Read, think, experiment, write, evolve — the AI research agent with memory that compounds across every project.
Thanks to everyone who's been trying AutoSci — the community response has been amazing! AutoSci evolved from our earlier OmegaWiki prototype into what we're building toward: a next-generation research agent that can handle the full scientific lifecycle. We're actively testing and iterating on new features, and more capabilities are on the way. Jump in, break things, and tell us what you think — your feedback and ideas are what's shaping where this goes next. 🙏
🌿 Which branch?
mainremains the stable Claude Code version.autosci-codexis the official Codex Preview, andautosci-opencodeis the official OpenCode Preview. These are separate runtime adaptations; the existing Claude Code and Codex versions remain available. The full system described in our paper — SciMem · SciFlow · SciDAG · SciEvolve — lives on thepaperbranch (frozen as tagarxiv-v1).
Try the OpenCode adaptation without changing your Claude Code or Codex checkout:
git clone -b autosci-opencode https://github.com/skyllwt/AutoSci.git
cd AutoSci
./setup.sh --lang en
opencode
# Then ask OpenCode to run the init skill for your research topic.Current boundary:
| Area | Status |
|---|---|
| Local OpenCode skills | Preview supported via generated .opencode/skills |
| Runtime instructions | Root AGENTS.md, generated from the selected language |
| Shared skill source | i18n/<lang>/skills remains the bilingual source of truth |
| Review LLM | Local llm-review MCP configured through generated opencode.json |
| Daily arXiv | Recommendation-only; standalone OpenAI-compatible API with deterministic fallback and optional email |
The OpenCode preview does not replace the Claude Code stable release or the Codex Preview.
Try the Codex preview without changing your main checkout:
git clone -b autosci-codex https://github.com/skyllwt/AutoSci.git
cd AutoSci
./setup.sh --lang en
codex
# Then invoke: $init [your-research-topic]Current boundary:
| Area | Status |
|---|---|
| Local Codex skills | Preview supported via .agents/skills |
| Runtime scope | Codex-only; Claude Code remains available separately on main |
| Shared skill source | i18n/<lang>/skills regenerates the active .agents/skills tree |
| Review LLM | Optional llm-review MCP configured through the Codex config example |
| Daily arXiv | CI is recommendation-only; no repository writeback or unattended ingest |
See docs/codex-preview.md for the preview notes and known boundaries.
If you find AutoSci useful in your research, please cite our paper.
Published a separate OpenCode adaptation while keeping the existing Claude Code stable release and Codex Preview available. The OpenCode branch provides bilingual project skills under .opencode/skills, root AGENTS.md instructions, generated machine-local configuration, and llm-review MCP integration. Its daily-arXiv automation is recommendation-only and uses a standalone OpenAI-compatible API with deterministic fallback, optional best-effort email, and digest artifacts without repository writeback.
Published a separate Codex-only adaptation while keeping the stable Claude Code release on main and the OpenCode Preview on autosci-opencode. The Codex branch provides bilingual skills under .agents/skills, root AGENTS.md instructions, Codex-specific setup and Review LLM configuration, and recommendation-only daily-arXiv CI without Claude Action authentication, automatic ingest, or repository writeback. The $research workflow delegates cold-wiki bootstrap to $init and proceeds only after bootstrap completes.
A possible usage process:/ideate [research-direction-or-topic](You can use --skip-pilot to decide whether to conduct preliminary experiments) -> /exp-design <idea-slug>-> For each experimental block,recommended flow: /exp-run <slug> [--env local|remote] to deploy → /exp-status to monitor → /exp-run <slug> --collect to collect.->/exp-eval <experiment-slug>
✨ : New Skills
/exp-pilot-run — Pilot experiment execution: write code, deploy, monitor, collect raw results.
/exp-pilot-eval — Pilot result evaluation: read results, apply lenient verdict logic
These two skills are built into Phase5 of /ideate
🛠️ : Modified Skills
/ideate
5 structured generation paths (A-E) for both Claude and Review LLM.
Phase restructuring: Filter & Validation merged into Phase 3, Write Wiki moved to Phase 4.
Phase 5: Finish pilot design and workflow invocation
Your ideas will follow a clearer path, and a more reasonable screening mechanism will be established through pilot experiments.
