# Research Paper

> >-

- **Type:** Skill
- **Install:** `agentstack add skill-geronimo-iia-agent-skills-research-paper`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [geronimo-iia](https://agentstack.voostack.com/s/geronimo-iia)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [geronimo-iia](https://github.com/geronimo-iia)
- **Source:** https://github.com/geronimo-iia/agent-skills/tree/main/research-paper
- **Website:** https://geronimo-iia.github.io/agent-skills/

## Install

```sh
agentstack add skill-geronimo-iia-agent-skills-research-paper
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# Research Paper Processing

Processes an academic paper into the knowledge repository following the standard
`sources → extract → analysis → studies → synthesis` pipeline.

> For document format and frontmatter standards, follow the authoring guide in
> `agent-foundation/docs/authoring-guide.md` ([github.com/geronimo-iia/agent-foundation](https://github.com/geronimo-iia/agent-foundation)).

## Knowledge base location

The knowledge base path depends on the workspace context:
- If a workspace rule or directive specifies a knowledge base path, use that
- If the user provides a path explicitly, use that
- Otherwise, ask the user before proceeding

Each topic is a subdirectory within the knowledge base root.

## Step 1 — Identify the paper and topic

Ask the user (or infer from context):
- The paper source: URL or local PDF path
- The target topic directory within the knowledge base
- Create the topic directory if it does not exist

## Step 2 — Acquire the source

### URL

Download the PDF to `/sources/.pdf` using `curl -L`:

```bash
curl -L "" -o "/sources/.pdf"
```

If the file already exists, skip the download.

### Local PDF

Copy or symlink the PDF to `/sources/.pdf` if not already there.

## Step 3 — Extract text

Use the `marker-pdf` skill if available, otherwise use `pdftotext`:

```bash
# preferred
marker_single "/sources/.pdf" --output_dir "/extract/"

# fallback
pdftotext "/sources/.pdf" "/extract/.txt"
```

The extracted file goes to `/extract/.txt` (or the marker-pdf output directory).

## Step 4 — Produce a structured analysis

Read the extracted text and write a comprehensive analysis to
`/analysis/analysis--comprehensive.md`.

The analysis must cover:

1. **Publication details** — title, authors, year, venue, DOI
2. **Core thesis** — main research question and central claim in 2–3 sentences
3. **Key contributions** — bullet list of concrete contributions
4. **Mathematical foundations** — equations, proofs, formal definitions (if present)
5. **Algorithms** — pseudocode or step-by-step descriptions of all algorithms
6. **Architecture / system design** — diagrams described in prose, component relationships
7. **Experimental results** — datasets, metrics, key findings
8. **Limitations and open problems** — what the paper acknowledges as unsolved
9. **Relation to existing knowledge** — how this paper connects to other documents already
   in `/analysis/` and `/synthesis/`
10. **Glossary** — definitions of domain-specific terms introduced

Use the frontmatter format:

```yaml
---
title: "Analysis: "
summary: ""
read_when:
  - 
status: active
last_updated: ""
source: ".pdf"
---
```

## Step 5 — Update the topic README / analysis index

If `/analysis/README.md` exists, add an entry for the new paper.
If it does not exist, create it with a minimal index.

## Step 6 — Assess synthesis impact

Read the existing synthesis documents in `/synthesis/` and determine:

- Does this paper introduce new concepts not yet in the synthesis?
- Does it contradict or refine existing synthesis claims?

If yes, either:
- Update the relevant synthesis document directly (for small additions)
- Create a new study in `/studies/` documenting the integration work needed

Report your assessment to the user.

## Output summary

After completing all steps, report:

```
✓ Source saved:   /sources/.pdf
✓ Text extracted: /extract/.txt
✓ Analysis:       /analysis/analysis--comprehensive.md
✓ Index updated:  /analysis/README.md
~ Synthesis:      
```

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [geronimo-iia](https://github.com/geronimo-iia)
- **Source:** [geronimo-iia/agent-skills](https://github.com/geronimo-iia/agent-skills)
- **License:** MIT
- **Homepage:** https://geronimo-iia.github.io/agent-skills/

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** yes
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-geronimo-iia-agent-skills-research-paper
- Seller: https://agentstack.voostack.com/s/geronimo-iia
- Browse the marketplace: https://agentstack.voostack.com/browse

---
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