Academic Research Suite for Codex
Imbad0202/academic-research-skills-codex
A router skill that sends academic work such as literature reviews, drafting, citation checks, peer review and revision to the right workflow in the ARS suite.
Runs multi-round research in three stages with a persisted state file, evidence tracking and a long-form report with per-claim citations.
$ npx skills add TokenRhythm/opensquilla --skill deep-research -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install TokenRhythm/opensquilla deep-research --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/TokenRhythm/opensquilla.git skills-src && mkdir -p .claude/skills && cp -r skills-src/src/opensquilla/skills/bundled/deep-research .claude/skills/deep-research && 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 "deep-research" agent skill from https://github.com/TokenRhythm/opensquilla/tree/main/src/opensquilla/skills/bundled/deep-research into .claude/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", 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/TokenRhythm/opensquilla/tree/main/src/opensquilla/skills/bundled/deep-researchType 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 TokenRhythm/opensquilla --skill deep-research -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install TokenRhythm/opensquilla deep-research --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TokenRhythm/opensquilla.git skills-src && mkdir -p .agents/skills && cp -r skills-src/src/opensquilla/skills/bundled/deep-research .agents/skills/deep-research && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "deep-research" agent skill from https://github.com/TokenRhythm/opensquilla/tree/main/src/opensquilla/skills/bundled/deep-research into .agents/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", 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 TokenRhythm/opensquilla --skill deep-research -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install TokenRhythm/opensquilla deep-research --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TokenRhythm/opensquilla.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/src/opensquilla/skills/bundled/deep-research .cursor/skills/deep-research && 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 "deep-research" agent skill from https://github.com/TokenRhythm/opensquilla/tree/main/src/opensquilla/skills/bundled/deep-research into .cursor/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", 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/TokenRhythm/opensquilla.git --path src/opensquilla/skills/bundled/deep-research--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 TokenRhythm/opensquilla --skill deep-research -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install TokenRhythm/opensquilla deep-research --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TokenRhythm/opensquilla.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/src/opensquilla/skills/bundled/deep-research .gemini/skills/deep-research && 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 "deep-research" agent skill from https://github.com/TokenRhythm/opensquilla/tree/main/src/opensquilla/skills/bundled/deep-research into .gemini/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", 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 TokenRhythm/opensquilla deep-researchInstalls 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 TokenRhythm/opensquilla --skill deep-research -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/TokenRhythm/opensquilla.git skills-src && mkdir -p .github/skills && cp -r skills-src/src/opensquilla/skills/bundled/deep-research .github/skills/deep-research && 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 "deep-research" agent skill from https://github.com/TokenRhythm/opensquilla/tree/main/src/opensquilla/skills/bundled/deep-research into .github/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", 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 TokenRhythm/opensquilla --skill deep-research -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install TokenRhythm/opensquilla deep-research --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TokenRhythm/opensquilla.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/src/opensquilla/skills/bundled/deep-research .opencode/skills/deep-research && 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 "deep-research" agent skill from https://github.com/TokenRhythm/opensquilla/tree/main/src/opensquilla/skills/bundled/deep-research into .opencode/skills/deep-research/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "deep-research", 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.
deep-researchRuns multi-round research in three stages with a persisted state file, evidence tracking and a long-form report with per-claim citations.
The skill structures an investigation as plan, iterate and compile, with all progress kept in one JSON state file that can resume the work at any point. It does not fetch the web itself: it prints a fetch list for the host agent to run with its own web tools and records the evidence that comes back. It is meant for deep dives, research reports and literature reviews, where a single-pass summary would lose too much.
Planning splits a question into sub-questions according to a depth setting: overview, thorough or exhaustive, with 3-5, 6-10 or 12-20 sub-questions and growing source targets. Each iteration round records evidence and updates coverage per sub-question until the plan's done flag flips. Sources are judged on authority, recency, evidence, bias and corroboration. Compile then writes a Markdown report that starts with an executive summary. The plan.py, iterate.py and compile.py scripts do the work, with references on methodology and sources.
3 steps, taken from the step headings in SKILL.md.
Read from SKILL.md and the folder at commit 4494195. 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.
