# Awesome Research Agents

> A curated collection of research agents, skill libraries, autonomous research loops, paper-writing pipelines, MCP servers, and benchmarks built around Claude Code, OpenAI Codex CLI, and adjacent coding-agent CLIs for AI/ML research.

- **Type:** MCP server
- **Install:** `agentstack add mcp-chrisliu298-awesome-research-agents`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [chrisliu298](https://agentstack.voostack.com/s/chrisliu298)
- **Installs:** 0
- **Category:** [AI & ML](https://agentstack.voostack.com/c/ai-and-ml)
- **Latest version:** 0.1.0
- **License:** CC0-1.0
- **Upstream author:** [chrisliu298](https://github.com/chrisliu298)
- **Source:** https://github.com/chrisliu298/awesome-research-agents

## Install

```sh
agentstack add mcp-chrisliu298-awesome-research-agents
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# 🔍 Awesome Research Agents

  
  
  
  

Curated resources for building, evaluating, and stress-testing research agents around Claude Code, OpenAI Codex CLI, and adjacent coding-agent CLIs — across AI/ML research workflows: literature, hypothesis design, implementation, experiments, analysis, writing, review, rebuttal, and project memory.

**New here?** Read [Start Here](#start-here). **Shipping a workflow?** Skip to [Coding-Agent Substrates and Hosts](#coding-agent-substrates-and-hosts) and [Skills, Workflow Packs, and Reusable Procedures](#skills-workflow-packs-and-reusable-procedures).

> If you maintain a research-agent project that should be on this list, or spot a mistake, broken link, or stale entry, please open an issue or pull request.

## Contents

- [Start Here](#start-here)
- [Research Stage Map](#research-stage-map)
- [Coding-Agent Substrates and Hosts](#coding-agent-substrates-and-hosts)
- [Skills, Workflow Packs, and Reusable Procedures](#skills-workflow-packs-and-reusable-procedures)
- [Literature Discovery and Evidence Grounding](#literature-discovery-and-evidence-grounding)
- [Lab Integrations, Notebooks, Experiment Tracking, and Memory](#lab-integrations-notebooks-experiment-tracking-and-memory)
- [Autonomous Execution Loops](#autonomous-execution-loops)
- [End-to-End Research and Hypothesis Systems](#end-to-end-research-and-hypothesis-systems)
- [Manuscript, Figure, Reproduction, and Paper-to-Agent Systems](#manuscript-figure-reproduction-and-paper-to-agent-systems)
- [Review and Rebuttal Systems](#review-and-rebuttal-systems)
- [Benchmarks and Research Arenas](#benchmarks-and-research-arenas)
- [Practitioner Reports, Methodology Essays, and Agent Frameworks](#practitioner-reports-methodology-essays-and-agent-frameworks)
- [Open Problems and Gaps](#open-problems-and-gaps)
- [Contributing](#contributing)
- [Citation](#citation)
- [License](#license)

## Tagging

Tags are conservative and used for within-section ordering (CLI-native → CLI-compatible → adjacent):

- **CLI-native** — ships explicit Claude Code/Codex skills, configs, docs, or workflows.
- **CLI-compatible** — usable from these CLIs but not primarily built for them.
- **adjacent** — informs research-agent design without being a CLI workflow.

## Start Here

1. **[Claude Code](https://docs.anthropic.com/en/docs/claude-code/overview)** — core Claude-native substrate: repo editing, shell, skills, hooks, subagents, memory, MCP.
2. **[OpenAI Codex CLI / Codex](https://github.com/openai/codex)** — OpenAI-native substrate: local CLI, `AGENTS.md`, skills, MCP, cloud/background tasks, parallel work.
3. **[AI-Research-SKILLs](https://github.com/Orchestra-Research/AI-Research-SKILLs)** — broadest reusable research-skill library before writing your own.
4. **[ARIS](https://arxiv.org/abs/2605.03042)** — strongest Claude/Codex-facing autonomous research loop with claim-audit patterns.
5. **[PaperOrchestra](https://arxiv.org/abs/2604.05018)** — main paper-writing and figure-generation reference.
6. **[PaperQA2](https://arxiv.org/abs/2409.13740)** — literature-grounded retrieval instead of model memory for citations.
7. **[ResearchArena (CLI-agent arena)](https://youarespecialtome.github.io/ResearchArena/index.html)** — calibrates expectations on direct CLI research-agent evaluation.
8. **[Stop Automating Peer Review Without Rigorous Evaluation](https://arxiv.org/abs/2605.03202)** — read before deploying review/rebuttal agents.
