Sciatlas Idea Grounding
zjunlp/SciAtlas
Use only SciAtlas search-papers to take a novice user from zero setup to final prior-art grounding for a research idea, including setup, registration guidance, configuration, retrieval, artifact…
A skill your agent uses when the deliverable is a FACT — not code, not a design, not a gap catalog.
$ npx skills add nubjs/nub --skill research-thread -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install nubjs/nub research-thread --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/nubjs/nub.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/research-thread .claude/skills/research-thread && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "research-thread" agent skill from https://github.com/nubjs/nub/tree/main/.claude/skills/research-thread into .claude/skills/research-thread/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-thread", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/nubjs/nub/tree/main/.claude/skills/research-threadType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add nubjs/nub --skill research-thread -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install nubjs/nub research-thread --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/nubjs/nub.git skills-src && mkdir -p .agents/skills && cp -r skills-src/.claude/skills/research-thread .agents/skills/research-thread && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "research-thread" agent skill from https://github.com/nubjs/nub/tree/main/.claude/skills/research-thread into .agents/skills/research-thread/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-thread", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add nubjs/nub --skill research-thread -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install nubjs/nub research-thread --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/nubjs/nub.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/.claude/skills/research-thread .cursor/skills/research-thread && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "research-thread" agent skill from https://github.com/nubjs/nub/tree/main/.claude/skills/research-thread into .cursor/skills/research-thread/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-thread", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/nubjs/nub.git --path .claude/skills/research-thread--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add nubjs/nub --skill research-thread -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install nubjs/nub research-thread --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/nubjs/nub.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/.claude/skills/research-thread .gemini/skills/research-thread && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "research-thread" agent skill from https://github.com/nubjs/nub/tree/main/.claude/skills/research-thread into .gemini/skills/research-thread/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-thread", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install nubjs/nub research-threadInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add nubjs/nub --skill research-thread -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/nubjs/nub.git skills-src && mkdir -p .github/skills && cp -r skills-src/.claude/skills/research-thread .github/skills/research-thread && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "research-thread" agent skill from https://github.com/nubjs/nub/tree/main/.claude/skills/research-thread into .github/skills/research-thread/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-thread", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add nubjs/nub --skill research-thread -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install nubjs/nub research-thread --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/nubjs/nub.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/.claude/skills/research-thread .opencode/skills/research-thread && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "research-thread" agent skill from https://github.com/nubjs/nub/tree/main/.claude/skills/research-thread into .opencode/skills/research-thread/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "research-thread", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
research-threadA skill your agent uses when the deliverable is a FACT — not code, not a design, not a gap catalog.
Research Thread is an agent skill from nubjs/nub. Use when the deliverable is a FACT — not code, not a design, not a gap catalog. A prior-art survey, "how has X already been solved", "what did they try and abandon", a long empirical sweep, or any non-trivial question whose answer will be cited for months. Produces a living write-up at wiki/research/<topic.md. Auto-triggers on "research this", "prior art", "survey", "find out how X works", "what's the state of the art", "dig into whether".
Its SKILL.md is about 2.2k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Legal & Compliance, covering Intellectual property and Literature review. The repository describes itself as: The fast all-in-one Node.js toolkit. The licence is MIT.
6 steps, taken from the first numbered list in SKILL.md.
Read from SKILL.md and the folder at commit 568e73a. It shows what the files ask for, not the result of running them.
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Shell commands in SKILL.md call:
gitFrom the folder's file list and the shell code blocks in SKILL.md.
No URLs in SKILL.md. Its commands use git, which can reach the network depending on how they are called.
From URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Research Thread loads about 2.2k tokens when it runs. Until then it costs about 116 tokens; SKILL.md has 1,262 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
The full file from nubjs/nub at commit 568e73a, republished under its MIT licence (© nubjs). 1,262 words, ~2,162 tokens.
.claude/skills/research-thread/SKILL.md (or your agent's skills folder).A research thread is one of the four thread profiles, alongside the implementation thread (build-the-decided-thing, the implementation-thread skill), the plan thread (settle-the-approach, the plan-thread skill), and the audit thread (verify-parity, the audit-thread skill). Its deliverable is a fact, written down — wiki/research/<topic>.md. It is the thread you open when what is true is the open question.
Most questions are not. The alternative to guessing is not only "dispatch a researcher" — it is "go read it". A few greps and the file they land in answer nearly every question about this codebase, first-hand and faster than a second-hand claim you must re-verify. AGENTS.md's prior-art reflex — spend the first few minutes finding out how a thing has already been solved — fires on EVERY non-trivial work item, and that scan is not a thread.