Ships 3 files in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
pythonFrom the folder's file list and the shell code blocks in SKILL.md.
No URLs in SKILL.md.
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.
Deep Research Workflow loads about 1.3k tokens when it runs, and up to ~3k if it reads all its reference files. Until then it costs about 180 tokens; SKILL.md has 467 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); the scripts in this folder are not scanned.
The full file from TokenRhythm/opensquilla at commit 4494195, republished under its Apache-2.0 licence (© TokenRhythm). 467 words, ~1,336 tokens.
.claude/skills/deep-research/SKILL.md (or your agent's skills folder). This skill also uses 6 other files; get the full folder from GitHub.Investigate a question by walking it through three explicit stages with a
persisted state file. Use this when a single-pass summarize would lose too
much, or when the user asks for a "research report" / "literature review".
The host agent does the web fetching; this skill structures the work and
keeps a paper trail.
| Need | Use |
|---|---|
| One-line summary of an article | summarize |
| Multi-round investigation with citations | this skill |
| Quick lookup, single source | direct web search |
| Continuous monitoring of a topic | a digest/cron skill |
Scope → Plan → Iterate (×N) → Compile → DeliverState persists in a single JSON file you pass between stages. The file is the contract; if you can describe the file, you can resume the research at any point.
python {baseDir}/scripts/plan.py \
--question "How did Manus differentiate from competing AI agents in 2025?" \
--depth thorough \
--out plan.json--depth choices:
overview — 3-5 sub-questions, target 1 source per sub-questionthorough — 6-10 sub-questions, target 2-3 sources per sub-questionexhaustive — 12-20 sub-questions, target 5+ sources per sub-questionThe plan is a pydantic model serialized to JSON; see
references/methodology.md for the schema and
the system-review approach the depth choices implement.
Each round: read the plan, decide which sub-questions need attention, print the fetch list for the host agent to execute, and (after the agent returns results) record evidence back into the plan.
# Show the host what to fetch this round
python {baseDir}/scripts/iterate.py --plan plan.json --round 1 --print-fetches
# After the host fetches, record results back
python {baseDir}/scripts/iterate.py --plan plan.json --round 1 \
--record evidence_round_1.jsonevidence_round_1.json:
[
{
"subquestion_id": "sq-002",
"url": "https://...",
"title": "...",
"excerpt": "...",
"relevance": 0.85,
"fetched_at": "2026-05-06T10:14:00Z"
}
]The script updates per-sub-question coverage estimates. When all
sub-questions reach the depth-target coverage, the plan's done flag flips
to true and the iteration loop terminates.
See references/sources.md for the 5-axis source evaluation (Authority, Recency, Evidence, Bias, Corroboration) you should apply when judging relevance.
python {baseDir}/scripts/compile.py --plan plan.json --out report.mdOutput is markdown with:
[^N]Citations link to the references block. The compile step never invents
sources — every [^N] in the body must correspond to an entry recorded in
stage 2.
summarizesummarize takes one document and produces a shorter version. This skill
takes one question and produces a researched report drawing on many
documents, with explicit evidence tracking. They share no trigger words by
design — summarize triggers on "summarize", "shorten", "tl;dr"; this
skill triggers on "research", "investigate", "literature review", "deep
dive".
© TokenRhythm, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
SKILL.md and 6 other files (scripts, references) in src/opensquilla/skills/bundled/deep-research of TokenRhythm/opensquilla.
Open the folder on GitHubat commit 4494195
Deep Research Workflow 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 |
|---|---|---|---|---|---|---|
| Deep Research Workflow this skillTokenRhythm/opensquilla | 7.1k | — | ~1.3k | Automated safety check: Pass | Apache-2.0 | |
| Academic Research Suite for CodexImbad0202/academic-research-skills-codex | 12k | — | ~12k | Automated safety check: Pass | Custom licence | |
| Deep Research Literature SurveyHKUSTDial/Supervisor-Skills | 8.4k | — | ~2.4k | Automated safety check: Pass | CC-BY-NC-SA-4.0 | |
| Live Researchbrightdata/skills | 264 | — | ~1.8k | Automated safety check: Pass | MIT | |
| Academic Researcheraiskillstore/marketplace | 430 | 3 repos | ~2.1k | Automated safety check: Pass | MIT | |
| Ulw Researchrlaope/oh-my-hermes | 3.2k | — | ~4.2k | Automated safety check: Pass | MIT |
Imbad0202/academic-research-skills-codex
A router skill that sends academic work such as literature reviews, drafting, citation checks, peer review and revision to the right workflow in the ARS suite.
