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literature-search

literature-search is a skill for Claude Code, Codex from yojiro253-del/BioForge. It costs 33 tokens per session (258 once invoked), scanned A, original, MIT.

An academic literature search tool for synthetic-biology and microbiology research. It searches Semantic Scholar and returns ranked papers with citation details, links, and abstract excerpts.

In plain words
What is it for?
Use it to find papers on a specific research topic, such as biofilms or antimicrobial surfaces, and create a citable list for review or further extraction.
Why use it?
It reduces the time needed to find relevant published papers and prepares sources for a later paper-extraction step.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

not rated 1repo 4mo ago A scan 33 tokens original MIT

Good fit Use it to find papers on a specific research topic, such as biofilms or antimicrobial surfaces, and create a citable list for review or further extraction.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/yojiro253-del/bioforge/literature-search
View source ↗ yojiro253-del/BioForge
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 yojiro253-del/BioForge --skill literature-search
Clone the repo
git clone --depth 1 https://github.com/yojiro253-del/BioForge

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 literature-search

README.md
[![agentmods](https://agentmods.dev/badge/skills/yojiro253-del/bioforge/literature-search/github.svg)](https://agentmods.dev/skills/yojiro253-del/bioforge/literature-search)
Your own site
<a href="https://agentmods.dev/skills/yojiro253-del/bioforge/literature-search"><img src="https://agentmods.dev/badge/skills/yojiro253-del/bioforge/literature-search/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 literature-search

Your own site · 80×15
<a href="https://agentmods.dev/skills/yojiro253-del/bioforge/literature-search"><img src="https://agentmods.dev/badge/skills/yojiro253-del/bioforge/literature-search.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 33 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 258 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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00033 $0.00258
Opus 5.5 $0.00013 $0.00103
Sonnet 5.5 $0.00007 $0.00052
Haiku 4.5 $0.00003 $0.00026

Measured 2mo ago against content hash 18255a25ad0b, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

literature-search 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 2mo ago.

The scan reads SKILL.md. This mod also ships 1 executable file (scripts/search_papers.py), 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.

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.

skills/literature-search/SKILL.md · 30 lines

What it actually says

When to use this

When the user wants to find papers on a topic before reading them:

  • "Find recent papers on dispersin B and biofilms."
  • "Get me sources for my iGEM lit review on antimicrobial surfaces."

What you produce

A ranked, citable list of papers (title, authors, year, citations, link, abstract snippet) to cite or hand to the paper-extractor skill.

How to run it

python scripts/search_papers.py "<topic>" --limit 10
python scripts/search_papers.py "<topic>" --json

No API key needed. For higher rate limits, add a free Semantic Scholar key to ~/keys.md as: S2_API_Key:

  • Downstream: paper-extractor (feed a chosen paper in to pull organisms, genes, methods).

Safety

Search and summarize published research only. See SAFETY.md at the repo root.

Files

What ships with it

1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

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. 2mo ago First seen · 30 lines · 33 tokens per session scan A 18255a25ad0b

Subscribe to this mod's changes

literature-search is a skill published in the GitHub repository yojiro253-del/BioForge (1 stars, last pushed 4mo ago), licensed MIT. It adds 33 tokens to every session and 258 once invoked, about $0.0001 per session on Opus 5.5. 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 2026-08-31.

LiteratureResearchScientificagent-skillsbioinformaticsclaude-skillsigemsynthetic-biology
Related

literature-search compared with skills from other repositories

literature-search next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
literature-searchyojiro253-del/BioForgeSkill14mo agoMITA33Claude Code, Codex
imaging-data-commonsK-Dense-AI/scientific-agent-skillsSkill56k5d agoMITA73Claude Code, Codex
genomic-intelligenceK-Dense-AI/scientific-agent-skillsSkill56k5d agoMITA151Claude Code, Codex
lab-hardware-cadK-Dense-AI/scientific-agent-skillsSkill56k5d agoMITA108Claude Code
scikit-bioK-Dense-AI/scientific-agent-skillsSkill56k5d agoMITA54Claude Code
statistical-analysisK-Dense-AI/scientific-agent-skillsSkill56k5d agoMITA111Claude Code, Codex
analytical-method-validationK-Dense-AI/scientific-agent-skillsSkill56k5d agoMITA281Claude Code