A research thread earns its own effort when the question needs breadth you cannot hold in one pass: a survey across several projects, independent sources that must be reconciled, a long empirical sweep, or a decision that will be cited for months. If the answer fits in a paragraph of your handoff, write the paragraph and skip the doc.
The order is the point — each step is cheaper than the one after it, and each kills theories the next would otherwise have to disprove.
git clone --depth 1 <repo> .repos/<name> (gitignored), then grep and read a whole consistent tree. Check what .repos/ already holds first — it carries 290 clones today, node/, bun/, pnpm/ and tsx/ among them. Never modify anything under .repos/.rustc file, or a differential run against the real tool answers "what does it actually do" faster and more reliably than tracing source. Ground every claim in code or an experiment, never memory — and label UNVERIFIED anything you could not run.Reversing a conclusion on new evidence is correct, not flip-flopping. State the current verdict, keep probing, and let evidence move you rather than defend the first answer.
wiki/ is TRACKED and PUBLICRead AGENTS.local.md → "What goes in the PUBLIC wiki/ vs the PRIVATE internal/" before writing a line. Default to internal/: a wrong exclusion costs a later copy, a wrong inclusion is permanent. Four things never go public — unimplemented roadmap, the narrative of a dead end pursued too long, competitor SCORECARDS (a factual technical statement about another tool is fine and makes the mechanism legible), and any deliberation about how benchmark results were framed.
A doc that is mostly publishable with one bad section gets the section cut, not the doc dropped — then re-read the remainder for framing that only made sense next to what you removed. Separately, even a perfectly publishable doc about an UNSHIPPED feature stays on that feature's branch until it ships.
wiki/research/<topic>.md, kebab-case slug, never the repo root. Research docs do not carry the YAML front matter that wiki/runtime/ and wiki/commands/ use.
The shape the existing 70 docs converge on:
| Part | Convention |
|---|---|
| Title | # <topic> — the question or the finding, not "Research doc for X" |
| Orientation block | Directly under the title: status + date, the QUESTION it answers, the headline answer, and links to sibling docs |
## TL;DR | Findings as a short numbered list — 40 of 70 docs. Write one whenever the body runs long |
| Body | The evidence, every load-bearing claim carrying its citation or its reproduction |
## Sources | The external links — 31 of 70 |
## Changelog | Mandatory — 68 of 70 |
Research docs are living documents. Edit in place: the body always reads as current best understanding, with no history inside it. Every change appends - YYYY-MM-DD — <what changed and why> under ## Changelog; a new doc's first entry is - YYYY-MM-DD — Initial write-up. A major reversal gets a leading **REVERSAL:** marker. Never blow away a prior conclusion silently — say that the doc previously said X, now says Y, and what evidence moved it. When two docs overlap, merge into one canonical, record the merge in the survivor's changelog, and note the supersession at the top of the absorbed doc before deleting it.
| The open question | The profile |
|---|---|
| What is true? | research → wiki/research/<topic>.md |
| How should we do it? | plan → a settled design (plan-thread) |
| Where do we diverge from a reference? | audit → a verified gap catalog, also under wiki/research/ (audit-thread) |
| Build the decided thing | implementation → a held, green PR (implementation-thread) |
An audit is the special case of research whose question is parity — it inherits this method and adds five hard gates against false positives. Use audit-thread for it, not this skill. A plan thread that needs a fact to decide spins a research effort, folds the result back, and keeps deciding: the plan owns the decision, the research owns the fact.
A research thread does not land code. But a clear bug with a clear fix found along the way gets run down, not parked under "still open" — the context that found it is the cheapest context that will ever exist for it. That fix is an implementation thread and is held to the implementation gates: reproduce it, prove the fix with a differential, sweep fixtures against a built binary, read the diff. "I chased it and it dissolved" is a first-class successful outcome and usually takes minutes.
wiki/ is markdown, so it commits direct to main with no PR. From the shared tree: sync first (git fetch origin && git merge --ff-only origin/main), commit path-scoped (git commit -- wiki/research/<topic>.md) so a sibling's WIP stays out, push, and read the push's exit code.wiki/ is public will write roadmap into it. Put both in the prompt. If you are yourself a dispatched sub-agent, the repo-wide depth cap in AGENTS.local.md applies: run the method inline and return.© nubjs, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Just SKILL.md in .claude/skills/research-thread of nubjs/nub.