9. **[AI for Auto-Research: Roadmap & User Guide](https://arxiv.org/abs/2605.18661)** — comprehensive lifecycle survey of the whole field as one map.

## Research Stage Map

| Stage | Useful entries |
|---|---|
| Idea & literature | AI-Research-SKILLs, ARIS, PaperQA2, LitLLM, OpenScholar, OpenNovelty, STORM, ResearchAgent, ai-skill-scholar, paper-search-mcp |
| Experiment design | ARIS, The Agentic Researcher, Agent Laboratory, AI co-scientist, EvoScientist, AAAR-1.0 |
| Coding | Claude Code, OpenAI Codex CLI, Aider, Gemini CLI, OpenHands, PaperCoder / Paper2Code |
| Execution | ARIS, W&B MCP Server, MLflow MCP Server, MLE-bench, MLAgentBench, CORE-Bench, RE-Bench, tinyKaggleClaw |
| Analysis | Jupyter MCP Server, W&B Skills, MLflow MCP Server, data-to-paper, PaperOrchestra |
| Writing | PaperOrchestra, Agent Laboratory, The AI Scientist, data-to-paper, GPT Researcher |
| Peer review | ResearchArena, Stanford Agentic Reviewer, AgentReview, The AI Scientist, LLM-REVal, Re2 |
| Rebuttal | Paper2Rebuttal, DRPG, ARIS, claude-code-my-workflow, ICML 2026 Peer Review FAQ |
| Project memory | Claude Code, OpenAI Codex CLI, Letta Code, Obsidian Memory, Zotero MCP / ZotPilot, PARNESS, AgentRxiv |

## Coding-Agent Substrates and Hosts

- [Claude Code](https://docs.anthropic.com/en/docs/claude-code/overview) *(2025, [CLI-native])* — Terminal-native coding agent that reads repos, edits files, runs commands, and composes with `CLAUDE.md`, skills, subagents, hooks, permissions, MCP, and SDK workflows.
- [OpenAI Codex CLI / Codex](https://github.com/openai/codex) *(2025, [CLI-native])* — Local and cloud/background coding agent with `AGENTS.md`, skills, MCP, subagents, worktrees, and parallel task support for implementation, evals, analysis, and reports.
- [OpenAI Codex cloud/background tasks](https://developers.openai.com/codex/app) *(2026, [CLI-native])* — Codex web/cloud mode for delegating tasks into isolated GitHub-connected environments; maps to ablations, eval additions, and report-generation threads.
- [Aider](https://github.com/aider-ai/aider) *(2023, [CLI-compatible])* — Terminal pair-programming agent with repo maps, file editing, lint/test loops, broad model support, and automatic git commits.
- [Gemini CLI](https://github.com/google-gemini/gemini-cli) *(2025, [CLI-compatible])* — Open-source terminal agent with file tools, shell, web fetch, Google Search grounding, MCP, and `GEMINI.md` customization.
- [OpenHands](https://github.com/OpenHands/OpenHands) *(2024, [CLI-compatible])* — Model-agnostic software-agent platform with SDK, CLI, local GUI, cloud/enterprise modes, and benchmark infrastructure.
- [goose](https://github.com/aaif-goose/goose) *(2025, [CLI-compatible])* — Provider-agnostic agent for code, workflows, research, writing, automation, and data analysis with MCP extensions, recipes, subagents, and CLI/desktop/API modes.
- [Cursor](https://www.cursor.com/) *(2023, [adjacent])* — IDE-oriented coding agent frequently mentioned as a compatible host for skill packs and MCP workflows.

## Skills, Workflow Packs, and Reusable Procedures

- [Anthropic Agent Skills and Claude Code skills](https://code.claude.com/docs/en/skills) *(2025, [CLI-native])* — Skills as progressively loaded folders with `SKILL.md`, scripts, resources, and optional dynamic context; native packaging pattern.
- [OpenAI Codex Skills and plugins](https://developers.openai.com/codex/skills) *(2026, [CLI-native])* — Codex skills with progressive disclosure, skill locations, and plugin packaging for skills, app mappings, and MCP config.
- [AI-Research-SKILLs](https://github.com/Orchestra-Research/AI-Research-SKILLs) *(2026, [CLI-native])* — Broad skill library across ideation, literature, model work, evaluation, MLOps, agents, RAG, and paper writing for Claude Code, Codex, and Gemini-style hosts.
- [academic-research-skills](https://github.com/Imbad0202/academic-research-skills) *(2026, [CLI-native])* — Claude Code skill suite for academic research, writing, review, revision, finalization, response-to-reviewer artifacts, integrity reports, reviewer simulation, and reproducibility checks.
