NORA (Night Owl Research Agent)

A fully automatic, domain-aware AI research agent for Geoscientists, Remote Sensing researchers, and GIScientists — powered entirely by Claude Code skills.

---

Quick Start

NORA runs inside Claude Code. There is no Python entry point, no server to spin up, and no build step — you just drop the skills into Claude Code's skill directory and invoke the launcher.

Step 1 — Install Claude Code

Install Claude Code first. Any of the official distributions works:

• CLI (recommended):

  npm install -g @anthropic-ai/claude-code
  claude --version

• Desktop app (macOS / Windows): download from https://claude.com/claude-code
• VS Code extension: install "Claude Code" from the Marketplace
• Web: https://claude.ai/code

Sign in once with your Anthropic account so Claude Code can reach the API.

Step 2 — Get NORA onto your machine

git clone https://github.com/GRIND-Lab-Core/night_owl_research_agent.git
cd night_owl_research_agent

Step 3 — Install the skills into Claude Code

Claude Code looks for skills under ~/.claude/skills/ (user-level, available in every project) or <project>/.claude/skills/ (project-local). Copy the entire skills/ folder from this repo into one of those locations.

macOS / Linux (user-level — recommended):

mkdir -p ~/.claude/skills
cp -R skills/* ~/.claude/skills/

Windows PowerShell (user-level):

New-Item -ItemType Directory -Force -Path "$env:USERPROFILE\.claude\skills" | Out-Null
Copy-Item -Recurse -Force .\skills\* "$env:USERPROFILE\.claude\skills\"

Windows bash / Git Bash:

mkdir -p "$USERPROFILE/.claude/skills"
cp -R skills/* "$USERPROFILE/.claude/skills/"

Project-local alternative (skills only visible when Claude Code is opened in this folder):

mkdir -p .claude/skills
cp -R skills/* .claude/skills/

Also copy the launcher slash command so /launcher is available:

# macOS / Linux
mkdir -p ~/.claude/commands
cp .claude/commands/launcher.md ~/.claude/commands/

# Windows PowerShell
New-Item -ItemType Directory -Force -Path "$env:USERPROFILE\.claude\commands" | Out-Null
Copy-Item -Force .\.claude\commands\launcher.md "$env:USERPROFILE\.claude\commands\"

Verify the install — open Claude Code and run:

/skills

You should see the NORA skills (full-pipeline, lit-review, idea-discovery-pipeline, deploy-experiment, paper-draft, …) listed.

Step 4 — Start a research session

Open the night_owl_research_agent folder in Claude Code (this gives NORA access to CLAUDE.md, RESEARCH_PLAN.md, output/, memory/, and tools/), then pick one of the two entry points:

Option A — interactive launcher (best for first-time users):

/launcher

The launcher walks you through a short questionnaire — research topic, stage to start from, control flags (AUTO_PROCEED, HUMAN_CHECKPOINT, COMPACT_MODE, REVIEWER_DIFFICULTY) — and routes to the correct skill.

Option B — end-to-end pipeline (best when you already know what you want to run):

Skill: full-pipeline
"Your research direction here, e.g. 'urban soundscape inequality via street-view + audio foundation models'"

or, if you prefer a slash-style invocation:

/full-pipeline "your research direction"

full-pipeline chains all four stages: idea-discovery-pipeline → deploy-experiment → auto-review-loop → generate-report and then hands off to paper-writing-pipeline for the manuscript.

Tip: for reproducibility, fill in RESEARCH_PLAN.md (or BRIEF.md) in the project root before launching. When either file is present, skills read it as the authoritative brief and ignore conflicting $ARGUMENTS.

Step 5 — (Optional) Enable extras

• MCP servers — edit .mcp.json and register with Claude Code (/mcp inside the chat) to enable filesystem, fetch, arxiv_mcp, geo_mcp, github, and brave_search. See mcp/README_MCP.md.
• Hooks — settings.json wires harness/hooks/*.sh into Claude Code's lifecycle (writes handoff.json on session end, validates tool use, sends desktop notifications). On Windows, run the hook scripts via Git Bash or WSL.
• W&B — if your experiments use Weights & Biases, run wandb login once on the host where deploy-experiment will launch training.
• API keys — set ANTHROPIC_API_KEY (for Claude Code), plus any optional keys you want to use (SEMANTIC_SCHOLAR_API_KEY, GITHUB_TOKEN, BRAVE_API_KEY).

