🎓 Academic Forge

Branch model

• site-first: the project's main (default) branch, and the single source for GitHub Pages, registry/skills.json, and installer scripts.
• the old submodule-based architecture (master) has been retired and is no longer maintained or updated weekly.

✨ New: 32 built-in Claude Science skills (by Anthropic)

• covers protein structure & design, genomics, single-cell, publication figures, literature review, remote compute, and more
• installable without a Claude Science subscription, usable across agents (Claude Code / OpenCode / Codex), and works on Windows (PowerShell installer)
• shipped as a locally maintained collection under skills/claude-science, filed in the catalog under "Workflow & Process · Claude Science", with each sub-skill re-classified into research / writing / figures, etc.

🔨 What Academic Forge Is

Academic Forge is a site-first catalog + installer. Much like Minecraft Forge loads mods into the game, it forges scattered academic AI skills into one handy toolbox. 🎓

Instead of cloning a whole bundle into every project, just three steps:

1. 🖱️ browse and check the packs you need on the site
2. 📋 generate an install command in one click
3. ⚡ run it from your project root

Core rules:

• 🧩 the site, generated commands, and installers all read the same registry/skills.json
• 🌿 site-first is the only public line
• 📦 two things are maintained locally in this repository: skills/scientific-visualization and skills/claude-science (Anthropic's built-in Claude Science collection)

🚀 Quick Start

🖱️ Option 1: Use the configurator site

Open https://hughyau.github.io/AcademicForge/, check the skill packs you need, pick your platform (Claude Code / OpenCode / Codex), and generate the install command in one click.

⌨️ Option 2: Run the installer directly

macOS / Linux:

cd your-project
curl -sSL https://raw.githubusercontent.com/HughYau/AcademicForge/refs/heads/site-first/scripts/forge-install.sh | bash -s -- \
  --tool claude \
  --skills humanizer,superpowers

Windows PowerShell:

cd your-project
$script = Join-Path $PWD 'forge-install.ps1'
Invoke-WebRequest -Uri 'https://raw.githubusercontent.com/HughYau/AcademicForge/refs/heads/site-first/scripts/forge-install.ps1' -OutFile $script
& $script -Tool claude -Skills 'humanizer,superpowers'
Remove-Item $script

Already-installed skills with the same name are skipped with a warning; add --force (-Force in PowerShell) to overwrite.

🤖 Option 3: Let your AI pick for you

Not sure what to pick? Hand this prompt to your AI agent (Claude Code / OpenCode / Codex):

Fetch and read https://hughyau.github.io/AcademicForge/agents.md, then follow its instructions: ask about my research needs, pick matching academic skills from the AcademicForge catalog, and build the install command for me.

The "Not sure what to pick?" card on the site copies this prompt in one click (with your selected tool and platform baked in). Agent-readable catalog endpoints:

• Guide: https://hughyau.github.io/AcademicForge/agents.md
• Slim index: https://hughyau.github.io/AcademicForge/index.slim.json
• Full registry mirror: https://hughyau.github.io/AcademicForge/skills.json

Verify installation:

ls .claude/skills/
ls .opencode/skills/
ls .codex/skills/

📦 Local Content Kept in This Branch

The local skill content that remains checked in on site-first is:

• skills/scientific-visualization — a single local skill

• skills/claude-science — the Claude Science (Anthropic) built-in collection, 32 skills. The collection root is filed under "Workflow & Process" as Claude Science by Anthropic; each sub-skill is then re-classified into research / writing / figures, etc. Because it is hosted directly in this repo, it installs via sparse-checkout without a Claude Science subscription, and is usable across agents including on Windows.

  After editing that directory, rebuild just this collection's index (no network clone of the other collections):

  node scripts/build-skill-index.mjs --only claude-science
  node scripts/build-slim-index.mjs
  

All other packs are installed from the sources described in registry/skills.json.

