Claude Scholar - Personal Claude Code configuration system for academic research and software development
Mission: Cover the complete academic research lifecycle (from ideation to publication) and software development workflows, with plugin development and project management capabilities.
- Degree: Computer Science PhD
- Target Venues:
- Top conferences: NeurIPS, ICML, ICLR, KDD
- High-impact journals: Nature, Science, Cell, PNAS
- Focus: Academic writing quality, logical coherence, natural expression
Python Ecosystem:
- Package manager:
uv- modern Python package manager - Config management: Hydra + OmegaConf (config composition, overrides, type safety)
- Model training: Transformers Trainer
Git Standards:
- Commit convention: Conventional Commits
Type: feat, fix, docs, style, refactor, perf, test, chore Scope: data, model, config, trainer, utils, workflow - Branch strategy: master/develop/feature/bugfix/hotfix/release
- Merge strategy: rebase for feature branch sync, merge --no-ff for integration
- Respond in English to the user
- Keep technical terms in English (e.g. NeurIPS, RLHF, TDD, Git)
- Do not translate proper nouns or names
- Plan documents:
/planfolder - Temporary files:
/tempfolder - Auto-create folders if they don't exist
- Discuss approach before breaking down complex tasks
- Run example tests after implementation
- Make backups, avoid breaking existing functionality
- Clean up temporary files after completion
- Task management: Use TodoWrite to track progress, plan before executing complex tasks, prefer existing skills
- Communication: Ask proactively when uncertain, confirm before important operations, follow hook-enforced workflows
- Code style: Python follows PEP 8, comments in English, identifiers in English
Ideation → ML Development → Experiment Analysis → Paper Writing → Self-Review → Submission/Rebuttal → Post-Acceptance
| Stage | Core Tools | Commands |
|---|---|---|
| 1. Research Ideation | research-ideation skill + literature-reviewer agent + Zotero MCP |
/research-init, /zotero-review, /zotero-notes |
| 2. ML Project Dev | architecture-design skill + code-reviewer agent |
/plan, /commit, /tdd |
| 3. Experiment Analysis | results-analysis skill + data-analyst agent |
/analyze-results |
| 4. Paper Writing | ml-paper-writing skill + paper-miner agent |
- |
| 5. Self-Review | paper-self-review skill |
- |
| 6. Submission & Rebuttal | review-response skill + rebuttal-writer agent |
/rebuttal |
| 7. Post-Acceptance | post-acceptance skill |
/presentation, /poster, /promote |
- Automation: 5 Hooks auto-trigger at session lifecycle stages (skill evaluation, env init, work summary, security check)
- Zotero Integration: Automated paper import, collection management, full-text reading, and citation export via Zotero MCP
- Knowledge Extraction:
paper-minerandkaggle-mineragents continuously extract knowledge from papers and competitions - Skill Evolution:
skill-development→skill-quality-reviewer→skill-improverthree-step improvement loop
- research-ideation: Research startup (5W1H, literature review, gap analysis, research question formulation, Zotero integration)
- results-analysis: Experiment result analysis (statistical tests, visualization, ablation studies)
- citation-verification: Citation verification (multi-layer: format→API→info→content)
- daily-paper-generator: Daily paper generator for research tracking
- ml-paper-writing: ML/AI paper writing assistance
- Top conferences: NeurIPS, ICML, ICLR, ACL, AAAI, COLM
- Journals: Nature, Science, Cell, PNAS
- writing-anti-ai: Remove AI writing patterns, bilingual (Chinese/English)
- paper-self-review: Paper self-review (6-item quality checklist)
- review-response: Systematic rebuttal writing
- post-acceptance: Post-acceptance processing (presentation, poster, promotion)
- doc-coauthoring: Document co-authoring workflow
- latex-conference-template-organizer: LaTeX conference template organization
- daily-coding: Daily coding checklist (minimal mode, auto-triggered)
- git-workflow: Git workflow standards (Conventional Commits, branch management)
- code-review-excellence: Code review best practices
- bug-detective: Debugging and error investigation (Python, Bash/Zsh, JavaScript/TypeScript)
- architecture-design: ML project code architecture and design patterns
- verification-loop: Verification loops and testing
- skill-development: Skill development guide
- skill-improver: Skill improvement tool
- skill-quality-reviewer: Skill quality review
- command-development: Slash command development
- command-name: Plugin structure guide
- agent-identifier: Agent development configuration
- hook-development: Hook development and event handling
- mcp-integration: MCP server integration
- planning-with-files: Planning and progress tracking with Markdown files
- uv-package-manager: uv package manager usage
- webapp-testing: Local web application testing
- kaggle-learner: Kaggle competition learning
