Genome Forge

Genome Forge is a local-first DNA design, cloning, validation, and bioinformatics workbench with a modern web UI, reproducible workflows, and real-world training materials.

It combines:

• interactive plasmid and sequence visualization
• cloning and assembly planning
• primer, PCR, trace, and verification workflows
• CRISPR/design-assist tooling
• project history, sharing, and lightweight review
• a 39-lesson self-study tutorial built on real biological examples

Latest release:

• Genome Forge v0.1.7

Why Genome Forge

Genome Forge is built for practical sequence work across the full “design -> validate -> explain -> hand off” loop:

• plasmid mapping and feature annotation
• restriction digest planning and cloning simulation
• primer design, PCR, and mutagenesis workflows
• alignment, trace review, and construct verification
• CRISPR helper workflows
• reference libraries, auto-flagging, and siRNA design
• project persistence, sharing, audit, and lightweight review workflows

For the full capability and maturity matrix, see FEATURE_COVERAGE.md.

Visual Tour

The tutorial now has a publication-style textbook layout with a clearer learning path, a broader screenshot atlas, dataset guidance, biological framing, and ambiguity-aware examples built around real records rather than toy strings.

Learn With Real Data

The tutorial package is meant to teach both the software and the biology behind the workflows.

Included training records and case bundles cover examples built around:

• EGFP and mCherry reporter CDS records
• pUC19 multiple-cloning-site and lacZ alpha cloning logic
• a medically meaningful BRAF exon 15 hotspot fragment
• clearly labeled derived training variants for comparison and interpretation exercises

Start here:

• Tutorial HTML
• Tutorial PDF
• Training Case Playbook
• Tutorial Dataset Guide

Quickstart

Run directly from source:

python3 web_ui.py --port 8080

Open:

http://127.0.0.1:8080

Recommended editable install:

python3 -m venv .venv
. .venv/bin/activate
python3 -m pip install --upgrade pip
python3 -m pip install -e ".[dev,bio]"
genomeforge-web --port 8080

CLI entry point after install:

genomeforge input.fasta info

Validation Snapshot

Current shipped baseline:

• python3 -m unittest discover -s tests -p 'test_*.py' -> 34/34 passed
• python3 smoke_test.py -> 108/108 passed
• python3 real_world_functional_test.py -> 97/97 passed
• npm run test:e2e -> 12/12 passed

Documentation

Start with:

• Docs Index
• Install Guide
• User Guide
• Developer Guide
• Architecture
• API Reference
• Contributing Guide
• Modernization Plan
• Changelog

Community

Ways to engage:

• open an Issue for a reproducible bug or concrete feature request
• start a Discussion for workflow design, usage help, or broader product feedback
• use the Contributing Guide for setup, test expectations, and PR discipline

This repo now includes structured GitHub issue forms and discussion prompts tuned for scientific workflow feedback, not just generic software bug reports.

Roadmap Snapshot

flowchart LR
  A["Now<br/>Stabilize workflows<br/>Broaden browser regression<br/>Polish docs and training"] --> B["Next<br/>Typed frontend state<br/>Cleaner component boundaries<br/>Generated capability docs"]
  B --> C["Later<br/>Structured API layer<br/>Deeper collaboration flows<br/>Longer-term platform hardening"]

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For the fuller engineering roadmap, see docs/MODERNIZATION_PLAN.md.

Common Commands

Run the UI:

python3 web_ui.py --port 8080

Run docs validation:

python3 docs/validate_docs.py

Run focused unit tests:

python3 -m unittest discover -s tests -p 'test_*.py'

Run broad regression:

python3 smoke_test.py
python3 real_world_functional_test.py

If development dependencies are installed:

python3 -m pytest

If browser test dependencies are installed:

npm run test:e2e

Current Project Shape

• backend/: extracted backend workflow domains for record I/O, core sequence workflows, design-assist workflows, trace, search, reference, siRNA, project persistence, sharing, history, cloning/assembly, analysis/alignment, and biology-support workflows such as digest, enzyme, annotation, feature, and gel operations
• genomeforge_toolkit.py: sequence engine and CLI
• web_ui.py: local HTTP API server and thin dispatch/bootstrap layer
• webui/: browser app shell, extracted styles, and extracted frontend scripts
• bio/, compat/, collab/: helper modules
• smoke_test.py: broad endpoint regression
• real_world_functional_test.py: real-data workflow validation
• docs/: product docs, tutorial, release notes, and modernization roadmap

Scope Notes

• Genome Forge is intentionally local-first.
• Many workflows are practical heuristics rather than proprietary commercial implementations.
• Native proprietary .dna import is supported through optional Biopython-backed parsing when available.
• External aligners are optional for adapter-backed multiple-alignment workflows.

License

Genome Forge is licensed under the Apache License 2.0. See LICENSE.