Scientific Agent Skills is a collection of reusable procedures that give AI agents capabilities for scientific research across areas such as biology, chemistry, medicine, and drug discovery. It is used by researchers and by people building AI scientist workflows with compatible coding agents. The catalogue contains many of the project's skills and supporting instructions.
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.
npx skills add K-Dense-AI/scientific-agent-skills --skill pdfgit clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skillsWrote 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.
[](https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/pdf)<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/pdf"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/pdf/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.
<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/pdf"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/pdf.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- Socket pass
- Snyk pass
- NVIDIA SkillSpector pass
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 | $0.00092 | $0.02180 |
| Opus 5 | $0.00046 | $0.01090 |
| Sonnet 5 | $0.00018 | $0.00436 |
| Haiku 4.5 | $0.00009 | $0.00218 |
Grade A, and why
pdf 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 7d 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.
Copies of this mod
8 near-identical copies found in the catalogue:
How it starts
The opening of the file, as written. The whole thing — 323 lines — stays where its author put it; the contents beside it link to each section on GitHub.
PDF Processing Guide
Overview
This guide covers essential PDF processing operations using Python libraries and command-line tools. For advanced features, JavaScript libraries, and detailed examples, see reference.md. If you need to fill out a PDF form, read forms.md and follow its instructions.
Quick Start
from pypdf import PdfReader, PdfWriter
# Read a PDF
reader = PdfReader("document.pdf")
print(f"Pages: {len(reader.pages)}")
# Extract text
text = ""
for page in reader.pages:
text += page.extract_text()
Python Libraries
pypdf - Basic Operations
Merge PDFs
from pypdf import PdfWriter, PdfReader
writer = PdfWriter()
for pdf_file in ["doc1.pdf", "doc2.pdf", "doc3.pdf"]:
reader = PdfReader(pdf_file)
for page in reader.pages:
writer.add_page(page)
with open("merged.pdf", "wb") as output:
writer.write(output)
Split PDF
reader = PdfReader("input.pdf")
for i, page in enumerate(reader.pages):
writer = PdfWriter()
writer.add_page(page)
with open(f"page_{i+1}.pdf", "wb") as output:
writer.write(output)
Extract Metadata
reader = PdfReader("document.pdf")
meta = reader.metadata
print(f"Title: {meta.title}")
print(f"Author: {meta.author}")
print(f"Subject: {meta.subject}")
print(f"Creator: {meta.creator}")
Rotate Pages
reader = PdfReader("input.pdf")
writer = PdfWriter()
page = reader.pages[0]
page.rotate(90) # Rotate 90 degrees clockwise
writer.add_page(page)
with open("rotated.pdf", "wb") as output:
writer.write(output)
pdfplumber - Text and Table Extraction
Extract Text with Layout
import pdfplumber
with pdfplumber.open("document.pdf") as pdf:
for page in pdf.pages:
text = page.extract_text()
print(text)
Extract Tables
with pdfplumber.open("document.pdf") as pdf:
for i, page in enumerate(pdf.pages):
tables = page.extract_tables()
for j, table in enumerate(tables):
print(f"Table {j+1} on page {i+1}:")
for row in table:
print(row)
What ships with it
11 files 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.
- forms.md 12 KB
- LICENSE.txt 1.4 KB
- reference.md 16 KB
- scripts/check_bounding_boxes.py 2.7 KB runs code
- scripts/check_fillable_fields.py 268 B runs code
- scripts/convert_pdf_to_images.py 1008 B runs code
- scripts/create_validation_image.py 1.2 KB runs code
- scripts/extract_form_field_info.py 4.2 KB runs code
- scripts/extract_form_structure.py 3.9 KB runs code
- scripts/fill_fillable_fields.py 3.7 KB runs code
- scripts/fill_pdf_form_with_annotations.py 3.2 KB runs code
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.
- 7d ago First seen · 323 lines · 92 tokens per session scan A 78001c088c20
pdf is a skill published in the GitHub repository K-Dense-AI/scientific-agent-skills (44,220 stars, last pushed 4d ago), licensed MIT. It adds 92 tokens to every session and 2,180 once invoked, about $0.0005 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 2026-09-03.
Other skills, from other repositories
pdf-to-md
Convert PDFs and office documents to clean Markdown, with structured bundles for scientific papers. Use when extracting article structure, preparing a manuscript for analysis, or creating CSAG input.
slides-as-code
Build research slides with text-first source (Slidev/Marp/Reveal/Quarto) and reproducible export (PDF). Includes structure, figure reuse rules, and quality checklist for top-tier scientific presentations.
pdf-design
Designs PDF reports and proposals from HTML with previews and branding. Use to create, export, or securely upload a PDF.
fulltext-retrieval
Batch download open-access PDFs by DOI using legitimate OA APIs (Unpaywall, PMC, OpenAlex, Crossref). Optional PDF→Markdown conversion for token-efficient LLM analysis.
pdf-text-replace
Replace text in fillable PDF forms by updating form field values. This skill should be used when users need to update names, addresses, dates, or other text in PDF form fields.
discharge-summary-writer
Generate hospital discharge summaries from admission data, hospital course, diagnoses, procedures, and follow-up plans; use when a structured discharge document is required from clinical notes.