- frontend-design: Create distinctive, production-grade frontend interfaces
- ui-ux-pro-max: UI/UX design intelligence (50+ styles, 97 palettes, 57 font pairings, 9 stacks)
- web-design-reviewer: Visual website inspection for responsive, accessibility, and layout issues
| Command | Function |
|---|---|
/research-init |
Start Zotero-integrated research ideation workflow (auto-create collections, import papers, full-text analysis) |
/zotero-review |
Read papers from Zotero collection, generate structured literature review |
/zotero-notes |
Batch read Zotero papers, generate structured reading notes |
/analyze-results |
Analyze experiment results (statistical tests, visualization, ablation) |
/rebuttal |
Generate systematic rebuttal document |
/presentation |
Create conference presentation outline |
/poster |
Generate academic poster design |
/promote |
Generate promotion content (Twitter, LinkedIn, blog) |
| Command | Function |
|---|---|
/plan |
Create implementation plan |
/commit |
Commit code (following Conventional Commits) |
/update-github |
Commit and push to GitHub |
/update-readme |
Update README documentation |
/code-review |
Code review |
/tdd |
Test-driven development workflow |
/build-fix |
Fix build errors |
/verify |
Verify changes |
/checkpoint |
Create checkpoint |
/refactor-clean |
Refactor and clean up |
/learn |
Extract reusable patterns from code |
/create_project |
Create new project |
/setup-pm |
Configure package manager (uv/pnpm) |
/update-memory |
Check and update CLAUDE.md memory |
/sc agent- Agent dispatch/sc analyze- Code analysis/sc brainstorm- Interactive brainstorming/sc build- Build project/sc business-panel- Business panel/sc cleanup- Code cleanup/sc design- System design/sc document- Generate documentation/sc estimate- Effort estimation/sc explain- Code explanation/sc git- Git operations/sc help- Help info/sc implement- Feature implementation/sc improve- Code improvement/sc index- Project index/sc index-repo- Repository index/sc load- Load context/sc pm- Package manager operations/sc recommend- Recommend solutions/sc reflect- Reflection summary/sc research- Technical research/sc save- Save context/sc select-tool- Tool selection/sc spawn- Spawn subtasks/sc spec-panel- Spec panel/sc task- Task management/sc test- Test execution/sc troubleshoot- Issue troubleshooting/sc workflow- Workflow management
- literature-reviewer - Literature search, classification, and trend analysis (Zotero MCP integration: auto-import, full-text reading)
- data-analyst - Automated data analysis and visualization
- rebuttal-writer - Systematic rebuttal writing with tone optimization
- paper-miner - Extract writing knowledge from successful papers
- architect - System architecture design
- build-error-resolver - Build error fixing
- bug-analyzer - Deep code execution flow analysis and root cause investigation
- code-reviewer - Code review
- dev-planner - Development task planning and breakdown
- refactor-cleaner - Code refactoring and cleanup
- tdd-guide - TDD workflow guidance
- kaggle-miner - Extract engineering practices from Kaggle solutions
- ui-sketcher - UI blueprint design and interaction specifications
- story-generator - User story and requirement generation
Cross-platform Node.js hooks for automated workflow execution:
| Hook | Trigger | Function |
|---|---|---|
session-start.js |
Session start | Show Git status, todos, available commands |
skill-forced-eval.js |
Every user input | Force evaluate all available skills |
session-summary.js |
Session end | Generate work log, detect CLAUDE.md updates |
stop-summary.js |
Session stop | Quick status check, temp file detection |
security-guard.js |
File operations | Security validation (key detection, dangerous command interception) |
Global constraints, always active:
| Rule File | Purpose |
|---|---|
coding-style.md |
ML project code standards: 200-400 line files, immutable config, type hints, Factory & Registry patterns |
agents.md |
Agent orchestration: auto-invocation timing, parallel execution, multi-perspective analysis |
security.md |
Security standards: key management, sensitive file protection, pre-commit security checks |
experiment-reproducibility.md |
Experiment reproducibility: random seeds, config recording, environment recording, checkpoint management |
- Format: kebab-case (lowercase + hyphens)
- Form: prefer gerund form (verb+ing)
- Example:
scientific-writing,git-workflow,bug-detective
- Format: Title Case
- Abbreviations all caps: TDD, RLHF, NeurIPS, ICLR
- Example:
[Writing, Research, Academic]
- Person: third person
- Content: include purpose and use cases
- Example: "Provides guidance for academic paper writing, covering top-venue submission requirements"
After each task, proactively provide a brief summary:
📋 Operation Review
1. [Main operation]
2. [Modified files]
📊 Current Status
• [Git/filesystem/runtime status]
💡 Next Steps
1. [Targeted suggestions]