academic-research-skills-codex

Academic Research Skills for Codex

> Skill by ara.so ↗ — Codex Skills collection.

This skill provides a comprehensive suite of AI-assisted academic research workflows including deep research, paper writing, peer review, and end-to-end research pipelines. Originally designed for Claude Code, this Codex-native package routes requests to specialized research agents based on user intent.

What It Does

Academic Research Skills (ARS) for Codex provides five core workflows:

1. Deep Research - Literature reviews, systematic reviews, research question refinement, fact-checking

2. Academic Paper - Outlining, drafting, citation formatting, revision, AI disclosure

3. Academic Paper Reviewer - Manuscript review, simulated peer review, editorial decisions

4. Academic Pipeline - End-to-end research-to-publication workflow with integrity gates

5. Experiment Agent - Code experiment planning, study protocols, reproducibility validation

Installation

Install using the Codex skill installer with git method:

python "$HOME/.codex/skills/.system/skill-installer/scripts/install-skill-from-github.py" \
  --repo Imbad0202/academic-research-skills-codex \
  --ref main \
  --path skills/academic-research-suite \
  --method git

Update Existing Installation

rm -rf "$HOME/.codex/skills/academic-research-suite"
python "$HOME/.codex/skills/.system/skill-installer/scripts/install-skill-from-github.py" \
  --repo Imbad0202/academic-research-skills-codex \
  --ref main \
  --path skills/academic-research-suite \
  --method git

After installation, open a new Codex conversation to activate the skill.

Verify Installation

/skills

You should see one entry: academic-research-suite. You should NOT see separate entries for academic-paper, deep-research, etc.

Core Usage Patterns

Basic Invocation

Use $academic-research-suite followed by your research task:

Use $academic-research-suite to help me plan a systematic literature review on
AI adoption in higher education quality assurance.

The Codex adapter automatically routes to the appropriate workflow based on your request.

Workflow Selection

| Workflow | When to Use | Example Trigger |

|----------|-------------|-----------------|

| deep-research | Need research question refinement, literature review, fact-checking | "conduct a systematic review on..." |

| academic-paper | Need paper outline, drafting, citations, revision | "write a research paper about..." |

| academic-paper-reviewer | Need manuscript review, peer review simulation | "review this research manuscript..." |

| academic-pipeline | Need full research-to-publication workflow | "run end-to-end pipeline from topic to paper" |

| experiment-agent | Need code experiment design, study protocols | "plan a reproducible code experiment..." |

Structured Request Pattern

For best results, provide goal, current state, and constraints:

Use $academic-research-suite.

Goal: write a journal article on AI in higher education QA
Current materials: literature matrix and rough findings, no outline yet
Output needed: paper architecture and evidence checklist
Constraints: English, APA 7, policy audience

Command Aliases

Codex emulates Claude Code /ars-* commands as aliases:

| Alias | Workflow | Purpose |

|-------|----------|---------|

| ars-plan | academic-paper | Create paper plan/structure |

| ars-outline | academic-paper | Generate outline only |

| ars-abstract | academic-paper | Draft abstract |

| ars-lit-review | academic-paper | Build literature review |

| ars-citation-check | academic-paper | Verify citations |

| ars-disclosure | academic-paper | Generate AI disclosure statement |

| ars-format-convert | academic-paper | Convert between formats |

| ars-revision-coach | academic-paper | Get revision guidance |

| ars-revision | academic-paper | Execute revisions |

| ars-full | academic-pipeline | Run full pipeline |

Using Aliases

Either prefix style works:

Use $academic-research-suite: ars-plan my paper on AI governance

Or if your client supports it:

/ars-plan my paper on AI governance

Workflow Examples

Deep Research: Socratic Question Refinement

When you have a broad topic but no clear research question:

Use $academic-research-suite.

I want to write about AI adoption in higher education quality assurance.
I don't have a clear research question yet.
Use Socratic dialogue to help me narrow the question first.

Expected: ARS asks narrowing questions before producing an outline.

