---
title: "Agent Skills: scientific workflows for the AI assistant"
description: "Agent Skills give the Biocompile assistant written guides for PubMed, UniProt, Ensembl, PDB, BLAST and RNA-seq work, and let your organization add its own."
url: https://www.biocompile.com/docs/skills/
section: "Projects and assistant"
last_updated: 2026-10-23
app_url: https://app.biocompile.com/skills
---

# Agent Skills: scientific workflows for the AI assistant

> Agent Skills give the Biocompile assistant written guides for PubMed, UniProt, Ensembl, PDB, BLAST and RNA-seq work, and let your organization add its own.

Source: https://www.biocompile.com/docs/skills/. Index of all Biocompile documentation: https://www.biocompile.com/docs/index.md

An Agent Skill is a written guide that tells the Biocompile assistant how to handle one kind
of task: which database or method to use, how to prepare inputs, and how to read and report
the results. Biocompile ships curated skills for public databases, literature search,
structures, sequences and common analyses, and your organization can add its own.

Open **Agents → Agent Skills** to see every skill available to you.

## How the assistant uses skills

You do not pick a skill for each request. Describe the goal in a conversation and name your
input files. The assistant looks for a skill that matches and reads its guide before it
starts.

> Find homologues of the protein in `lipase_candidate.fasta` and tell me which
> characterized enzymes it is closest to.

> Plan a thermostability engineering campaign for the xylanase in `xynA.pdb` and suggest
> stabilizing mutations to test first.

The assistant only uses skills that its agent profile allows. In **Agents → Agent Profiles**,
open a profile and select its **Skills**. They are grouped into
**Biocompile skills**, which are available to every organization, and
**Organization skills**, which your organization created.

## Skills Biocompile provides

| Kind of task | Skills cover |
|---|---|
| Literature | PubMed abstracts and full text, OpenAlex works and citation metrics, arXiv, and bioRxiv and medRxiv preprints |
| Genes and variants | Ensembl identifiers, sequences and variant effect prediction, dbSNP, ClinVar, gnomAD frequencies and constraint, GTEx expression and eQTLs |
| Gene regulation | ENCODE candidate cis-regulatory elements, UCSC conservation scores and binding sites, JASPAR binding profiles, UniBind binding sites |
| Proteins and pathways | UniProt, InterPro domains and families, STRING interactions, Reactome pathways, QuickGO annotations, Human Protein Atlas, EMBL-EBI ontology lookup |
| Structures | PDB search and download, AlphaFold Database predictions and confidence, Foldseek structural search, PyMOL rendering and analysis |
| Chemistry, drugs and trials | ChEMBL, PubChem, Open Targets, openFDA, ClinicalTrials.gov |
| Sequences | NCBI sequence retrieval, protein homology search with MMseqs2 or BLAST, protein multiple sequence alignment with Clustal Omega, choosing an alignment approach |
| Analysis and design | RNA-seq analysis (bulk, single-cell and spatial), enzyme thermostability engineering, synthetic bacterial promoter design, model selection for biomedical tabular data |
| Lab and publication work | Laboratory protocol authoring with parameters, controls and acceptance criteria, publication-ready scientific figures |

Biocompile skills are read-only. Open one from the list to read its guide.

## Create an organization skill

1. Open **Agents → Agent Skills** and choose **New skill → Organization skill**.
2. Enter a **Name**. The assistant refers to skills by name, so it must be unique.
3. Add a one-sentence **Short description** and any **Tags**.
4. Write the **Guide (markdown)**: the approach, the inputs to check, and how results
   should be reported.
5. Choose **Create**.

An organization skill with the same name as a Biocompile skill takes its place for your
organization. Deleting a skill removes the assistant's access to its guide immediately.

## Limitations

- Some skills run helper code. Your organization's security policy can block a helper, and
  the policy preview lists the skill helpers a change blocks. See
  [Review and activate a change](https://www.biocompile.com/docs/organization-security.md#review-and-activate-a-change).
- A skill guides the assistant's approach; it does not make the underlying database or
  method more reliable than its source.

## Common questions

### Do I have to choose a skill for each request?

No. Describe the goal in a conversation and the assistant looks for a matching skill and
reads its guide before it starts. The agent profile decides which skills it may use.

### Can my organization add its own skills?

Yes. Under **Agents → Agent Skills**, choose **New skill → Organization skill** and write a
guide the assistant follows across your organization. A guide can cover your lab's plasmid
naming rules or your standard qPCR analysis.

### Can an organization skill replace a Biocompile skill?

Yes. An organization skill with the same name as a Biocompile skill takes its place for
your organization.

## Related

- [AI research assistant: ask your files and the literature](https://www.biocompile.com/docs/ai-research-assistant.md)
- [Organization security: AI models, tools and EU processing](https://www.biocompile.com/docs/organization-security.md)

## Get access to Biocompile

Biocompile is used in the browser at https://app.biocompile.com. It is free to start and no payment method is required: sign up at https://app.biocompile.com/signup?mc_cta=docs-md&mc_path=/docs/skills.md. If your team already uses Biocompile, ask an organization admin to invite you. Research teams that want hands-on setup can apply for the founder-led pilot at https://www.biocompile.com/pilot/. Questions: https://www.biocompile.com/contact/.