Prerequisites summary

Requirement	Why
Claude Code (CLI / desktop / web / VS Code)	Runtime for skills
Anthropic account + API credit	Powers the agent
Python 3.10+ with pip install arxiv requests	tools/arxiv_fetch.py, tools/semantic_scholar_fetch.py
Conda env with geopandas, pysal, libpysal, esda, spreg, mgwr, rasterio, xarray	Track B (spatial) experiments
CUDA GPU (local / remote SSH / Modal)	Track A (deep-learning) experiments — optional

---

What It Does

NORA automates the complete academic research lifecycle using Claude Code skills — Markdown-defined workflows that Claude reads and executes, selecting appropriate tools and methods based on context.

1. Literature review — searches ArXiv, Semantic Scholar, local papers, Zotero, and Obsidian; synthesizes findings and identifies ranked research gaps.
2. Idea discovery — generates 8–12 research ideas from literature gaps, validates novelty via multi-source search + external reviewer, and pilot-tests the top candidates. Pilots run a mandatory local-GPU presence check first (nvidia-smi → CUDA, then MPS, then none); when a local GPU is detected, every pilot launches on it instead of silently falling back to CPU or remote.
3. Method refinement — iteratively refines vague research directions into problem-anchored, implementation-ready proposals via adversarial review (up to 5 rounds, score ≥ 9 target).
4. Experiment design & execution — produces claim-driven experiment roadmaps and deploys to local, remote SSH, or Modal serverless GPU (Track A), or runs spatial/GIScience methods on CPU (Track B), or both for mixed GeoAI. The same mandatory local-GPU check runs at Step 0 of deploy-experiment so any ML/DL workload (pilot or full) executes on the local GPU when present.
5. Data acquisition — discovers, evaluates, downloads, validates, and documents datasets from government portals, APIs, cloud archives, and open repositories with full provenance.
6. Spatial analysis — guideline-driven: classifies the analytical objective, runs ESDA, and applies geospatial diagnostics conditionally on the research question. MAUP discussion, GWR/MGWR, residual Moran's I, alternative spatial weights, and spatial CV are triggered only when the claim depends on them; when in doubt the skill pauses for a human checkpoint instead of running heavyweight checks (or skipping reviewer-expected ones) by reflex.
7. Adversarial review — up to 4 rounds of generator–evaluator-separated review with per-criterion hard floors; medium / hard / nightmare reviewer modes via Codex MCP, codex exec, or a Claude subagent. Domain personas (giscience, remote-sensing, spatial-data-science) apply geo-specific must-checks only where the paper's claims actually depend on them instead of penalizing every paper for missing MAUP / GWR discussion.
8. Report + paper writing — consolidates every pipeline artifact into output/NARRATIVE_REPORT.md, then runs paper-writing-pipeline to produce a journal-ready manuscript (Markdown → LaTeX → PDF/DOCX) with journal-specific profiles for IJGIS, IEEE TGRS, ISPRS JPRS, RSE, AAG, TGIS, and more.

---

Architecture

NORA is a skills-first system. All research logic lives in Markdown skill files that Claude reads and executes.

Skills describe workflow logic in Markdown. Claude reads a skill to understand the workflow, then decides the exact sequence of actions based on context — the skill provides guidelines and decision frameworks, not rigid procedures.

You (or /launcher)
    ↓ invokes
Skill SKILL.md  ←─── reads domain knowledge from skills/knowledge/
    ↓ Claude decides what to do
CLI tools (tools/arxiv_fetch.py, etc.) + inline Python + MCP servers as needed
    ↓ produce
Output files (reports, paper-cache, figures, manuscript)
    ↓ read by
Next skill in pipeline

The single installed slash command is /launcher. Every other skill is invoked by name (Claude Code's native Skill tool) or by being called internally from another skill.

---

Skills

23 workflow skills in skills/ plus domain knowledge in skills/knowledge/. Each skill is a self-contained Markdown workflow file.

