academic-research-skills-codex

name academic-research-skills-codex description AI-assisted academic research workflows for literature review, paper writing, peer review, and research pipelines triggers ["help me write an academic paper","conduct a literature review","review this research manuscript","plan a systematic review","generate research paper outline","format academic citations","run academic research pipeline","peer review simulation"] 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: Deep Research - Literature reviews, systematic reviews, research question refinement, fact-checking Academic Paper - Outlining, drafting, citation formatting, revision, AI disclosure Academic Paper Reviewer - Manuscript review, simulated peer review, editorial decisions Academic Pipeline - End-to-end research-to-publication workflow with integrity gates 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 $academic-research-suite: ars-revision [attach draft.md and reviewer_comments.txt] Execute revisions based on Reviewer 2 methodology concerns. Track changes: show original -> revised for each section. Update Material Passport with revision metadata. Troubleshooting Skill Not Found If /skills doesn't show academic-research-suite : Verify installation path: ls -la "$HOME/.codex/skills/academic-research-suite" Reinstall using update command above 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.