The Agent Skills Directory

[PROMPT_INJECTION]: The skill processes complex biological data from external files and remote databases, which introduces a surface for indirect prompt injection.
Ingestion points: Uses Bio.SeqIO.parse in references/sequence-io.md, Bio.Entrez.read in references/databases.md, and Bio.Blast.NCBIXML.read in references/blast.md to ingest external sequence data and search results.
Boundary markers: Code examples do not demonstrate the use of delimiters or instructions to ignore embedded commands within processed data.
Capability inventory: The skill can execute local binaries via subprocess wrappers (e.g., NcbiblastnCommandline in references/blast.md) and perform file system operations (e.g., SeqIO.write in references/sequence-io.md).
Sanitization: Relies on standard Biopython library parsers without additional sanitization for potentially malicious content within sequences or metadata fields.
[COMMAND_EXECUTION]: The skill uses command-line wrappers to execute local bioinformatics binaries.
Evidence: Wrappers like NcbiblastnCommandline, ClustalOmegaCommandline, and MuscleCommandline in references/blast.md and references/alignment.md are used to run external tools such as BLAST+, Clustal Omega, and MUSCLE.
[EXTERNAL_DOWNLOADS]: The skill interacts with well-known biological databases and search services.
Evidence: Facilitates network requests to official NCBI (National Center for Biotechnology Information) endpoints using Bio.Entrez and Bio.Blast.NCBIWWW to retrieve records and perform remote searches.

biopython