Hypothesis Generation
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
Reads projects, searches project feeds, and retrieves recommendations and canonical papers in Paperzilla through the pz CLI.
$ npx skills add K-Dense-AI/scientific-agent-skills --skill paperzilla -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install K-Dense-AI/scientific-agent-skills paperzilla --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/K-Dense-AI/scientific-agent-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/paperzilla .claude/skills/paperzilla && 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 "paperzilla" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/paperzilla into .claude/skills/paperzilla/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paperzilla", 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/K-Dense-AI/scientific-agent-skills/tree/main/skills/paperzillaType 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 K-Dense-AI/scientific-agent-skills --skill paperzilla -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install K-Dense-AI/scientific-agent-skills paperzilla --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/paperzilla .agents/skills/paperzilla && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "paperzilla" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/paperzilla into .agents/skills/paperzilla/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paperzilla", 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 K-Dense-AI/scientific-agent-skills --skill paperzilla -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install K-Dense-AI/scientific-agent-skills paperzilla --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/paperzilla .cursor/skills/paperzilla && 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 "paperzilla" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/paperzilla into .cursor/skills/paperzilla/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paperzilla", 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/K-Dense-AI/scientific-agent-skills.git --path skills/paperzilla--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 K-Dense-AI/scientific-agent-skills --skill paperzilla -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install K-Dense-AI/scientific-agent-skills paperzilla --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/paperzilla .gemini/skills/paperzilla && 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 "paperzilla" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/paperzilla into .gemini/skills/paperzilla/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paperzilla", 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 K-Dense-AI/scientific-agent-skills paperzillaInstalls 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 K-Dense-AI/scientific-agent-skills --skill paperzilla -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/paperzilla .github/skills/paperzilla && 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 "paperzilla" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/paperzilla into .github/skills/paperzilla/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paperzilla", 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 K-Dense-AI/scientific-agent-skills --skill paperzilla -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install K-Dense-AI/scientific-agent-skills paperzilla --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/paperzilla .opencode/skills/paperzilla && 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 "paperzilla" agent skill from https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/paperzilla into .opencode/skills/paperzilla/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paperzilla", 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.
paperzillaReads projects, searches project feeds, and retrieves recommendations and canonical papers in Paperzilla through the pz CLI.
Paperzilla is an agent skill from K-Dense-AI/scientific-agent-skills. Reads projects, searches project feeds, and retrieves recommendations and canonical papers in Paperzilla through the pz CLI. Supports recent recommendations, paper details, markdown-based summaries, recommendation feedback, JSON export, and Atom feed URLs.
Its SKILL.md is about 2.3k tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files, including reference files (for example `references/cli-contracts.md`). Compatibility notes: Requires the pz CLI, network access, and a Paperzilla account with CLI access. Source builds require Go 1.23 or later.
It sits in Research & Science. The repository describes itself as: Turn any AI agent into an AI Scientist. The 1 Agent Skills library for science, used by 250,000+ scientists worldwide. 177 ready-to-use validated skills plus 100+ scientific… The licence is MIT.
Read from SKILL.md and the folder at commit 92ace75. 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:
brewFrom the folder's file list and the shell code blocks in SKILL.md.
Hosts in commands or code, which the agent is likely to contact:
github.compaperzilla.aiAlso links to:
docs.paperzilla.aiFrom 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.
Requires the pz CLI, network access, and a Paperzilla account with CLI access. Source builds require Go 1.23 or later.
From compatibility in the SKILL.md frontmatter.
Paperzilla loads about 2.3k tokens when it runs, and up to ~4.2k if it reads all its reference files. Until then it costs about 67 tokens; SKILL.md has 999 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 K-Dense-AI/scientific-agent-skills at commit 92ace75, republished under its MIT licence (© K-Dense-AI). 999 words, ~2,324 tokens.
.claude/skills/paperzilla/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.Use this skill when you want to chat with your agent about projects, recommendations, and canonical papers in Paperzilla.
This is the core Paperzilla skill. It gives your agent direct access to Paperzilla data, but it does not impose a workflow or external delivery integration.
Use the official pz CLI. This skill targets 0.7.1, checked against the
official release source and binary. Command examples use placeholder IDs; replace
them with records returned by your account. CLI behavior was tested against a
local mock server, not an authenticated Paperzilla account.
Start with pz --version, then list projects, select a project, browse or search
its feed, and inspect selected recommendations. Keep project recommendations
separate from the underlying canonical paper when summarizing or exporting.
brew install paperzilla-ai/tap/pzIf Homebrew 6 or later rejects this formula as untrusted, the official guide uses
brew trust --formula paperzilla-ai/tap/pz, then retries installation. Trust only
that formula. Installation and upgrade commands were documentation-checked, not
executed during this review.
scoop bucket add paperzilla-ai https://github.com/paperzilla-ai/scoop-bucket
scoop install pzUse the official Linux install guide:
See the CLI repository for source builds:
Check whether your CLI is up to date and get install-specific upgrade steps:
pz updateIf detection is ambiguous, override it explicitly:
pz update --install-method homebrew
pz update --install-method scoop
pz update --install-method release
pz update --install-method sourceSupported values are auto, homebrew, scoop, release, and source.
pz loginLogin sends a one-time code to the account email and saves the session locally. Complete it interactively before running JSON exports: missing or expired credentials can trigger login prompts on stdout. The CLI checks account access and refreshes tokens automatically; report access/upgrade errors rather than treating them as an empty feed.
