The Agent Skills Directory

[COMMAND_EXECUTION]: The skill provides examples of using the subprocess module to call external bioinformatics tools like blastn, clustalo, and muscle. The documentation explicitly advises users to maintain fixed argument lists and avoid constructing command strings from unsanitized input, which is a key security measure against command injection.
[EXTERNAL_DOWNLOADS]: The skill guides the installation of the well-known biopython library and facilitates data retrieval from official NCBI (National Center for Biotechnology Information) web services. These network operations are standard requirements for scientific workflows and are performed through legitimate, authenticated channels.
[SAFE]: The skill processes biological data from external files (e.g., FASTA, PDB, GenBank). It demonstrates high security awareness by recommending the use of Biopython version 1.87 or later to address a specific historical XML parsing vulnerability (CVE-2025-68463), ensuring that the agent uses patched tools when handling potentially untrusted data.

biopython