HKUSTDial/Supervisor-Skills
Runs a survey-grade literature investigation: fixes the research questions, searches from adversarial angles, verifies citations and writes an evidence-first report.
brightdata/skills
Produce a deep, multi-source, cited research brief on a topic from live web data using Bright Data's Discover API (intent-ranked web search + parsed page content).
aiskillstore/marketplace
Academic research assistant for literature reviews, paper analysis, and scholarly writing.
rlaope/oh-my-hermes
[omh] Deep dive before a decision: deep research engine - grounding for specs and decisions: study open-source reference implementations with pinned refs, gather live web evidence with citation…
revfactory/harness-100
A pipeline where an agent team systematically performs academic research assistance.
TokenRhythm/opensquilla
Deterministic PDF operations through bundled scripts: extract text and tables, merge files or page ranges, split by range, fill form fields and build PDFs from data.
TokenRhythm/opensquilla
Inspects, edits in place or creates Word .docx files with bundled Python scripts, keeping existing styles intact when content changes.
TokenRhythm/opensquilla
Guides semantic, accessible HTML work: pages, forms, media and HTML5 APIs, plus how to deliver a runnable webpage project with a preview.
TokenRhythm/opensquilla
Reads, edits in place, or creates PowerPoint .pptx decks, picking one of three paths based on what tools and files are available.
TokenRhythm/opensquilla
Inspects, edits in place or creates Microsoft Excel .xlsx workbooks with openpyxl, treating each cell as a typed number, string, datetime or formula value.
TokenRhythm/opensquilla
Hands a self-contained coding task to Codex, Claude Code, OpenCode or Pi as a non-interactive background process, using OpenSquilla's exec_command and process tools.
Categories
Runs multi-round research in three stages with a persisted state file, evidence tracking and a long-form report with per-claim citations. The skill structures an investigation as plan, iterate and compile, with all progress kept in one JSON state file that can resume the work at any point. It does not fetch the web itself: it prints a fetch list for the host agent to run with its own web tools and records the evidence that comes back.
Deep Research Workflow fits situations like: producing a research report with a citation for each claim; running a multi-round literature review that can be resumed; scoping a broad question into sub-questions and tracking coverage.
Run `npx skills add TokenRhythm/opensquilla --skill deep-research -a claude-code`. Or copy the skill folder (src/opensquilla/skills/bundled/deep-research in TokenRhythm/opensquilla) into .claude/skills/deep-research in your project. Claude Code loads it when a task matches its description.
Run `npx skills add TokenRhythm/opensquilla --skill deep-research -a codex`. Or copy the skill folder (src/opensquilla/skills/bundled/deep-research in TokenRhythm/opensquilla) into .agents/skills/deep-research 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 TokenRhythm/opensquilla --skill deep-research -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/deep-research, .gemini/skills/deep-research, .github/skills/deep-research and .opencode/skills/deep-research in your project.
Going by SKILL.md and its folder, Deep Research Workflow needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python, for plan.py, iterate.py and compile.py; Web fetching tools in the host agent.
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
Deep Research Workflow is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
About 1.3k tokens (SKILL.md is roughly 5.3k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 1.6k tokens, read only when the agent opens those files.
Skills that share tags, products or a category with Deep Research Workflow: Academic Research Suite for Codex (Imbad0202/academic-research-skills-codex, 12k stars), Deep Research Literature Survey (HKUSTDial/Supervisor-Skills, 8.4k stars), Live Research (brightdata/skills, 264 stars) and Academic Researcher (aiskillstore/marketplace, 430 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
TokenRhythm (a GitHub organization) maintains it in TokenRhythm/opensquilla, which has 7,087 GitHub stars. The repository holds 8 skills in this directory. The repository was last updated on October 4, 2026.
Source: TokenRhythm/opensquilla on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.