Workflow Skills

Skill	What it does
full-pipeline	Master pipeline: idea discovery → experiment → review → report → paper
lit-review	Search + synthesize + gap analysis (ArXiv, Semantic Scholar, local papers, Zotero, Obsidian)
idea-discovery-pipeline	Full idea pipeline: lit-review → generate-idea → novelty-check → idea-review → experiment-design-pipeline
generate-idea	Brainstorm 8–12 ideas, filter, pilot-test top 3, rank (called by idea-discovery-pipeline)
novelty-check	Verify idea novelty via multi-source search + external reviewer
idea-review	External critical review of research ideas (Codex MCP)
refine-research	Iterative method refinement via external review (up to 5 rounds, score ≥ 9)
experiment-design	Claim-driven experiment roadmap with run order, budget, decision gates
experiment-design-pipeline	One-shot wrapper: refine-research → experiment-design
deploy-experiment	Deploy experiments — mandatory local-GPU check at Step 0, then Track A (GPU ML) and/or Track B (CPU spatial)
data-download	Discover, evaluate, download datasets with provenance tracking
spatial-analysis	Research-question-driven spatial analysis: classification → ESDA → method → conditional diagnostics → interpretation, with a human checkpoint before adding or skipping heavyweight spatial checks
auto-review-loop	Up to 4 adversarial review rounds with per-criterion floors
generate-report	Consolidate lit-review + idea + experiment + review artifacts into output/NARRATIVE_REPORT.md
paper-writing-pipeline	Orchestrates paper-plan → paper-figure-generate → paper-draft → paper-review-loop → paper-covert
paper-plan	Build section outline + figure plan (output/PAPER_PLAN.md)
paper-figure-generate	Generate publication-quality figures, maps, diagrams, and captions
paper-draft	Turn output/PAPER_PLAN.md into a journal-quality Markdown manuscript
paper-review-loop	Reviewer-editor review of the draft manuscript and iterative revision
paper-covert	Convert final manuscript into venue submission package (modular LaTeX, PDF, DOCX)
submit-check	Validate manuscript against target-journal requirements
training-check	Monitor running experiments for stalls/failures

Domain Knowledge

File	Domain
spatial-methods.md	Spatial statistics, regression, autocorrelation
geoai-domain.md	GeoAI, spatial deep learning, foundation models
academic-writing.md	Academic writing conventions
apa-citations.md	APA 7th edition citation formatting
disaster-resilience.md	Disaster management, community resilience
environmental-health.md	Environmental epidemiology, exposure assessment
literature-mining.md	Literature search and synthesis strategies
research-iteration.md	Iterative research refinement patterns

---

Control Flags

Edit CLAUDE.md before starting a long run:

AUTO_PROCEED: false       # true = auto-select top idea after discovery; false = wait for approval
HUMAN_CHECKPOINT: true    # true = pause after each review round; false = run autonomously
COMPACT_MODE: false       # true = use output/PROJ_NOTES.md instead of full logs (saves context)
EXTERNAL_REVIEW: false    # true = use Claude subagent / external reviewer LLM

full-pipeline also accepts REVIEWER_DIFFICULTY = medium | hard | nightmare and ARXIV_DOWNLOAD = true | false. Overrides can be passed inline, e.g.:

/full-pipeline "topic — AUTO_PROCEED: false, difficulty: nightmare"

---

Harness Engineering

Claude Code's hook system automates lifecycle management (configured in settings.json):

Hook	When	What it does
PreToolUse	Before Bash/Write	Validates paths, blocks dangerous commands, logs intent
PostToolUse	After tool execution	Updates state, caches results
SkillUse	Before/after each Skill tool call	harness/hooks/skill_marker.sh writes per-stage markers feeding tools/telemetry_stage_marker.py
Stop	Agent session ends	Writes handoff.json, updates memory/MEMORY.md, runs tools/telemetry_aggregate.py to emit output/TELEMETRY.jsonl and output/TELEMETRY_STAGES.jsonl, sends notification
Notification	Long tasks finish	Desktop alert via notify-send / osascript

---

Autoresearch Scoring Loop

paper-draft writes draft
    ↓
paper-review-loop scores it (separate context — generator–evaluator separation)
    ↓
All 5 dimension floors met AND weighted avg ≥ 7.5? → ACCEPT
    ↓ (else)
paper-draft revises (max 3 attempts total)
    ↓
If still not accepted → flag for human review

Dimension	Weight	Hard floor
Novelty	30%	≥ 6.5
Rigor	25%	≥ 7.0
Literature coverage	20%	≥ 6.5
Clarity	15%	≥ 6.0
Impact	10%	≥ 6.0

Accept requires weighted avg ≥ 7.5 and all five floors met.

---

Journal Templates & Profiles

Templates enforce correct structure, section ordering, word limits, and formatting. paper-covert additionally loads a YAML profile that drives LaTeX conversion.

Markdown templates (templates/)

Category	Journals
geoscience/	Nature Geoscience, Geophysical Research Letters
remote_sensing/	Remote Sensing of Environment, IEEE TGRS, ISPRS JPRS
giscience/	IJGIS, Transactions in GIS, Annals of AAG

Submission profiles (skills/paper-covert/profiles/)

aag_annals.yaml, generic.yaml, ieee_tgrs.yaml, ijgis.yaml, isprs_jprs.yaml, rse.yaml, tgis.yaml.

---

MCP Servers

Declared in .mcp.json. Setup notes in mcp/README_MCP.md.