Academic Paper: From Notes to Draft

Use $academic-research-suite.

Task: Turn these research notes into an IMRaD paper.
Materials: [attach notes.md, data_summary.csv]
Target: 6000-8000 words, APA 7, submit to Higher Education Research
Output: Full outline with section word counts, then draft intro

Paper Review: Simulated Peer Review

Use $academic-research-suite to review this manuscript.

Mode: full review
Focus: methodology, contribution, citation integrity, desk-reject risks
Output: reviewer reports + editorial decision letter

[attach manuscript.pdf or manuscript.md]

Academic Pipeline: Staged Execution

For checkpoint-based workflow:

Use $academic-research-suite to start an academic-pipeline run.

Begin with Stage 0 intake and stop after producing the pipeline dashboard.
Wait for my approval before Stage 1.

Experiment Agent: Reproducible Study Design

Use $academic-research-suite experiment-agent.

Plan a code experiment comparing three ML models on education dataset.
Requirements: reproducible, statistical rigor, version control, artifact storage
Output: experiment protocol + reproducibility checklist

Configuration

Environment Variables

For cross-model verification (optional):

export ARS_CROSS_MODEL=claude-opus-4.7
export ANTHROPIC_API_KEY=your_api_key_here

Without these, ARS runs entirely within Codex/OpenAI. Cross-model review uses Anthropic API when explicitly requested.

Material Passport

ARS tracks research artifacts through "Material Passports" - metadata files that follow:

{
  "artifact_id": "paper_v1_outline",
  "created": "2026-05-17T10:30:00Z",
  "workflow": "academic-paper",
  "stage": "outline",
  "integrity_checks": ["citation_format", "structure"],
  "sources": ["source1.pdf", "source2.pdf"],
  "status": "approved"
}

Reset Material Passport by starting a new Codex conversation.

Working with Citations

Citation Check

Use $academic-research-suite: ars-citation-check

[paste paper text with citations]

Verify all citations are formatted correctly in APA 7.
Flag any unverifiable sources.

Expected output:

• Citation format compliance report
• Unverifiable citations flagged
• Suggested corrections

Literature Review Mode

Use $academic-research-suite: ars-lit-review

Topic: AI ethics in higher education
Scope: 2020-2026, peer-reviewed only
Output: thematic synthesis with citation matrix

Paper Formatting and Conversion

Format Conversion

Use $academic-research-suite: ars-format-convert

Input: [attach paper.md]
From: Markdown
To: LaTeX (IEEE conference template)
Preserve: citations, figures, tables

AI Disclosure Statement

Use $academic-research-suite: ars-disclosure

Paper stage: final draft before submission
AI tools used: Codex for literature search, outline generation, citation formatting
Human contribution: research design, analysis, interpretation, revision
Output: journal-ready disclosure statement

Revision Workflow

Revision Coach

For guidance without executing changes:

Use $academic-research-suite: ars-revision-coach

[attach draft.md and reviewer_comments.txt]

Analyze reviewer feedback and suggest revision strategy.
Prioritize major vs minor revisions.
Do not rewrite yet - provide plan only.

Execute Revisions

Use $academic-research-suite: ars-revision

[attach draft.md and reviewer_comments.txt]

Execute revisions based on Reviewer 2 methodology concerns.
Track changes: show original -> revised for each section.
Update Material Passport with revision metadata.

Troubleshooting

Skill Not Found

If /skills doesn't show academic-research-suite:

1. Verify installation path: ls -la "$HOME/.codex/skills/academic-research-suite"

2. Reinstall using update command above

3. Open a new Codex conversation (old sessions cache skills)

Multiple ARS Skills Showing

If you see academic-paper, deep-research, etc. as separate skills:

# Remove all ARS skills
rm -rf "$HOME/.codex/skills/academic-"*
rm -rf "$HOME/.codex/skills/deep-research"
rm -rf "$HOME/.codex/skills/experiment-agent"

# Reinstall single suite
python "$HOME/.codex/skills/.system/skill-installer/scripts/install-skill-from-github.py" \
  --repo Imbad0202/academic-research-skills-codex \
  --ref main \
  --path skills/academic-research-suite \
  --method git

Wrong Workflow Selected

If ARS routes to the wrong workflow, be more explicit:

Use $academic-research-suite deep-research workflow in socratic mode.

