What is research-init?

A guided startup command for a research project and literature review, using Zotero, a tool for organizing research papers and references. It creates or audits sources and research-question cards, but only writes a proposal when the evidence is sufficient.

Use it to start or audit literature research, define research questions, check available sources, and prepare a proposal when the evidence gate passes.

It prevents a polished proposal from being produced when Zotero, full-paper evidence, or a focused research question is missing. In those cases it returns an intake or source-audit result instead.

research-init — Command for Claude Code by Galaxy-Dawn

About the project

Claude Scholar is a semi-automated research assistant for academic research and software development, supporting literature review, coding, experiments, reporting, writing, and project knowledge management. Computer science and AI researchers use it across the research workflow with several coding-agent platforms; the catalogue contains its skills, commands, agents, hooks, plugin, and instruction.

Galaxy-Dawn/claude-scholar · 5,381 stars · on GitHub

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Clone the repo

git clone --depth 1 https://github.com/Galaxy-Dawn/claude-scholar

Made for: Claude Code.

Or install claude-scholar, the plugin that ships this one along with the rest of its 45 skills, 34 commands, 6 agents, 5 hooks.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/commands/galaxy-dawn/claude-scholar/research-init.svg)](https://agentmods.dev/commands/galaxy-dawn/claude-scholar/research-init)

Your own site

<a href="https://agentmods.dev/commands/galaxy-dawn/claude-scholar/research-init"><img src="https://agentmods.dev/badge/commands/galaxy-dawn/claude-scholar/research-init.svg" alt="Measured on agentmods" height="20"></a>

Per session 40 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.

When invoked 4,403 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00040	$0.04403
Opus 5	$0.00020	$0.02201
Sonnet 5	$0.00008	$0.00881
Haiku 4.5	$0.00004	$0.00440

Measured 9d ago against content hash 6d0f6ee4158e, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-08, from the pricing page.

Security

Grade A, and why

research-init scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

commands/research-init.md · 293 lines

How it starts

The opening of the file, as written. The whole thing — 293 lines — stays where its author put it; the contents beside it link to each section on GitHub.

/research-init - Zotero-Integrated Research Startup Workflow

Launch a project-scoped literature startup workflow for the research topic "$topic", with scope "$scope" and output type "$output_type".

Default behavior is evidence-first: if Zotero is unavailable, if full-paper evidence is insufficient, or if the selected Research Question Card is not ready, produce an intake/audit result instead of forcing a polished proposal.

Usage

Basic Usage

/research-init "transformer interpretability"

Specify Scope

/research-init "few-shot learning" focused

Specify All Parameters

/research-init "neural architecture search" broad both

Workflow

Execute the following steps in order:

Step 0: Intake and Capability Gate

Before creating collections or writing files:

Confirm the practical purpose: new project intake, literature review, proposal draft, or source audit.
Check whether Zotero MCP is configured and writable.
If Zotero MCP is unavailable, read-only, or the user asks for dry-run mode:
- do not create collections,
- do not import papers,
- produce research-question-card.md and a source candidate/audit section,
- either skip references.bib or create a stub that clearly says canonical BibTeX is unavailable unless reliable BibTeX can be generated from existing sources,
- stop before literature-review.md or research-proposal.md unless the user explicitly provides sufficient local evidence.
If the topic, target venue/audience, or project boundary is ambiguous enough to change the search strategy, ask a short clarifying question before acting.

Step 1: Create Zotero Research Collection

Call the Zotero MCP tool zotero_create_collection to create the main collection, named Research-{Topic}-{YYYY-MM} (extract a short PascalCase keyword from the topic, use the current year and month)
Create sub-collections under the main collection:
- Core Papers
- Methods
- Applications
- Baselines
- To-Read
Record the collection_key for each sub-collection (needed for import in Step 2)

Read the full file on GitHub · 293 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

9d ago First seen · 293 lines · 40 tokens per session scan A 6d0f6ee4158e

Subscribe to this mod's changes

research-init is a command published in the GitHub repository Galaxy-Dawn/claude-scholar (5,381 stars, last pushed 12d ago), licensed MIT. It adds 40 tokens to every session and 4,403 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Claude Code Paper Search Research Zotero academic-research ai-agents claude codex-cli developer-tools literature-review

research-init