- [claude-code-my-workflow](https://github.com/pedrohcgs/claude-code-my-workflow) *(2026, [CLI-native])* — Personal Claude Code setup for papers, slides, data analysis, replication packages, preregistration, review, and referee responses; notable "contractor mode" and adversarial QA loops.
- [claude-scholar](https://github.com/Galaxy-Dawn/claude-scholar) *(2026, [CLI-native])* — Semi-automated research assistant for CS/AI across literature, coding, experiments, reports, writing, rebuttal, and knowledge management; skills + commands + agents + rules + hooks + Zotero + optional Obsidian.
- [W&B Skills](https://github.com/wandb/skills) *(2026, [CLI-native])* — Installable Claude Code / Codex skills for W&B experiments, traces, evals, and reports (training, run comparison, failure-mode analysis, report generation).
- [Organon](https://github.com/krmdel/organon) *(2026, [CLI-native])* — Claude Code scientific OS covering literature search, hypothesis testing, data analysis, manuscript drafting, scheduled jobs, and science communication, with verification gates that block fabricated citations and unsupported claims.
- [MedSci Skills](https://github.com/Aperivue/medsci-skills) *(2026, [CLI-native])* — Medical-science Claude Code skill suite (~39 skills) across topic discovery, literature search, study design, statistics, figures, writing, compliance, peer review, revision, and presentations with PubMed/Semantic Scholar/CrossRef-verified citations.
- [Claude Code for an Academic Researcher](https://github.com/flonat/claude-research) *(2026, [CLI-native])* — Full Claude Code infrastructure for academics with 48 skills, 6 agents, 9 hooks, rules, context libraries, LaTeX, bibliography tooling, Notion integration, and reviewer roles (domain reviewer, paper critic, peer reviewer, referee).
- [scientific-agent-skills](https://github.com/K-Dense-AI/scientific-agent-skills) *(2026, [CLI-compatible])* — Agent Skills catalog across biology, chemistry, medicine, ML, materials, physics, engineering, data analysis, and scientific communication with Cursor / Claude Code / Codex compatibility.
- [ai-skill-scholar](https://github.com/dsebastien/ai-skill-scholar) *(2026, [CLI-compatible])* — Three skills for scholarly search, citation analysis, and literature review via OpenAlex; two-pass orchestrator with persistent session state.
- [EvoSkills](https://github.com/EvoScientist/EvoSkills) *(2026, [CLI-compatible])* — Installable research-skill library for ideation, paper planning, experiment pipelines, writing, review, rebuttal, memory, paper navigation, and surveys across Claude Code, Codex, Gemini CLI, Cursor, OpenCode, and DeepAgents.
- [ML Experiment Tracking Setup skill](https://mcpmarket.com/tools/skills/ml-experiment-tracking-setup-9) *(2026, [CLI-compatible])* — Skill for scaffolding MLflow or W&B experiment-tracking before agent-driven iteration; verify adoption before depending on it.
- [ResearchClaw](https://github.com/ymx10086/ResearchClaw) *(2025, [CLI-compatible])* — Personal research assistant exposing extensible skills for retrieval, analytics, code execution, and document understanding.

## Literature Discovery and Evidence Grounding

- [paper-search-mcp](https://github.com/openags/paper-search-mcp) *(2026, [CLI-native])* — Searches and downloads papers from arXiv, PubMed, bioRxiv via MCP tools and a Claude Code skill; discovery layer only — ranking discipline still needed.
- [LitLLM](https://github.com/LitLLM/LitLLM) *(2025, [CLI-native])* — Literature-review toolkit and Claude Code skill for retrieving, ranking, and synthesizing related work over OpenAlex, Google Scholar, embedding search, and LLM reranking.
- [PaperQA2](https://arxiv.org/abs/2409.13740) *(2024, [CLI-compatible])* — Scientific RAG over papers, text, Office files, and code with cited evidence; callable as a literature-QA backend for related work, contradiction checks, paper writing, and rebuttals. [](https://github.com/future-house/paper-qa)
- [GPT Researcher](https://github.com/assafelovic/gpt-researcher) *(2024, [CLI-compatible])* — Long-form cited research reports over web and local sources with planning, crawling, source tracking, MCP, and Claude Skill install; scholarly claims still need verification.
- [Zotero MCP / ZotPilot](https://github.com/54yyyu/zotero-mcp) *(2025, [CLI-compatible])* — Zotero library, citations, summaries, PDFs, and annotations via MCP; ZotPilot adds semantic search and lit-review drafting over local data.
