deep-science-writer

deep-science-writer is a skill for Claude Code, Codex from CYC2002tommy/Deep-Research-Agent. It costs 35 tokens per session (8,036 once invoked), scanned A, original, MIT.

A research-writing workflow for scientific articles, literature reviews, and deep research reports. It combines source searching, browser-based collection, academic synthesis, citations, and review.

In plain words
What is it for?
Use it for scientific writing, literature reviews, or research reports that need comprehensive source gathering, APA 7 citations, and iterative peer review.
Why use it?
It helps turn scattered scientific sources into a checked, referenced report with a natural reading flow. It is designed for work requiring broad research and academic citations.

Skill for Claude CodeCodex

Which agent this was written for is unclear — built for hermes-agent. Also seen: mentions subagents; mentions Claude Code; built for hermes-agent.

Good fit Use it for scientific writing, literature reviews, or research reports that need comprehensive source gathering, APA 7 citations, and iterative peer review.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/cyc2002tommy/deep-research-agent/deep-science-writer
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.

Any agent
npx skills add CYC2002tommy/Deep-Research-Agent --skill deep-science-writer
Clone the repo
git clone --depth 1 https://github.com/CYC2002tommy/Deep-Research-Agent

Made for: Claude Code, Codex.

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.

agentmods badge for deep-science-writer

README.md
[![agentmods](https://agentmods.dev/badge/skills/cyc2002tommy/deep-research-agent/deep-science-writer/github.svg)](https://agentmods.dev/skills/cyc2002tommy/deep-research-agent/deep-science-writer)
Your own site
<a href="https://agentmods.dev/skills/cyc2002tommy/deep-research-agent/deep-science-writer"><img src="https://agentmods.dev/badge/skills/cyc2002tommy/deep-research-agent/deep-science-writer/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for deep-science-writer

Your own site · 80×15
<a href="https://agentmods.dev/skills/cyc2002tommy/deep-research-agent/deep-science-writer"><img src="https://agentmods.dev/badge/skills/cyc2002tommy/deep-research-agent/deep-science-writer.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 35 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 8,036 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector warn 7 Sept 2026
SkillSpector: 4 findings, up to medium

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

  • medium Data Exfiltration · line 154
    Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.
    Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
  • medium Data Exfiltration · line 164
    Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.
    Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
  • medium Data Exfiltration · line 189
    Data is being sent to an external URL. This could be legitimate telemetry or data exfiltration. Manual review is recommended.
    Fix: Verify the destination URL is trusted and necessary. Remove or replace with documented APIs. Ensure no secrets, tokens, or PII are transmitted.
  • medium Excessive Agency · line 218
    Skill enables autonomous high-impact decisions without human-in-the-loop verification. Critical operations (destructive commands, financial transactions, data deletion) should require explicit user confirmation.
    Fix: Add human-in-the-loop confirmation for destructive, irreversible, or high-impact operations. Never auto-execute commands that modify files, send data, or alter system state.
How audits are shown
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 5.1 $0.00035 $0.08036
Opus 5 $0.00017 $0.04018
Sonnet 5 $0.00007 $0.01607
Haiku 4.5 $0.00003 $0.00804

Measured 10d ago against content hash 17c077e5aca5, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

deep-science-writer scanned grade A with 1 finding 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 10d ago.

The scan reads SKILL.md. This mod also ships 7 executable files (scripts/mermaid_to_png.py, scripts/node/extract_pdf_text.js, scripts/node/fetch_openalex_papers.js, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

2. **DOI/URL Liveness Test**: Use the `Bash` tool (via `curl -I`), Exa Search MCP, or a Python script (e.g., `requests.get` / `urllib`) to ping every DOI or URL in the reference list. For bulk or programmatic URL resolut
skills/deep-science-writer/SKILL.md · 245 lines

How it starts

The opening of the file, as written. The whole thing — 245 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Deep Science Writer (End-to-End Pipeline)

This skill orchestrates a multi-stage pipeline for scientific research, combining neural search, browser automation, academic synthesis, and humanized writing. It merges the capabilities of Exa Search, Playwright, Google Science Skills, Deep Research, and Text Humanization into one cohesive workflow.

🎯 Trigger Conditions

  • User asks to write a scientific article, literature review, or deep-dive research report.
  • User requests comprehensive research using web searching and scraping (Exa + Playwright).
  • The output requires rigorous academic citations (APA 7th) but a highly natural, human-like reading flow.

📋 Workflow Steps

Phase 0: Mandatory Deep Context Gathering & Research Plan

  1. Incorporate academic rigor, structured literature parsing, and cross-validation techniques into your approach and keep those principles active in context. Reference material for these lives in the local repos C:/Users/User/workspace/nature-skills/, C:/Users/User/workspace/academic-research-skills/, and C:/Users/User/workspace/superpowers/ — these are not installed skills, so read from them with Read/Grep rather than trying to invoke them.
  2. Mandatory Interrogation: You MUST deeply understand the user's current research topic before doing anything else. If the user's initial prompt is too brief, you MUST actively interrogate them to extract their exact pain points, research hypotheses, and core objectives. Do NOT proceed until you fully grasp the context.
  3. Mandatory Pre-Flight Discussion: Once the context is understood, formulate a preliminary research plan (proposed keywords, target databases, expected article structure, and goals).
  4. Present this blueprint to the user to discuss the research direction. Focus on delegating the heavy lifting to parallel subagents via Agent to protect the main context window.
  5. Halt & Wait: You MUST wait for the user's "Explicit Approval" of the research plan before proceeding to Phase 0.5.

Read the full file on GitHub · 245 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.

  1. 10d ago First seen · 245 lines · 35 tokens per session scan A 17c077e5aca5

Subscribe to this mod's changes

deep-science-writer is a skill published in the GitHub repository CYC2002tommy/Deep-Research-Agent (301 stars, last pushed 17d ago), licensed MIT. It adds 35 tokens to every session and 8,036 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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