Agent Skills: scientific workflows for the AI assistant

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

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