- [semantic-scholar-mcp](https://github.com/akapet00/semantic-scholar-mcp) *(2026, [CLI-compatible])* — Lightweight MCP server for searching and analyzing papers through the Semantic Scholar API; unofficial and small.
- [arxiv-mcp-server](https://github.com/blazickjp/arxiv-mcp-server) *(2025, [CLI-compatible])* — Search, download, store, and analyze arXiv papers via MCP, with security guidance on adversarial paper text and prompt injection.
- [PubMed MCP Server](https://chat.mcp.so/server/pubmed-mcp-server/cyanheads) *(rolling, [CLI-compatible])* — PubMed / NCBI E-utilities MCP with article search, retrieval, research-plan generation, filtering, citation analysis, metadata visualization, and biomedical research-agent scaffolding.
- [ChatPaper](https://github.com/kaixindelele/ChatPaper) *(2023, [CLI-compatible])* — Open-source paper-summarization and literature-synthesis tool widely adopted as an early LLM-assisted reading workflow.
- [Tongyi DeepResearch](https://github.com/Alibaba-NLP/DeepResearch) *(2025, [CLI-compatible])* — Alibaba open-source agentic LLM specialized for long-horizon deep information seeking and report synthesis.
- [OpenScholar](https://arxiv.org/abs/2411.14199) *(2024, [adjacent])* — Retrieval-augmented scholarly assistant over a large open-access corpus with ScholarQABench-style evaluation; canonical grounding layer, not a CLI workflow. [](https://github.com/akariasai/openscholar)
- [STORM](https://arxiv.org/abs/2402.14207) *(2024, [adjacent])* — Long-form grounded articles via perspective discovery, simulated writer-expert chat, outline organization, and drafting from retrieved sources; Co-STORM adds collaborative discourse. [](https://github.com/stanford-oval/storm)
- [Gemini Deep Research Agent](https://ai.google.dev/gemini-api/docs/interactions/deep-research) *(2026, [adjacent])* — API-level deep-research agent for planning, executing, and synthesizing multi-step research with background execution, planning viz, MCP, and document input.
- [OpenNovelty](https://arxiv.org/abs/2601.01576) *(2026, [adjacent])* — Agentic novelty-assessment pipeline that extracts claims, retrieves prior work, builds a hierarchical taxonomy, compares contributions against full texts, and produces evidence-grounded novelty reports. [](https://github.com/january-blue/OpenNovelty)
- [LitLLM (paper)](https://arxiv.org/abs/2402.01788) *(2024, [adjacent])* — Literature-review toolkit paper integrating LLMs with academic databases for dense retrieval over scientific corpora.
- [PaSa](https://arxiv.org/abs/2501.10120) *(2025, [adjacent])* — LLM agent for academic search that issues follow-up queries and iteratively refines candidate paper sets like a human probing a topic.
- [AutoSurvey](https://arxiv.org/abs/2406.10252) *(2024, [adjacent])* — Single-pass automated survey-writing system establishing baseline feasibility for turning retrieved literature into structured drafts.
- [SurveyX](https://arxiv.org/abs/2502.14776) *(2025, [adjacent])* — Academic survey-automation system evaluated separately on content quality, structure quality, and citation accuracy.
- [SurveyForge](https://arxiv.org/abs/2503.04629) *(2025, [adjacent])* — Survey-writing system learning outline heuristics from human surveys and using memory-driven content generation.
- [LiRA](https://arxiv.org/abs/2510.05138) *(2025, [adjacent])* — Multi-agent literature-review generator splitting retrieval, verification, organization, and writing into specialized roles.
- [Agentic AutoSurvey](https://arxiv.org/abs/2509.18661) *(2025, [adjacent])* — Agentic survey-generation workflow with dedicated agents for retrieval, organization, and narrative synthesis.
- [IterSurvey](https://arxiv.org/abs/2510.21900) *(2025, [adjacent])* — Literature-survey agent treating outline generation as iterative planning with stability checks.
- [InteractiveSurvey](https://arxiv.org/abs/2504.08762) *(2025, [adjacent])* — Interact

…

## Source & license

This open-source MCP server is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [chrisliu298](https://github.com/chrisliu298)
- **Source:** [chrisliu298/awesome-research-agents](https://github.com/chrisliu298/awesome-research-agents)
- **License:** CC0-1.0

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/mcp-chrisliu298-awesome-research-agents
- Seller: https://agentstack.voostack.com/s/chrisliu298
- Browse the marketplace: https://agentstack.voostack.com/browse

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Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.