Version-specific discrepancy: the online guides describe anonymous canonical
paper access, but the 0.7.1 binary requires login and a CLI-access check even for
pz paper. Its subsequent canonical-paper HTTP request uses a public route. Do
not promise an anonymous CLI workflow for this release.
If the current profile uses pz, these are the core commands.
pz project list
pz project list --jsonpz project <project-id>
pz project <project-id> --jsonThe list JSON is an array containing id, name, mode, and visibility.
The single-project JSON also includes keywords, watched sources, and categories.
pz feed <project-id>Useful flags:
--must-read--since YYYY-MM-DD--limit N--offset N (zero-based results to skip)--json--atomExamples:
pz feed <project-id> --must-read --since 2026-03-01 --limit 5
pz feed <project-id> --limit 20 --offset 20 --json
pz feed <project-id> --json
pz feed <project-id> --atom--since filters when recommendations were ready, not paper publication date.
Browse JSON contains items, total, limit, and offset. A command fetches
one page; it does not export the entire feed automatically. Retain the same
filters, advance from the returned offset by the number of items received, and
stop on an empty page or when the returned total is reached. Deduplicate by
recommendation ID if the live feed changes while paging.
Feed output can include existing recommendation feedback markers:
[↑] upvote[↓] downvote[★] starpz feed search --project-id <project-id> --query "latent retrieval" --json
pz feed search --project-id <project-id> --query "retrieval" --feedback-filter starred --must-read --limit 20 --offset 20 --jsonSearch ranks results across the whole project feed. Use a trimmed query of
3–200 characters and a positive --limit up to 100. --offset must be
nonnegative. Feedback filters are all, unrated, liked, disliked, starred,
not-relevant, and low-quality; these hyphenated filters differ from the
underscored downvote reasons below. Search does not accept --since.
Search JSON contains items, limit, offset, has_more, and query, with no
exact total. Request the next offset only while has_more is true, keeping the
query and filters unchanged. Stop and report an inconsistent empty page rather
than looping indefinitely. The second example illustrates a subsequent page.
pz paper <paper-id>
pz paper <paper-id> --json
pz paper <paper-id> --markdown
pz paper <paper-id> --project <project-id>pz rec <project-paper-id>
pz rec <project-paper-id> --json
pz rec <project-paper-id> --markdownpz feedback <project-paper-id> upvote
pz feedback <project-paper-id> star
pz feedback <project-paper-id> downvote --reason not_relevant
pz feedback clear <project-paper-id>Feedback changes account data; use it when the user requests that change.
Downvote reasons are not_relevant or low_quality, and --reason applies only
to a downvote. Add --json to get the feedback object; clearing returns
{"project_paper_ref": "...", "cleared": true}. clear is a subcommand before
the recommendation ID.
A canonical paper-id identifies the paper; a project-paper-id identifies its
recommendation within a project. Take both from returned records and retain the
project association when exporting results. Use the recommendation ID for rec
and feedback operations, even if the same paper appears in several projects.
In feed JSON, items[].id/items[].short_id are recommendation identifiers;
items[].paper.id/items[].paper.short_id are canonical paper identifiers.
Do not infer recommendation IDs from a DOI or canonical paper ID. See the
official CLI documentation.
When markdown is still being prepared, report that state and summarize only the metadata or abstract actually returned. A retry message is not full-text evidence.
--json for machine parsing after completing login. paper and rec
reject combining --json with --markdown.pz paper --markdown only returns markdown when it is already prepared.pz rec --markdown and project-scoped pz paper --project ... --markdown
can queue markdown generation. A pending message can exit successfully; check
the content before treating stdout as full text. Avoid repeated immediate
retries and report the pending state.--atom returns a personal feed URL for feed readers and can create a feed
token. Anyone holding that URL can read the feed; keep its token out of logs,
public reports, and repositories. It does not return Atom XML or page JSON,
and browse filters are not applied to the generated URL.export PZ_API_URL="https://paperzilla.ai"The default already points to Paperzilla; change it only for a trusted service
or a local test server. Authenticated requests send session credentials there.
PZ_TOKENS_PATH optionally selects a session file; by default the CLI uses
~/.paperzilla/tokens.json. Never export that file as research data.
See the verified CLI contracts for request routes, response shapes, pagination, and the documentation/source discrepancy.