/exp-design
A brand-new experimental design process:method candidate generation + 5 experiment block types + iterative ablation loop
/exp-run
Add the code decision gate, code optimization and config check
Run the poster skill after paper-draft and paper-compile (/poster in Claude Code, $poster in Codex) to turn your finished draft into a self-contained 1400×900 HTML poster and a print-quality PNG. Figures, booktabs tables, and math macros are extracted automatically from your LaTeX source; the agent walks you through picking which figures land in which sections and customizing the header (venue, affiliation logo). Export to PDF from your browser's print dialog. Pipeline adapted from PaperX (arXiv:2602.03866).
Use /discover --venue iclr --year 2024 in Claude Code or $discover --venue iclr --year 2024 in Codex (or any conference/year) and get a personalized shortlist of papers from that venue, ranked by relevance to what's already in your wiki. Instead of scrolling a 7000-paper proceedings, you see the dozen that actually matter for your research direction, each with a rationale tied to topics and methods you already track. No new API keys, no ingest side-effects on your wiki — just a ranked reading list. Supports NeurIPS, ICLR, ICML, and other venues covered by Paper Copilot.
Use /daily-arxiv in Claude Code or $daily-arxiv in Codex for a one-off pass. The GitHub Actions scheduler supports Codex CLI for unattended inform recommendations, with legacy Claude Code Action and Review LLM fallbacks; CI auto-ingest remains on the legacy Claude Action path until Codex writeback is separately verified. The skill builds an evidence packet from arXiv + Semantic Scholar + DeepXiv, lets the LLM rank candidates against your wiki interests, and delivers a digest by e-mail. Explicit --mode auto-ingest calls the ingest skill for high-confidence picks; inform mode just notifies.
Your research graph now has two ways to explore:
- Web UI — run
python3 tools/serve.py, openhttp://localhost:8765/#/graph. Click any node to highlight its neighborhood via BFS, filter by entity type or edge category, double-click to open the full page in the Reader. - Obsidian — run
/visualize --obsidianto generate a color-coded graph config, or/visualize --canvasto produce a force-layout Canvas with labeled semantic edges.
Scientific research has traditionally been human-intensive: researchers coordinate literature, ideas, experiments, manuscripts, and review responses across long project cycles. AutoSci is a memory-centric agentic system that automates the full research lifecycle — from paper ingestion to rebuttal — while maintaining structured persistent memory across projects and improving its own procedures over time.
The following papers were generated end-to-end using AutoSci — from literature ingestion and idea generation to experiment execution and manuscript writing.
| Paper | Domain | |
|---|---|---|
| Agent-driven iterative optimization of Triton GPU kernels | GPU kernel optimization | |
| PTM-aware degrader target nomination via calibrated ternary-complex scoring | Biomedical drug discovery | |
| Forced Honesty Dissociates Polite Speech from Motivated Cognition in LLM Attitude Ratings | LLMs as cognitive models |
Have you used AutoSci in your own research? We'd love to feature your work here — open a PR or drop us a message!
Prerequisites: Python 3.9+, Node.js 18+, and OpenCode
# 1. Clone the OpenCode Preview branch
git clone -b autosci-opencode https://github.com/skyllwt/AutoSci.git
cd AutoSci
# 2. Verify OpenCode
opencode --version
# 3. Generate the local environment, skills, AGENTS.md, and opencode.json
chmod +x setup.sh && ./setup.sh --lang en
# 4. Add your papers and optional notes
# raw/papers/ raw/notes/ raw/web/
# 5. Start OpenCode and load the init skill
opencodeThe generated .opencode/ tree and opencode.json are machine-local and should not be committed. The English and Chinese sources under i18n/ remain authoritative.
