AcademicForge

🎓 Academic Forge

✨ 新增： Claude Science内置的 32 个技能

• 覆盖发表级图表、文献综述、远程算力、蛋白质结构与设计、基因组、单细胞等
• 无需订阅 Claude Science 即可安装，跨 agent 通用（Claude Code / OpenCode / Codex），支持 Windows（PowerShell 安装脚本）
• 作为本地维护集合收录在 skills/claude-science，在目录中归类为「流程与方法 · Claude Science」，其下每个技能再按科研 / 写作 / 图表等分类展示

🔨 什么是 Academic Forge

"Forge（锻造台）" 灵感来自 Minecraft 的模组加载器系统——就像 Minecraft Forge 整合包为特定游戏体验集成各种模组一样，Academic Forge 把散落各处的学术 AI 技能，锻造成一套趁手的工具箱。🎓

不用整仓复制全部 skill，三步搞定：

1. 🖱️ 在站点里浏览、勾选需要的 pack
2. 📋 一键生成安装命令
3. ⚡ 在自己的项目根目录里执行

🚀 快速开始

🖱️ 方式一：使用选配站

打开 https://hughyau.com/AcademicForge/，勾选需要的 skill pack、选择你的平台（Claude Code / OpenCode / Codex），一键生成安装命令。

⌨️ 方式二：直接运行安装脚本

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

已安装的同名 skill 会被跳过并提示；追加 --force（PowerShell 为 -Force）可覆盖更新。

🤖 方式三：让你的 AI 替你挑选

不知道选什么？把下面这段提示词交给你的 AI 智能体（Claude Code / OpenCode / Codex 均可）：

请获取并阅读 https://hughyau.github.io/AcademicForge/agents.md，按其中的说明了解我的研究需求，然后从 AcademicForge 目录中为我挑选合适的学术 skills 并生成安装命令。

🔬 Claude Science 技能清单（32 个）

下面按主题整理了 skills/claude-science 收录的全部 32 个技能。只想安装这一套：

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

六大主题：🧬 结构预测与对接 · ✏️ 蛋白质设计与嵌入 · 🧫 基因组与单细胞 · 📊 图表与可视化 · ✍️ 文献与写作 · ⚙️ 算力与工作流

展开查看全部 32 个 Claude Science 技能

🧬 结构预测与对接（6）

Skill	用途
alphafold2	AlphaFold2 / AF2-Multimer 折叠单体与复合物（ColabFold 运行器）
openfold3	AlphaFold3 的开源权重 PyTorch 复现（AlQuraishi Lab）
boltz	Boltz-2 预测蛋白 / 核酸 / 小分子复合物，可选结合亲和力
chai1	Chai-1 基础模型预测抗体-抗原、蛋白-配体复合物
esmfold2	Biohub ESMFold2 / ESMFold2-Fast 全原子共折叠
diffdock	DiffDock-L 预测小分子结合构象（分子对接）

✏️ 蛋白质设计与嵌入（4）

Skill	用途
proteinmpnn	对蛋白骨架逆折叠生成氨基酸序列
ligandmpnn	带配体 / 核酸 / 金属上下文的逆折叠
solublempnn	面向可溶性重训的 ProteinMPNN 变体
fair-esm2	用 Meta ESM-2 生成蛋白质嵌入表征

🧫 基因组与单细胞（4）

Skill	用途
borzoi	从 DNA 序列预测全基因组功能轨迹（RNA-seq/CAGE/DNase/ChIP）
evo2	长上下文基因组基础模型：打分 / 嵌入 / 生成 DNA
scgpt	单细胞基础模型 scGPT：嵌入与细胞注释
scvi-tools	概率式单细胞 RNA-seq（scVI / scANVI + 贝叶斯差异表达）

📊 图表与可视化（4）

Skill	用途
figure-composer	组合出版级多面板图
figure-style	出版级图表正确性与可读性规范
algorithmic-art	用 p5.js 创作算法 / 生成艺术
web-artifacts-builder	构建复杂的 claude.ai HTML 交互产物（React/Tailwind/shadcn）

✍️ 文献与写作（4）

Skill	用途
literature-review	检索、核验并综合科学文献
paper-narrative	审视并重塑论文图表讲述的“故事线”
indication-dossier	生成治疗适应症档案（indication dossier）
pdf-explore	跨整篇 PDF / 论文定位、比较与抽取内容

⚙️ 算力与工作流（10）

Skill	用途
compute-env-setup	在远程算力上搭建运行环境
remote-compute-modal	在你自己的 Modal 账户上运行 GPU 任务
remote-compute-ssh	SSH / SLURM 主机的提交 → 等待 → 回收工作流
managed-model-endpoints	注册本地 / 远程模型服务端点
using-model-endpoint	通过原生 HTTP API 调用已注册的模型端点
self-awareness	对 Claude Science 会话数据库 / SDK 做自省
skill-creator	创建、改进并评测 skill
customize	自定义 agent 画像并创作新 skill
learn	面向“理解原理”的学习 / 讲解型 skill
product-self-knowledge	涉及 Anthropic 产品事实时先自查核对

📚 文档

• 快速入门
• Skill 归属

⭐ Star History

Star History

---

📄 许可证

• 仓库结构、站点、脚本和本地内容采用 MIT
• 第三方 skill 保留其各自许可证与作者信息

🎓 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

---

📄 License

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