© K-Dense-AI, MIT. 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 1 other file (references) in skills/paperzilla of K-Dense-AI/scientific-agent-skills.
Open the folder on GitHubat commit 92ace75
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in K-Dense-AI/scientific-agent-skills, which our catalogue first saw on October 7, 2026.
Paperzilla 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 |
|---|---|---|---|---|---|---|
| Paperzilla this skillK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~2.3k | Automated safety check: Pass | MIT | |
| Hypothesis Generationspacering-net/codeg | 3.9k | 14 repos | ~3.6k | Automated safety check: Notes | MIT | |
| GitHub Deep Researchbytedance/deer-flow | 84k | 4 repos | ~1.3k | Automated safety check: Pass | MIT | |
| Nature Paper CardYuan1z0825/nature-skills | 47k | 2 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| Content Research Writerweapp-tailwindcss/weapp-tailwindcss | 1.9k | 25 repos | ~3.5k | Automated safety check: Pass | MIT | |
| Peer Reviewspacering-net/codeg | 3.9k | 17 repos | ~5.9k | Automated safety check: Notes | MIT |
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
bytedance/deer-flow
Researches a GitHub repository over four rounds using the GitHub API and web search, then writes a structured markdown report with timeline, metrics and Mermaid diagrams.
Yuan1z0825/nature-skills
Builds a structured deep-reading card for one scientific paper, covering methods, how experiments support claims, limitations and research ideas, with a script to prepare the source.
weapp-tailwindcss/weapp-tailwindcss
Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section.
spacering-net/codeg
Structured manuscript/grant review with checklist-based evaluation.
mvanhorn/last30days-skill
Research what people actually say about any topic in the last 30 days.
K-Dense-AI/scientific-agent-skills
Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.
K-Dense-AI/scientific-agent-skills
Plans, runs, and documents analytical method validation, verification, or transfer studies under ICH Q2(R2)/Q14, USP, ICH M10, CLSI EP, or ISO/IEC 17025.
K-Dense-AI/scientific-agent-skills
Runs Cantera constant-volume or constant-pressure ignition simulations and reports temperature-based ignition delay with mechanism provenance and checks.
K-Dense-AI/scientific-agent-skills
Predicts how small molecules bind to a protein with DiffDock, covering batch docking, pose ranking by confidence and checks on the results; not for binding affinity.
K-Dense-AI/scientific-agent-skills
Plans and audits runs of the HypoGeniC and HypoRefine packages, which propose hypotheses from labeled text datasets, with local checks before any model call.
K-Dense-AI/scientific-agent-skills
Organizes scope, controlled documents, risk files and traceability into draft evidence for human review against ISO 13485, 14971, 17025 and 15189.
Categories
Reads projects, searches project feeds, and retrieves recommendations and canonical papers in Paperzilla through the pz CLI. Paperzilla is an agent skill from K-Dense-AI/scientific-agent-skills. Reads projects, searches project feeds, and retrieves recommendations and canonical papers in Paperzilla through the pz CLI.
Paperzilla fits situations like: research & Science work in your project.
Run `npx skills add K-Dense-AI/scientific-agent-skills --skill paperzilla -a claude-code`. Or copy the skill folder (skills/paperzilla in K-Dense-AI/scientific-agent-skills) into .claude/skills/paperzilla in your project. Claude Code loads it when a task matches its description.
Run `npx skills add K-Dense-AI/scientific-agent-skills --skill paperzilla -a codex`. Or copy the skill folder (skills/paperzilla in K-Dense-AI/scientific-agent-skills) into .agents/skills/paperzilla 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 K-Dense-AI/scientific-agent-skills --skill paperzilla -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/paperzilla, .gemini/skills/paperzilla, .github/skills/paperzilla and .opencode/skills/paperzilla in your project.
Going by SKILL.md and its folder, Paperzilla needs the command-line tools its instructions call (brew). Compatibility (from SKILL.md): Requires the pz CLI, network access, and a Paperzilla account with CLI access. Source builds require Go 1.23 or later..
SKILL.md names 3 domains. In commands or code: github.com and paperzilla.ai; the agent is likely to contact these when it follows the instructions. As links in the text: docs.paperzilla.ai. 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.
Paperzilla is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
About 2.3k tokens (SKILL.md is roughly 9.3k 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 1.8k tokens, read only when the agent opens those files.
Skills that share tags, products or a category with Paperzilla: Hypothesis Generation (spacering-net/codeg, 3.9k stars), GitHub Deep Research (bytedance/deer-flow, 84k stars), Nature Paper Card (Yuan1z0825/nature-skills, 47k stars) and Content Research Writer (weapp-tailwindcss/weapp-tailwindcss, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
K-Dense-AI (a GitHub organization) maintains it in K-Dense-AI/scientific-agent-skills, which has 48,095 GitHub stars. The repository holds 153 skills in this directory. The repository was last updated on October 5, 2026.
Source: K-Dense-AI/scientific-agent-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.