Prerequisites: Python 3.9+, Node.js 18+
# 1. Clone the Codex Preview branch
git clone -b autosci-codex https://github.com/skyllwt/AutoSci.git
cd AutoSci
# 2. Install and sign in to Codex
# Follow your Codex/OpenAI setup path, then verify:
codex --version
# 3. One-click setup
chmod +x setup.sh && ./setup.sh # Linux / macOS
# Windows (PowerShell):
# powershell -ExecutionPolicy Bypass -File .\setup.ps1
# setup creates .venv and syncs the Codex `.agents/skills` tree
# 4. Put your own papers in raw/papers/ (.tex or .pdf)
# Optional: intent notes in raw/notes/, saved pages in raw/web/
# 5. Build your research memory and start a project
codex
# Then invoke: $init [your-research-topic]Claude Code users should use the stable main branch instead:
git clone -b main https://github.com/skyllwt/AutoSci.git
cd AutoSci
npm install -g @anthropic-ai/claude-code
claude login
claude
# Then type: /init [your-research-topic]Manual setup (Linux / macOS)
python3 -m venv .venv && source .venv/bin/activate
pip install -r requirements.txt
cp .env.example .env # Edit to add API keys
mkdir -p .agents/skills/shared-references
cp -R i18n/en/skills/. .agents/skills/
cp i18n/en/shared-references/*.md .agents/skills/shared-references/
mkdir -p .claude/skills/shared-references
cp -R i18n/en/skills/. .claude/skills/
cp i18n/en/shared-references/*.md .claude/skills/shared-references/
cp config/settings.local.json.example .claude/settings.local.json # Claude Code compatibilityManual setup (Windows / PowerShell)
python -m venv .venv
.\.venv\Scripts\Activate.ps1
pip install -r requirements.txt
Copy-Item .env.example .env # Edit to add API keys
New-Item -ItemType Directory -Force .agents\skills\shared-references | Out-Null
Copy-Item i18n\en\skills\* .agents\skills -Recurse -Force
Copy-Item i18n\en\shared-references\*.md .agents\skills\shared-references -Force
New-Item -ItemType Directory -Force .claude\skills\shared-references | Out-Null
Copy-Item i18n\en\skills\* .claude\skills -Recurse -Force
Copy-Item i18n\en\shared-references\*.md .claude\skills\shared-references -Force
Copy-Item config\settings.local.json.example .claude\settings.local.json # Claude Code compatibilityNote: native Windows is supported for the local pipeline. Remote-GPU
experiments via /exp-run --env remote rely on ssh/rsync/screen
and are best run from WSL2 or Linux/macOS.
| Key | Required? | How to get | What it enables |
|---|---|---|---|
| Agent runtime auth | Yes | Claude Code: claude login; Codex: sign in through Codex |
Powers the interactive coding-agent skills |
OPENAI_API_KEY or CODEX_ACCESS_TOKEN |
Optional | OpenAI / Codex account | GitHub Actions Codex CLI recommender for daily-arxiv inform mode |
ANTHROPIC_API_KEY |
Claude Code only (or use a third-party compatible API — see below) | claude login (automatic) |
Powers Claude Code skills |
CLAUDE_CODE_OAUTH_TOKEN |
Optional | claude setup-token |
GitHub Actions legacy Claude Code auth for Pro/Max users and daily-arxiv auto-ingest |
SEMANTIC_SCHOLAR_API_KEY |
Optional | semanticscholar.org/product/api (free) | Citation graph, paper search |
DEEPXIV_TOKEN |
Optional | setup.sh auto-registers |
Semantic search, TLDR, trending |
LLM_API_KEY + LLM_BASE_URL + LLM_MODEL |
Optional | Any OpenAI-compatible API | Cross-model review; /daily-arxiv inform recommendations |
Don't have an Anthropic API key? You can use Codex, or use Claude Code with any Anthropic-protocol-compatible provider — DeepSeek, Kimi, MiMo, GLM, and more. See the LLM API Configuration section below for Claude Code provider snippets.
Cross-model review: AutoSci uses a second LLM as an independent reviewer for ideas, experiments, and paper drafts. Works with any OpenAI-compatible API — DeepSeek, OpenAI, Qwen, OpenRouter, SiliconFlow, etc. If not configured, skills still work in single-agent mode.
AutoSci runs on Claude Code or Codex. Claude Code speaks the Anthropic API protocol: you can use Claude directly, or route Claude Code to any third-party provider that exposes an Anthropic-compatible endpoint by overriding a few environment variables. Codex uses the Codex/OpenAI sign-in path and reads the repo skills from .agents/skills.
AutoSci 支持 Claude Code 与 Codex。Claude Code 使用 Anthropic API 协议通信:你既可以直接使用 Claude, 也可以通过覆盖几个环境变量, 把 Claude Code 指向任意支持 Anthropic 协议的第三方供应商。Codex 使用 Codex/OpenAI 登录路径,并从 .agents/skills 读取 repo skills。
claude login # OAuth, no manual config / OAuth 登录,无需手动配置Pick a provider below, paste the snippet into ~/.claude/settings.json (or the project's .claude/settings.json), and replace the <...> placeholder with your own API key. Model names and extra options follow each provider's official Claude Code docs.
