The Agent Skills Directory

[COMMAND_EXECUTION]: The skill provides instructions and numerous code examples for executing external bioinformatics command-line tools via the Python subprocess module.
Specific examples include the execution of clustalo, muscle, blastn, makeblastdb, and dssp using explicit argument lists.
These operations depend on standard bioinformatics binaries typically managed separately in a research environment.
[EXTERNAL_DOWNLOADS]: The skill documentation describes and facilitates the programmatic retrieval of data from external biological repositories.
It utilizes Bio.Entrez to search and download records from NCBI (National Center for Biotechnology Information) databases, including PubMed, GenBank, and Protein.
It uses Bio.Blast.NCBIWWW to transmit sequence data to NCBI servers for remote BLAST analysis.
It uses Bio.PDB.PDBList to fetch macromolecular structure files from the Protein Data Bank (PDB).
These network operations target established scientific and governmental infrastructure.
[INDIRECT_PROMPT_INJECTION]: The skill is designed to ingest and process a variety of biological data formats (such as FASTA, GenBank, XML, and PDB) which may be sourced from external, untrusted providers.
Ingestion points: Data enters the context through Bio.SeqIO.parse, Bio.Entrez.read, Bio.Blast.NCBIXML.read, and structural parsers like PDBParser and MMCIFParser.
Capability inventory: The skill has access to the Bash tool and uses subprocess.run to interact with the local operating system.
Sanitization: The skill documentation proactively recommends using Biopython version 1.87 or later to address CVE-2025-68463, a vulnerability related to parsing untrusted Entrez XML files.
Boundary markers: The provided examples do not implement specific boundary markers or instructions to the agent to disregard natural language commands that might be embedded within biological sequence comments or metadata fields.

biopython