Medical Research Agent Skills is a library of agent instructions for medical and biomedical research, covering evidence analysis, study protocol design, data analysis, and academic writing. Researchers use it to guide compatible coding agents through common scientific workflows. The catalogue contains many of the library's skills and commands.
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 aipoch/medical-research-skills --skill ppi-network-analysisgit clone --depth 1 https://github.com/aipoch/medical-research-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/aipoch/medical-research-skills/ppi-network-analysis)<a href="https://agentmods.dev/skills/aipoch/medical-research-skills/ppi-network-analysis"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/ppi-network-analysis/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/aipoch/medical-research-skills/ppi-network-analysis"><img src="https://agentmods.dev/badge/skills/aipoch/medical-research-skills/ppi-network-analysis.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- 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 | $0.00069 | $0.02366 |
| Opus 5 | $0.00034 | $0.01183 |
| Sonnet 5 | $0.00014 | $0.00473 |
| Haiku 4.5 | $0.00007 | $0.00237 |
Grade A, and why
ppi-network-analysis 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 12d 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.
How it starts
The opening of the file, as written. The whole thing — 173 lines — stays where its author put it; the contents beside it link to each section on GitHub.
PPI Network Analysis
When to Read External Files
| Situation | File to Read | Purpose |
|---|---|---|
| Need algorithm details | references/algorithm.md |
Explain local STRING mapping, interaction filtering, network metrics, and plot interpretation |
| Need to execute the analysis | scripts/main.R |
Run the CLI entry point with a complete Rscript command |
| Encounter an error | references/troubleshooting.md |
Map standardized error codes to causes and fixes |
| Need CLI examples or baseline usage | references/cli-guide.md |
Review installation notes, offline cache requirements, and runnable examples |
| Need a runnable smoke test | tests/data/ |
Use the bundled small gene list for verification |
Usage
Rscript scripts/main.R \
--genelist_file ./input/gene_list.csv \
--species human \
--threshold 700 \
--output_dir output/basic-run \
--seed 42 \
--timeout_seconds 600
Rscript scripts/main.R \
--plot_only TRUE \
--output_dir output/basic-run \
--seed 42 \
--timeout_seconds 600
Arguments
| Short | Long | Type | Default | Required | Description |
|---|---|---|---|---|---|
-g |
--genelist_file |
character | none | yes, unless --plot_only TRUE |
Gene list file in CSV, TSV, TXT, or XLSX format |
-s |
--species |
character | none | yes, unless --plot_only TRUE |
Species: human, mouse, 9606, or 10090 |
-t |
--threshold |
integer | none | yes, unless --plot_only TRUE |
STRING combined-score threshold from 400 to 1000 |
-o |
--output_dir |
character | output |
no | Output directory inside the skill root |
-p |
--plot_only |
logical | FALSE |
no | Reuse output_dir/data/ppi_result.rds and regenerate the network plot |
-d |
--seed |
integer | 42 |
no | Random seed used for layout reproducibility |
-u |
--timeout_seconds |
integer | 600 |
no | Elapsed time limit in seconds |
--string_cache_dir |
character | references/string_cache |
no | Local STRING cache directory; if omitted, the bundled cache inside the skill is used | |
--string_version |
character | auto |
no | Preferred STRING cache version; use auto, v11.5, or v12.0 when available |
|
--figure_family |
character | sans |
no | PDF font family: sans, serif, or mono |
|
--figure_width |
numeric | 12 |
no | Plot width in inches | |
--figure_height |
numeric | 10 |
no | Plot height in inches | |
--label |
character | node |
no | Label mode: node or none |
|
--label_size |
numeric | 0.8 |
no | Label size | |
--label_color |
character | black |
no | Label color | |
--label_dist |
numeric | 0 |
no | Label distance from the node center | |
--line_alpha |
numeric | 1 |
no | Edge alpha | |
--line_color |
character | built-in palette | no | Comma-separated edge colors | |
--line_size |
numeric | 0.8 |
no | Base edge width | |
--line_type |
character | solid |
no | Edge line type; supported values in plotting are solid, dashed, or dotted |
|
--mapping_link_alpha |
character | value |
no | Map edge alpha from interaction score: value or none |
|
--mapping_link_color |
character | value |
no | Map edge color from interaction score: value or none |
|
--mapping_link_size |
character | value |
no | Map edge width from interaction score: value or none |
|
--mapping_node_alpha |
character | none |
no | Map node alpha from degree: value or none |
|
--mapping_node_color |
character | none |
no | Map node color from degree: value or none |
|
--mapping_node_size |
character | value |
no | Map node size from degree: value or none |
|
--point_alpha |
numeric | 1 |
no | Node alpha | |
--point_color |
character | built-in palette | no | Comma-separated node border colors | |
--point_fill |
character | built-in palette | no | Comma-separated node fill colors | |
--point_shape |
character | circle |
no | Node shape: circle or square |
|
--point_size |
numeric | 12 |
no | Base node size | |
--style_layout |
character | nicely |
no | Layout style: kk, fr, nicely, circle, star, grid, or randomly |
|
--style_line |
character | straight |
no | Edge style: straight or curve |
|
--theme_size |
numeric | 0.8 |
no | Theme size placeholder retained for compatibility | |
--title |
character | empty | no | Main plot title |
What ships with it
26 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.
- eval_report_ppi-network-analysis_result.json 17 KB
- references/algorithm.md 8.2 KB
- references/cli-guide.md 8.1 KB
- references/string_cache/10090.protein.aliases.v11.5.txt.gz 13280 KB
- references/string_cache/10090.protein.info.v11.5.txt.gz 1796 KB
- references/string_cache/10090.protein.links.v11.5.txt.gz 82588 KB
- references/string_cache/9606.protein.aliases.v11.5.txt.gz 21218 KB
- references/string_cache/9606.protein.info.v11.5.txt.gz 1857 KB
- references/string_cache/9606.protein.links.v11.5.txt.gz 71014 KB
- references/troubleshooting.md 4.2 KB
- scripts/cli_options.R 86 B
- scripts/core_option_groups.R 1.7 KB
- scripts/functions.R 2.7 KB
- scripts/io.R 3.3 KB
- scripts/main.R 2.0 KB
- scripts/option_validation.R 3.1 KB
- scripts/path_utils.R 2.6 KB
- scripts/plot_option_groups.R 3.9 KB
- scripts/recording.R 173 B
- scripts/run_analysis.R 1.7 KB
- scripts/string_cache.R 5.0 KB
- scripts/utils.R 1.0 KB
- scripts/validation_utils.R 1.2 KB
- scripts/visualization.R 5.6 KB
- tests/data/gene_list.csv 48 B
- tests/run_tests.R 347 B
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.
- 12d ago First seen · 173 lines · 69 tokens per session scan A 80a91b540ff6
ppi-network-analysis is a skill published in the GitHub repository aipoch/medical-research-skills (1,855 stars, last pushed 1mo ago), licensed MIT. It adds 69 tokens to every session and 2,366 once invoked, about $0.0003 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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