The Agent Skills Directory

[INDIRECT_PROMPT_INJECTION]: The skill is designed to ingest and process data from various external biological file formats and databases, creating a potential vector for indirect prompt injection if those files contain adversarial instructions.
Ingestion points: The skill utilizes SeqIO.parse, Entrez.read, NCBIXML.read, PDBParser.get_structure, and Phylo.read to load data from external sources across several reference files.
Boundary markers: The provided code snippets and instructions do not implement explicit delimiters or warnings to ignore instructions embedded within the processed data.
Capability inventory: The skill has the capability to execute local binaries (e.g., BLAST+, MUSCLE) via command-line wrappers, perform network operations to NCBI services, and write files to the local system.
Sanitization: There is no evidence of input validation or sanitization of data fields before they are used in logic or displayed to the user.
[COMMAND_EXECUTION]: The skill provides instructions for wrapping and executing external bioinformatics command-line tools.
Evidence: The reference files (references/alignment.md, references/blast.md, references/structure.md) document the use of ClustalOmegaCommandline, MuscleCommandline, NcbiblastnCommandline, and the DSSP executable for sequence alignment, local BLAST searches, and secondary structure assignment.
[EXTERNAL_DOWNLOADS]: The skill facilitates the download of biological data and software dependencies from well-known scientific services.
Evidence: Instructions include installing biopython via a package manager and using Biopython's internal modules (Bio.Entrez, Bio.PDB.PDBList) to fetch sequences and protein structures from NCBI and PDB repositories.

biopython