The Agent Skills Directory

[INDIRECT_PROMPT_INJECTION]: The skill is designed to process external biological data files (FASTA, GenBank, FASTQ, PDB, etc.), which are untrusted inputs. This functionality, combined with the skill's ability to perform network operations and write files, creates an attack surface for indirect prompt injection. However, this behavior is standard for the bioinformatics domain and the library's intended purpose.
Ingestion points: SKILL.md (Loading and parsing various file formats using Bio.SeqIO, Bio.PDB, Bio.Phylo, and Bio.AlignIO).
Boundary markers: None mentioned in the provided examples.
Capability inventory: The skill utilizes network access via Bio.Entrez and Bio.Blast.NCBIWWW, and file system writes via Bio.SeqIO.write, Bio.Phylo.write, and pandas.to_csv (implicitly through workflow examples).
Sanitization: No explicit sanitization or validation of the content of biological files is shown in the examples.
[EXTERNAL_DOWNLOADS]: The skill references the installation of standard, well-known Python packages (biopython, numpy, matplotlib, pandas) from official registries. It also demonstrates how to programmatically download data from the National Center for Biotechnology Information (NCBI) via its public APIs (Entrez and BLAST), which are established and well-known services in the scientific community.

biopython-molecular-biology