Server	Purpose
filesystem	Read/write local files and datasets
fetch	Fetch web content (papers, data portals, journal pages)
geo_mcp	Spatial data: GADM, OSM Overpass, Census ACS, GEE (mcp/geo_mcp_server.py)
arxiv_mcp	ArXiv search, paper fetch, abstract parsing
github	GitHub repo reading and code management
brave_search	Web search for literature, datasets, documentation

---

Key Output Files

File	Written by
output/LIT_REVIEW_REPORT.md	lit-review
output/IDEA_REPORT.md / NOVELTY_REPORT.md / IDEA_REVIEW_REPORT.md	idea-discovery-pipeline
output/refine-logs/FINAL_PROPOSAL.md / REFINE_REPORT.md	refine-research
output/refine-logs/EXPERIMENT_PLAN.md / output/EXPERIMENT_TRACKER.md	experiment-design
output/experiment/EXPERIMENT_RESULT.md / EXPERIMENT_LOG.md	deploy-experiment
output/experiment/data/ / figures/ / scripts/	deploy-experiment, spatial-analysis
output/AUTO_REVIEW_REPORT.md / REVIEW_STATE.json / review-rounds/	auto-review-loop
output/METHOD_DESCRIPTION.md	auto-review-loop
output/NARRATIVE_REPORT.md	generate-report
output/PAPER_PLAN.md	paper-plan
output/figures/	paper-figure-generate
output/manuscript/	paper-draft, paper-review-loop
output/papers/	paper-covert
output/reports/submit_check_*.md	submit-check
data/DATA_MANIFEST.md, data/raw/	data-download
output/PROJ_NOTES.md	all skills (append-only, compact log)
output/TELEMETRY.jsonl (per-session) and output/TELEMETRY_STAGES.jsonl (per-skill)	tools/telemetry_aggregate.py (run by Stop hook)
output/CONTRACT_VIOLATION.md	any skill that detects a downgraded success criterion or other contract violation
memory/MEMORY.md, handoff.json	Stop hook

---

Project Structure

night_owl_research_agent/
├── CLAUDE.md                        ← Dashboard and project conventions
├── README.md                        ← This file
├── design_principle.md              ← Skill-level design principles (export → Excel via tools/)
├── design_principle_agents.md       ← Sub-agent design principles
├── settings.json                    ← Claude Code hooks, permissions, env vars
├── .mcp.json                        ← MCP server declarations
│
├── .claude/
│   ├── commands/
│   │   └── launcher.md              ← /launcher (only installed slash command)
│   └── agents/                      ← Specialist sub-agent definitions (9 total)
│       ├── orchestrator.md
│       ├── literature-scout.md
│       ├── synthesis-analyst.md
│       ├── gap-finder.md
│       ├── hypothesis-generator.md
│       ├── geo-specialist.md
│       ├── paper-writer.md
│       ├── peer-reviewer.md
│       └── citation-manager.md
│
├── skills/                          ← 22 workflow skills + knowledge/
│   ├── full-pipeline/SKILL.md
│   ├── lit-review/SKILL.md
│   ├── idea-discovery-pipeline/SKILL.md
│   ├── generate-idea/SKILL.md
│   ├── novelty-check/SKILL.md
│   ├── idea-review/SKILL.md
│   ├── refine-research/SKILL.md
│   ├── experiment-design/SKILL.md
│   ├── experiment-design-pipeline/SKILL.md
│   ├── deploy-experiment/SKILL.md
│   ├── data-download/SKILL.md
│   ├── spatial-analysis/SKILL.md
│   ├── auto-review-loop/SKILL.md
│   ├── generate-report/{SKILL.md, templates/}
│   ├── paper-writing-pipeline/SKILL.md
│   ├── paper-plan/SKILL.md
│   ├── paper-figure-generate/{SKILL.md, templates/}
│   ├── paper-draft/{SKILL.md, templates/}
│   ├── paper-review-loop/{SKILL.md, templates/}
│   ├── paper-covert/{SKILL.md, profiles/, templates/}
│   ├── submit-check/SKILL.md
│   ├── training-check/SKILL.md
│   └── knowledge/                   ← Domain reference files
│
├── tools/                           ← CLI utilities (called by skills + harness)
│   ├── arxiv_fetch.py
│   ├── semantic_scholar_fetch.py
│   ├── convert_skills_to_llm_chat.py
│   ├── export_design_principle_table.py        ← exports design_principle.md tables to Excel
│   ├── export_agent_design_principle_table.py  ← exports design_principle_agents.md tables
│   ├── telemetry_stage_marker.py               ← called by skill_marker hook (per-skill timing)
│   └── telemetry_aggregate.py                  ← called by Stop hook (session/stage telemetry)
│
├── configs/
│   └── default.yaml                 ← Scoring weights, domain keywords
│
├── templates/                       ← Project + paper templates
│   ├── EXPERIMENT_LOG_TEMPLATE.md
│   ├── EXPERIMENT_PLAN_TEMPLATE.md
│   ├── FINDINGS_TEMPLATE.md
│   ├── HANDOFF_TEMPLATE.json
│   ├── IDEA_CANDIDATES_TEMPLATE.md
│   ├── PAPER_PLAN_TEMPLATE.md
│   ├── RESEARCH_CONTRACT_TEMPLATE.md
│   ├── RESEARCH_PLAN_TEMPLATE.md
│   ├── REVIEW_STATE_TEMPLATE.json
│   ├── geoscience/ (nature_geoscience, grl_template)
│   ├── remote_sensing/ (ieee_tgrs, isprs_jprs, remote_sensing_env)
│   └── giscience/ (ijgis, transactions_gis, annals_aag)
│
├── harness/
│   ├── hooks/ (pre_tool_use, post_tool_use, skill_marker, stop_hook, notification)
│   └── prompts/system_geo.md
│
├── mcp/                             ← MCP server implementations
│   ├── geo_mcp_server.py
│   └── README_MCP.md
│
├── memory/MEMORY.md                 ← Persistent session memory
│
├── output/                          ← All generated outputs
│   ├── AUTO_REVIEW.md
│   ├── REVIEW_STATE.json
│   ├── ARCHITECTURE_DIAGRAM_PROMPTS.md
│   ├── papers/
│   ├── figures/
│   └── reports/
│
├── res/nora_architecture.png        ← Architecture diagram
│
└── archived/                        ← Retired skills and pre-skill Python modules

