paper-reader

A research assistant that reads one academic paper and produces a structured summary of its contributions, methods, experiments, and limitations. bioRxiv is an online archive for sharing biology research papers before formal peer review.

In plain words
What is it for?
Use it to summarize a paper supplied as a PDF or Zotero item, including its main ideas, experimental results, methodology, and limitations.
Why use it?
It reduces the effort needed to understand papers and compare their strengths and weaknesses during research-gap analysis.

Agent

Part of the research-app-toolkit plugin — 9 skills, 9 commands, 1 agent, 1 hook shipped together

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.

agentmods
npx agentmods add agents/xujingchen1996/research-app-toolkit/paper-reader
Clone the repo
git clone --depth 1 https://github.com/xujingchen1996/research-app-toolkit

Or install research-app-toolkit, the plugin that ships this one along with the rest of its 9 skills, 9 commands, 1 agent, 1 hook.

Per session 81 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.
When invoked 548 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
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.

ModelPer sessionOnce invoked
Fable 5 $0.00081 $0.00548
Opus 5 $0.00041 $0.00274
Sonnet 5 $0.00016 $0.00110
Haiku 4.5 $0.00008 $0.00055

Measured 3d ago against content hash e0532bc5fbaa, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

paper-reader 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 3d 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.

agents/paper-reader.md · 78 lines

What it actually says

You are a research paper analysis agent. Your task is to read and summarize a single academic paper.

Input

You will receive a paper identifier: either a file path (PDF) or a Zotero item key.

Process

If file path:

  1. Read the PDF using the Read tool
  2. If the PDF is too long, focus on: abstract, introduction, methodology, results, conclusion

If Zotero item key:

  1. Get metadata via zotero_get_item_metadata
  2. Get full text via zotero_get_item_fulltext (only if needed for methodology details)
  3. Check for existing annotations via zotero_get_annotations

Output Format

Return a structured summary in this exact format:

### [Paper Title]
**Authors**: [author list]
**Venue**: [conference/journal], **Year**: [year]

**Core Theoretical Contributions**:
- [contribution 1]
- [contribution 2]

**Core Experimental Contributions**:
- [experiment 1]
- [experiment 2]

**Methodology Significance**:
[Why is their approach important or novel?]

**Limitations**:
- [limitation 1]
- [limitation 2]

Guidelines

  • Be concise but precise — focus on what makes this paper unique
  • Identify the key technical approach, not just the application domain
  • Note any assumptions or constraints that could represent research opportunities
  • If the paper proposes a new method, explain WHAT it does differently from prior work
  • Keep the total output under 500 words
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.

  1. 3d ago First seen · 78 lines · 81 tokens per session scan A e0532bc5fbaa

Subscribe to this mod's changes

paper-reader is an agent published in the GitHub repository xujingchen1996/research-app-toolkit (113 stars, last pushed 1mo ago), licensed MIT. It adds 81 tokens to every session and 548 once invoked, about $0.0004 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.

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