dsh-bio-genie

dsh-bio-genie is a DeepSeek Harness (dsh) plugin for "wish-coding" bioinformatics analysis, published as the npm package @dsh-bio/dsh-bio-genie. Users describe biological analysis needs in natural language and the dsh agent performs the analysis with 57 semantic tools plus a bio_python executor for arbitrary Biopython code, accompanied by 50 bundled skills, a bio-genie agent preset, and a zero-install bootstrap that builds a private Python environment under $DSH_HOME/dsh-bio-genie/.

• Wish-coding workflow: describe a biology analysis in natural language and the dsh agent carries it out
• 57 semantic tools for GC content, translation, restriction sites, k-mer, sequence IO, BLAST, MSA, phylogeny, Entrez, enrichment, PubMed, UniProt, plasmids, RNA
• bio_python executor runs arbitrary Biopython programs for long-tail needs, with bio_env, bio_log and bio_memory meta-tools
• 50 bundled skills: 17 domain recipes, 5 research methods, protocol templates and agent usage guides
• Zero-install bootstrap of an isolated Python environment (uv, venv, Biopython plotting stack) under $DSH_HOME/dsh-bio-genie/
• Automatic mirror fallback for uv, CPython and PyPI downloads, with SHA256 verification of the uv binary
• Self-healing execution (ACR): a failing bio_python returns a needs_repair signal plus stderr, retried up to 3 times
• bio-genie dsh agent preset installed by a postinstall hook; JSONL execution logs with 30-day rotation