从下方任选一个供应商,把对应配置粘贴到 ~/.claude/settings.json(或项目的 .claude/settings.json),并把 <...> 占位符替换为你自己的 API key。模型名与额外选项均来自各供应商官方 Claude Code 文档。
MiMo / DeepSeek / Kimi / GLM 配置示例
{
"env": {
"ANTHROPIC_BASE_URL": "https://api.xiaomimimo.com/anthropic",
"ANTHROPIC_AUTH_TOKEN": "<your-mimo-key>",
"ANTHROPIC_MODEL": "mimo-v2.5",
"ANTHROPIC_DEFAULT_SONNET_MODEL": "mimo-v2.5",
"ANTHROPIC_DEFAULT_OPUS_MODEL": "mimo-v2.5-pro",
"ANTHROPIC_DEFAULT_HAIKU_MODEL": "mimo-v2.5"
}
}{
"env": {
"ANTHROPIC_BASE_URL": "https://api.deepseek.com/anthropic",
"ANTHROPIC_AUTH_TOKEN": "<your-deepseek-key>",
"ANTHROPIC_MODEL": "deepseek-v4-pro[1m]",
"ANTHROPIC_DEFAULT_OPUS_MODEL": "deepseek-v4-pro[1m]",
"ANTHROPIC_DEFAULT_SONNET_MODEL": "deepseek-v4-pro[1m]",
"ANTHROPIC_DEFAULT_HAIKU_MODEL": "deepseek-v4-flash",
"CLAUDE_CODE_SUBAGENT_MODEL": "deepseek-v4-flash",
"CLAUDE_CODE_EFFORT_LEVEL": "max"
}
}{
"env": {
"ANTHROPIC_BASE_URL": "https://api.moonshot.ai/anthropic",
"ANTHROPIC_AUTH_TOKEN": "<your-moonshot-key>",
"ANTHROPIC_MODEL": "kimi-k2.5",
"ANTHROPIC_DEFAULT_OPUS_MODEL": "kimi-k2.5",
"ANTHROPIC_DEFAULT_SONNET_MODEL": "kimi-k2.5",
"ANTHROPIC_DEFAULT_HAIKU_MODEL": "kimi-k2.5",
"CLAUDE_CODE_SUBAGENT_MODEL": "kimi-k2.5",
"ENABLE_TOOL_SEARCH": "false"
}
}{
"env": {
"ANTHROPIC_BASE_URL": "https://api.z.ai/api/anthropic",
"ANTHROPIC_AUTH_TOKEN": "<your-zai-key>",
"API_TIMEOUT_MS": "3000000"
}
}Z.AI applies a default server-side model mapping, so no explicit
ANTHROPIC_MODELis needed. Z.AI 默认在服务端做模型映射,无需显式设置ANTHROPIC_MODEL。
Skip the Claude Code onboarding / 跳过 Claude Code 初始引导: when using a third-party key, create or edit .claude.json (~/.claude.json on macOS/Linux) and add { "hasCompletedOnboarding": true }.
AutoSci ships with 30+ agent skills spanning the full research lifecycle.
- Claude Code: invoke skills as slash commands, for example
/init. - Codex: invoke skills with
$skill-nameor from/skills, for example$init.
View all skills
Each skill has the same name in both runtimes. Use the Claude Code slash form
inside Claude Code, and the Codex dollar form inside Codex or select the skill
from Codex /skills.