Open the folder on GitHubat commit 568e73a
Research Thread next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Research Thread this skillnubjs/nub | 4.4k | — | ~2.2k | Automated safety check: Pass | MIT | |
| Sciatlas Idea Groundingzjunlp/SciAtlas | 160 | — | ~1.1k | Automated safety check: Pass | MIT | |
| Mechanical Engineering Researchccplugins/awesome-claude-code-plugins | 967 | — | ~2.9k | Automated safety check: Pass | Apache-2.0 | |
| Aminer MCP ResearchDrchronx/ai-agent-research-starter-kit | 134 | — | ~1.1k | Automated safety check: Pass | Custom licence | |
| Paper to Chinese Patent DrafterYuan1z0825/nature-skills | 46k | 1 repos | ~1.1k | Automated safety check: Pass | Apache-2.0 | |
| NeuroarxivUditAkhourii/neuroarxiv | 433 | — | ~3.1k | Automated safety check: Pass | MIT |
zjunlp/SciAtlas
Use only SciAtlas search-papers to take a novice user from zero setup to final prior-art grounding for a research idea, including setup, registration guidance, configuration, retrieval, artifact…
ccplugins/awesome-claude-code-plugins
Research, write, code, analyze, present, and develop proposals for thermal-fluid mechanical engineering work with source-aware rigor.
Drchronx/ai-agent-research-starter-kit
Use AMiner MCP for academic knowledge graph tasks: scholar search, author profile lookup, institution or team analysis, paper and patent discovery, academic influence checks, and research trend…
Yuan1z0825/nature-skills
Drafts Chinese invention patent applications and technical disclosures from research papers or inventor materials, tying each claim feature to source evidence.
UditAkhourii/neuroarxiv
Grounds a coding agent's architecture decisions in real arXiv prior art before it builds something new.
boheling/deltasci
The grounding layer for AI-assisted research: scan the real prior art around an idea, gauge how crowded or open the gap is, and verify every citation against the source of truth.
nubjs/nub
Diagnose and clear CPU, memory, and disk contention on the maintainer's dev host.
nubjs/nub
Reclaim disk on the maintainer's Mac when the volume is full or filling — ENOSPC, "no space left on device", a failed build or agent harness, or a routine sweep of Rust build residue.
nubjs/nub
Build a performance chart for nubjs.com — the SVG bar figures in blog posts, docs pages and social posts (a runtime augmentation against plain node, an install or dispatch comparison, a cross-tool…
nubjs/nub
A skill your agent uses when running a compatibility/parity AUDIT — enumerating where nub diverges from a reference it claims parity with (pnpm CLI grammar, a lockfile format, a Node behavior, a…
nubjs/nub
Run ad-hoc Nub tests and debugging probes on real local Linux guests.
nubjs/nub
Performance-trace Nub package-manager installs using the existing phase timings, structured diagnostics, and sampling-profiler workflow.
Categories
A skill your agent uses when the deliverable is a FACT — not code, not a design, not a gap catalog. Research Thread is an agent skill from nubjs/nub. Use when the deliverable is a FACT — not code, not a design, not a gap catalog.
Research Thread fits situations like: the deliverable is a FACT — not code; not a gap catalog; find out how X works; whats the state of the art.
Run `npx skills add nubjs/nub --skill research-thread -a claude-code`. Or copy the skill folder (.claude/skills/research-thread in nubjs/nub) into .claude/skills/research-thread in your project. Claude Code loads it when a task matches its description.
Run `npx skills add nubjs/nub --skill research-thread -a codex`. Or copy the skill folder (.claude/skills/research-thread in nubjs/nub) into .agents/skills/research-thread in your project. Codex loads it when a task matches its description.
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add nubjs/nub --skill research-thread -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/research-thread, .gemini/skills/research-thread, .github/skills/research-thread and .opencode/skills/research-thread in your project.
Going by SKILL.md and its folder, Research Thread needs the command-line tools its instructions call (git).
SKILL.md contains no URLs. Its commands use git, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
Research Thread is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
About 2.2k tokens (SKILL.md is roughly 8.6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
Skills that share tags, products or a category with Research Thread: Sciatlas Idea Grounding (zjunlp/SciAtlas, 160 stars), Mechanical Engineering Research (ccplugins/awesome-claude-code-plugins, 967 stars), Aminer MCP Research (Drchronx/ai-agent-research-starter-kit, 134 stars) and Paper to Chinese Patent Drafter (Yuan1z0825/nature-skills, 46k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
nubjs (a GitHub organization) maintains it in nubjs/nub, which has 4,370 GitHub stars. The repository holds 31 skills in this directory. The repository was last updated on October 7, 2026.
Source: nubjs/nub on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.