdiffusion.sh): ranks ColabFold predictions by mean pLDDT, feeds top-N structures back into RFdiffusion as fixed motifs, re-runs ProteinMPNN and ColabFold for configurable iterations FB2 (feedback2_plddt_mpnn_resample.py): re-runs ProteinMPNN at higher sampling temperature on low-pLDDT backbones; marks unconverged designs after max_iterations FB3 (feedback3_blast_to_braker.sh): fetches BLAST hit subject sequences from NCBI, merges with original OrthoDB hints, re-runs BRAKER with the enriched protein hint set, writes annotation diff report FB4 (feedback4_domesticated_cds_revalidate.py): extracts domesticated CDS features from plasmid GenBank files, re-folds with ColabFold, flags sequences with pLDDT regression above configurable thresholds FB5 (feedback5_designed_proteins_to_annotation.sh): filters validated designs by pLDDT, merges with OrthoDB hints, optionally launches a fresh run on a related organism FB6 (feedback6_blast_taxonomy_rerun.py): resolves per-accession taxonomy, assigns each hit to its single most-specific OrthoDB partition keyword, detects and corrects wrong partition selections, re-runs BRAKER with GTF repair and gffread Master orchestrator - genomopipe.py (new) Single entry point for the full pipeline YAML, JSON, and plain-text config file support; CLI flags always override config values Per-phase sentinel files (.genomopipe_phase1.done, etc.) independent of genome_to_design.sh checkpoints --reset clears orchestrator sentinels without touching step-level checkpoints Pre-flight script validation before committing to a long run Structured summary report (genomopipe_summary.md) written after every run Desktop GUI - BioForge App (new) Electron desktop application. See v1.0.0 → v2.0.0 section above for full tab breakdown.Requirements added since v1.0.0 Node.js ≥ 18, Electron (npm install in app directory) pip install pyyaml pydna (orchestrator + plasmid design) pip install dnachisel[reports] (optional - substantially improves domestication) braker_env now also requires: repeatmodeler, repeatmasker, star, samtools, sra-tools, gffread Demo Image