| Skill | Claude Code | Codex | What it does |
|---|---|---|---|
| setup | /setup |
$setup |
Interactive API key configuration — checks .env state and walks through Semantic Scholar, DeepXiv, and Review LLM setup |
| reset | /reset |
$reset |
Destructive cleanup — reset wiki state to a clean scaffold by scope (wiki / raw / log / checkpoints / all) |
| Skill | Claude Code | Codex | What it does |
|---|---|---|---|
| prefill | /prefill |
$prefill |
Seed wiki/foundations/ with domain background so later ingest runs do not create duplicate concept pages for textbook material |
| init | /init |
$init |
Bootstrap the wiki from your source files, with optional discovery, then ingest the final paper set serially by default, with optional parallel worktree mode |
| ingest | /ingest |
$ingest |
Ingest a paper (local path or arXiv URL) — creates pages and builds all cross-references and graph edges |
| discover | /discover |
$discover |
Build a ranked shortlist of candidate papers (anchor-driven, topic-driven, venue-filtered, or from wiki state) without ingesting |
| edit | /edit |
$edit |
Add or remove raw sources, or update wiki content, per user request |
| ask | /ask |
$ask |
Ask the wiki a question — retrieve and synthesize relevant pages, optionally crystallize the answer back into the wiki |
| check | /check |
$check |
Scan the full wiki to detect health issues and produce a tiered fix-recommendation report |
| Skill | Claude Code | Codex | What it does |
|---|---|---|---|
| daily-arxiv | /daily-arxiv |
$daily-arxiv |
Run or schedule the daily arXiv recommendation feed; delivers a ranked digest by email with optional auto-ingest for high-confidence picks |
| ideate | /ideate |
$ideate |
Multi-phase research idea generation: landscape scan → dual-model brainstorm → filter & validation → write to wiki → pilot |
| exp-pilot-run | /exp-pilot-run |
$exp-pilot-run |
Pilot experiment execution — write code, deploy, monitor, collect raw results as part of the ideation pipeline |
| exp-pilot-eval | /exp-pilot-eval |
$exp-pilot-eval |
Pilot result evaluation — read results, apply success criteria, update idea page as part of the ideation pipeline |
| novelty | /novelty |
$novelty |
Multi-source novelty verification via WebSearch + Semantic Scholar + wiki + Review LLM; outputs novelty score and recommendations |
| review | /review |
$review |
Cross-model review of any research artifact — outputs structured scores, wiki entity mapping, and improvement suggestions |
| exp-design | /exp-design |
$exp-design |
Idea-driven experiment design with iterative ablation — method candidates → benchmark selection → sensitivity analysis → main experiment |
| exp-run | /exp-run |
$exp-run |
Full experiment execution pipeline — prepare code → deploy → monitor → collect results |
| exp-status | /exp-status |
$exp-status |
View the status of all running experiments; optionally auto-collect completed runs and advance the pipeline |
| exp-eval | /exp-eval |
$exp-eval |
Experiment verdict gate — Review LLM independently judges results and auto-updates the linked idea's status and graph edges |
| refine | /refine |
$refine |
Multi-round iterative improvement — repeatedly reviews an artifact, parses feedback, applies fixes, and updates wiki until target score |
| Skill | Claude Code | Codex | What it does |
|---|---|---|---|
| survey | /survey |
$survey |
Generate a Related Work section from wiki knowledge — thematic grouping → narrative structure → LaTeX output |
| paper-plan | /paper-plan |
$paper-plan |
Compile a paper outline from the idea graph — evidence map → narrative structure → section + figure + citation plan |
| paper-draft | /paper-draft |
$paper-draft |
Draft a LaTeX paper from PAPER_PLAN — write each section from wiki sources, generate figures/tables, verify BibTeX |
| paper-compile | /paper-compile |
$paper-compile |
LaTeX compile → PDF — latexmk compile + auto-fix + page count / anonymity / font checks + submission checklist |
| research | /research |
$research |
End-to-end research orchestrator — idea discovery → experiment design → execution → verdict → paper writing with human gates |
| rebuttal | /rebuttal |
$rebuttal |
Parse review comments → atomize concerns → map to wiki → stress-test with Review LLM → generate rebuttal |
| poster | /poster |
$poster |
Generate an academic poster from a drafted paper — distill sections into a single-page HTML poster with figures |
| Skill | Claude Code | Codex | What it does |
|---|---|---|---|
| visualize | /visualize |
$visualize |
Generate Obsidian graph configs and Canvas knowledge maps; the interactive web graph is served by tools/serve.py |
We welcome contributions and feedback — especially while we're in active iteration. See CONTRIBUTING.md.
Scan to join the AutoSci WeChat group / 扫码加入微信交流群
If you find AutoSci useful in your research, please cite our paper:
@misc{qian2026autosci,
title={AutoSci: A Memory-Centric Agentic System for the Full Scientific Research Lifecycle},
author={Weitong Qian and Beicheng Xu and Zhongao Xie and Bowen Fan and Guozheng Tang and Jiale Chen and Xinzhe Wu and Mingtian Yang and Chenyang Di and Jiajun Li and Lingching Tung and Peichao Lai and Yifei Xia and Ziyi Guo and Yanwei Xu and Yanzhao Qin and Shaoduo Gan and Xupeng Miao and Bin Cui},
year={2026},
eprint={2605.31468},
archivePrefix={arXiv},
primaryClass={cs.AI},
url={https://arxiv.org/abs/2605.31468},
}- Claude Code and Codex — supported coding-agent runtimes for AutoSci
- The
/posterpipeline is adapted from PaperX
MIT — use it, fork it, build on it.
Built for Claude Code and Codex
If this project helps your research, give it a ⭐