[your request]

Or use specific alias:

Use $academic-research-suite: ars-outline

[your request]

Citation Verification Fails

When citations cannot be verified:

• ARS should mark them as unverified rather than inventing support
• If verification is critical, provide DOIs or URLs for sources
• Use ars-citation-check mode with source files attached

Codex Warnings

These warnings are non-blocking:

• [features].codex_hooks is deprecated - update Codex config when convenient
• hooks need review before they can run - ARS Codex doesn't require hooks for normal use

Advanced Patterns

Staged Pipeline with Checkpoints

Use $academic-research-suite academic-pipeline workflow.

Stage 0: Intake and dashboard
STOP and show dashboard for approval

[After approval]

Stage 1: Research question refinement via Socratic dialogue
STOP and show refined question

[Continue stage by stage]

Parallel Literature Search

Use $academic-research-suite deep-research workflow.

Search strategy: parallel tracks
Track 1: Scopus, Web of Science - quantitative studies
Track 2: Google Scholar - grey literature, policy docs
Track 3: Specialized databases - ERIC, ProQuest Education

Synthesize results into single literature matrix.

Multi-Pass Review

Use $academic-research-suite academic-paper-reviewer workflow.

Pass 1: Structure and contribution (desk-reject check)
[Wait for my review]

Pass 2: Methodology rigor
[Wait for my review]

Pass 3: Citation integrity and ethics
[Final decision]

Integration with Research Tools

With Reference Managers

Use $academic-research-suite: ars-citation-check

Citation library: Zotero export attached (bibtex format)
Paper: [attach draft.md]

Cross-check all in-text citations against Zotero library.
Flag missing entries and formatting errors.

With Data Analysis Code

Use $academic-research-suite experiment-agent workflow.

Existing analysis: [attach analysis.py, results.csv]
Task: Create reproducible experiment protocol around this analysis
Output: protocol.md, requirements.txt, reproduction checklist

With Institutional Templates

Use $academic-research-suite: ars-format-convert

Input: [attach paper.md]
Template: University PhD thesis LaTeX template [attach template.tex]
Preserve: custom environments for theorems, university citation style

CLI Smoke Test

Test routing without full execution:

codex exec --ephemeral --sandbox read-only \
  -C /path/to/academic-research-skills-codex \
  'Use $academic-research-suite. Router smoke test only. Classify workflow and mode for: I want to write a paper on AI adoption but do not have a research question yet.'

Expected: Route to deep-research socratic mode.

Key Differences from Claude Code Version

This Codex package differs from the original Claude Code ARS:

| Feature | Claude Code | Codex Package |

|---------|-------------|---------------|

| Installation | Plugin marketplace | Git-based skill installer |

| Commands | Native /ars-* slash commands | Emulated aliases via router |

| Agent teams | Automatic background agents | Inline unless explicitly delegated |

| Hooks | SessionStart, SubagentStop | Vendored for traceability only |

| Cross-model review | GPT/Gemini secondary dispatch | Anthropic Claude API (explicit config) |

| Updates | Marketplace auto-update | Manual reinstall |

Version Information

• Codex Package Version: v0.1.6
• Vendored ARS Commit: 1d0c8625207c9cd8fc46132b1ef930f2cc012236
• License: CC BY-NC 4.0 (non-commercial use)
• Original Repository: https://github.com/Imbad0202/academic-research-skills

Additional Resources

• Codex Setup Guide: skills/academic-research-suite/ars/docs/SETUP.md
• Architecture Details: skills/academic-research-suite/ars/docs/ARCHITECTURE.md
• Claude Code Version: https://github.com/Imbad0202/academic-research-skills

For issues specific to the Codex packaging, open an issue at the Codex package repository. For ARS workflow issues, consult the original Claude Code repository.