🔬 Claude Science Skill List (32)

The full set of 32 skills in skills/claude-science, organized by theme. To install just this collection:

curl -sSL https://raw.githubusercontent.com/HughYau/AcademicForge/refs/heads/site-first/scripts/forge-install.sh | bash -s -- --tool claude --skills claude-science

Six themes: 🧬 Structure prediction & docking · ✏️ Protein design & embeddings · 🧫 Genomics & single-cell · 📊 Figures & visualization · ✍️ Literature & writing · ⚙️ Compute & workflow

Expand all 32 Claude Science skills

🧬 Structure prediction & docking (6)

Skill	What it does
alphafold2	Fold monomers & complexes with AlphaFold2 / AF2-Multimer (ColabFold runner)
openfold3	Open-weights PyTorch reproduction of AlphaFold3 (AlQuraishi Lab)
boltz	Boltz-2 protein / nucleic-acid / small-molecule complexes, optional binding affinity
chai1	Chai-1 foundation model for antibody-antigen & protein-ligand complexes
esmfold2	Biohub ESMFold2 / ESMFold2-Fast all-atom co-folding
diffdock	Predict small-molecule binding poses with DiffDock-L

✏️ Protein design & embeddings (4)

Skill	What it does
proteinmpnn	Inverse-fold a backbone into an amino-acid sequence
ligandmpnn	Inverse-folding with ligand / nucleic-acid / metal context
solublempnn	ProteinMPNN retrained on a soluble-PDB subset
fair-esm2	Protein embeddings with Meta AI's ESM-2

🧫 Genomics & single-cell (4)

Skill	What it does
borzoi	Predict genome-wide functional tracks (RNA-seq/CAGE/DNase/ChIP) from DNA
evo2	Long-context genomic foundation model: score / embed / generate DNA
scgpt	Single-cell foundation model scGPT: embed & annotate
scvi-tools	Probabilistic scRNA-seq (scVI / scANVI + Bayesian differential expression)

📊 Figures & visualization (4)

Skill	What it does
figure-composer	Compose a publication-grade multi-panel figure
figure-style	Publication-grade figure correctness & legibility rules
algorithmic-art	Create algorithmic / generative art with p5.js
web-artifacts-builder	Build elaborate claude.ai HTML artifacts (React/Tailwind/shadcn)

✍️ Literature & writing (4)

Skill	What it does
literature-review	Find, verify & synthesize scientific literature
paper-narrative	Judge & reshape the story a paper's figures tell
indication-dossier	Generate a therapeutic indication dossier
pdf-explore	Locate, compare & extract content across a whole PDF / paper

⚙️ Compute & workflow (10)

Skill	What it does
compute-env-setup	Set up a run environment on remote compute
remote-compute-modal	Run GPU jobs on your own Modal account
remote-compute-ssh	Submit → wait → harvest workflow for SSH / SLURM hosts
managed-model-endpoints	Register local / remote model service endpoints
using-model-endpoint	Call a registered endpoint over its native HTTP API
self-awareness	Introspect Claude Science's session DB / SDK
skill-creator	Create, improve & evaluate skills
customize	Customize agent profiles & author new skills
learn	Learning / explanation skill for understanding "why"
product-self-knowledge	Fact-check claims about Anthropic products

🛠️ Maintaining site-first

Common local commands:

npm run site:install
npm run build
npm run preview
npm run validate:registry
npm run ci:validate
node scripts/build-skill-index.mjs --check

Local installer smoke tests:

"D:\Application\Git\bin\bash.exe" scripts/tests/forge-install-local-registry.sh
pwsh -File scripts/tests/forge-install-local-registry.ps1

🌐 GitHub Pages

• GitHub Pages deploys only from site-first
• set Settings -> Pages -> Source to GitHub Actions
• use npm run preview for branch-local preview before pushing

📚 Documentation

• Quick Start
• Attributions
• site-first design spec
• site-first implementation plan

⭐ Star History

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📄 License

• repository structure, site, scripts, and local content are under MIT
• third-party skills retain their original licenses and authorship