---

Contributing

1. Fork this repository.
2. Add skills in skills/<name>/SKILL.md.
3. Add journal templates in templates/ (plus a YAML profile in skills/paper-covert/profiles/ if needed).
4. Add domain knowledge in skills/knowledge/.

---

License

MIT License. See LICENSE for details.

---

Design Principles

Two living documents describe the rules NORA's skills and sub-agents follow. Treat them as the source of truth when you write or change a skill.

File	Scope
design_principle.md	Skill-level principles: anchored problem, smallest adequate mechanism, generator–evaluator separation, conditional geospatial checks, mandatory local-GPU check before any pilot or full experiment, human-checkpoint pattern for synthesis decisions.
design_principle_agents.md	Sub-agent principles for the 9 specialists in .claude/agents/ (orchestrator, literature-scout, gap-finder, hypothesis-generator, geo-specialist, paper-writer, peer-reviewer, citation-manager, synthesis-analyst).

Both files can be exported to Excel for review or workshop use:

python tools/export_design_principle_table.py
python tools/export_agent_design_principle_table.py

---

Inspired By

NORA's design borrows ideas from several open-source projects. Credit and gratitude to their authors:

• BZBarrett/superpowers — skill-pack patterns for extending Claude Code with composable Markdown workflows.
• BZBarrett/get-shit-done — pragmatic harness patterns for getting long-running agentic work to actually finish.
• wanshuiyin/Auto-claude-code-research-in-sleep — "research while you sleep" autonomous-loop concept that motivated NORA's overnight pipelines, handoff.json recovery, and adversarial review loop.
• karpathy/autoresearch — generator–evaluator separation and the per-criterion floors + weighted-average scoring loop adapted into auto-review-loop and paper-review-loop.

If your project influenced NORA and is missing here, please open an issue and we will add it.

---

Citation

If you use NORA in your research, please cite the arXiv preprint:

Zhou, B., Wu, Q., Huang, X., Ning, H., Li, D., & Zhang, Z. (2026). NORA: Night Owl Research Agent — Autonomous AI Research for Geoscience, Remote Sensing, and GIScience. arXiv:2605.02092. https://arxiv.org/abs/2605.02092

@misc{zhou2026nora,
  title         = {NORA: Night Owl Research Agent --- Autonomous AI Research for Geoscience, Remote Sensing, and GIScience},
  author        = {Zhou, Bing and Wu, Qiusheng and Huang, Xiao and Ning, Huan and Li, Diya and Zhang, Ziyi},
  year          = {2026},
  eprint        = {2605.02092},
  archivePrefix = {arXiv},
  url           = {https://arxiv.org/abs/2605.02092},
  howpublished  = {\url{https://github.com/GRIND-Lab-Core/night_owl_research_agent}}
}