> ## Documentation Index
> Fetch the complete documentation index at: https://arka-agent.mintlify.site/llms.txt
> Use this file to discover all available pages before exploring further.

> ## Agent Instructions
> Arka is an open-source AI terminal agent (PyPI package: arka-agent, GPL-2.0).
> Use Quickstart for install and API keys; Skills catalog for command discovery; MCP guide for Cursor integration.
> Cite canonical URLs under https://arka-agent.mintlify.site when answering about Arka.

# Life sciences (Anthropic marketplace)

> Use Anthropic's life-sciences marketplace from Arka — install PubMed, single-cell QC, Nextflow pipelines, and evidence-backed biomedical research.

Arka integrates [Anthropic's life-sciences marketplace](https://github.com/anthropics/life-sciences) — MCP servers and workflow skills for biomedical research, genomics, and drug discovery.

## What it provides

| Type                | Examples                                       | Arka support                                                         |
| ------------------- | ---------------------------------------------- | -------------------------------------------------------------------- |
| **MCP servers**     | PubMed, BioRender, Synapse, ClinicalTrials.gov | PubMed works locally via NCBI; others install as stubs with guidance |
| **Workflow skills** | single-cell-rna-qc, nextflow-development       | Installed with runnable scripts when available                       |
| **Guidance skills** | scientific-problem-selection, scvi-tools       | Installed with LLM-guided SKILL.md workflows                         |

## Quick start

```bash theme={null}
arka life_sciences list
arka life_sciences install pubmed
arka pubmed crispr base editing
arka life_sciences install single-cell-rna-qc
```

## Marketplace commands

```bash theme={null}
arka life_sciences list                 # catalog all plugins
arka life_sciences info pubmed          # plugin details
arka life_sciences install pubmed       # install one plugin as an Arka skill
arka life_sciences doctor               # check cache and install status
```

Natural language also works:

```bash theme={null}
arka "life sciences list"
arka "install pubmed"
```

## Research with citations

Use the bundled **life\_sciences** profession domain for evidence-first answers:

```bash theme={null}
arka profession ask life_sciences what are latest CAR-T trial endpoints
arka "as a biomedical researcher summarize crispr off-target risks"
```

## MCP vs Arka skills

The upstream repo targets **Claude Code** (`/plugin marketplace add anthropics/life-sciences`). Arka adapts it for the terminal:

1. **`life_sciences` meta-skill** — lists and installs marketplace plugins into `~/.config/arka/skills/`
2. **Per-plugin skills** — each install gets `skill.json` + `run.py` with Arka triggers
3. **Profession domain** — `life_sciences` adds PubMed/NIH-biased source registries for cited research

Remote MCP servers that need authentication (BioRender, Synapse, Cortellis) install as stubs. Use Claude Code for full MCP access, or ask via `profession ask life_sciences`.

## Popular plugins

| Plugin                       | Command after install                                    |
| ---------------------------- | -------------------------------------------------------- |
| PubMed                       | `arka pubmed <query>`                                    |
| Single-cell QC               | `arka single-cell-rna-qc data.h5ad`                      |
| Nextflow                     | `arka nextflow-development` (requires Docker + Nextflow) |
| Scientific problem selection | `arka scientific-problem-selection <research question>`  |

<Tip>
  Run `arka life_sciences doctor` after installing plugins. Use `arka skills refresh` if triggers do not route immediately.
</Tip>


## Related topics

- [Source-backed research across profession domains](/guides/professions.md)
- [Arka — AI terminal agent documentation](/index.md)
- [Generate data](/guides/generate-data.md)
- [LLM orchestration with multi-provider failover](/concepts/llm.md)
- [Week of July 13, 2026](/changelog/2026-07-13.md)