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Skills

Each skill is a directory under skills/ with a required SKILL.md. The frontmatter gives the name and short description; the body gives instructions, inputs, outputs, quality gates, and references. Optional subdirectories hold examples, scripts, tool notes, literature summaries, and reusable assets.

The table below is a reader-facing map. The source SKILL.md files are still canonical.

Bioinformatics and Scientific Analysis

Skill Use when Main result
bio-foundation-housekeeping Starting a new bioinformatics project or normalizing an existing one. A reproducible project scaffold with environments, schemas, manifests, and data cataloging.
exploratory-data-analysis Inspecting an unfamiliar scientific data file before choosing a workflow. A Markdown report covering file type, structure, quality issues, and downstream analysis options.
bio-reads-qc-mapping Ingesting raw reads, trimming or filtering them, and mapping reads to references or assemblies. QC reports, cleaned reads, alignments, and coverage summaries.
bio-assembly-qc Building genome, metagenome, or long-read assemblies. Assemblies with QC metrics and assembly-level interpretation.
tracking-taxonomy-updates Reconciling taxonomy across NCBI, GTDB, ICTV, eukaryote frameworks, and QuickClade-first domain triage. Versioned taxonomy evidence and domain-specific routing decisions.
bio-binning-qc Recovering and refining metagenomic bins. MAG/bin sets with completeness, contamination, and chimerism checks.
bio-gene-calling Calling genes and basic features in prokaryotic, viral, or eukaryotic sequence sets. Predicted CDS, protein FASTA files, GFF annotations, and feature summaries.
bio-annotation Assigning function and taxonomy from sequence homology. Functional annotations, taxonomy calls, and evidence-ranked hit tables.
bio-fasta-database-curator Preparing sequence databases for BLAST, DIAMOND, MMseqs2, HMMER, pyhmmer, or custom reference searches. Curated FASTA/FAA files, stable headers, deduplicated records, mapping tables, and database statistics.
bio-phylogenomics Building marker-gene or protein alignments and trees. Alignments, phylogenetic trees, topology checks, and interpretation.
bio-protein-clustering-pangenome Clustering proteins into orthogroups or building pangenome matrices. Orthogroups, copy-number matrices, and core/accessory gene summaries.
bio-structure-annotation Adding structure-based evidence to protein interpretation. Predicted or searched structures, fold-level annotations, and confidence notes.
bio-viromics Detecting, classifying, and QCing viral contigs. Viral calls, quality summaries, taxonomy evidence, and candidate discovery tables.
bio-stats-ml-reporting Aggregating results, training models, or preparing final analysis reports. Validated statistics, model outputs, plots, and a reproducible report.
bio-prefect-dask-nextflow Designing executable bioinformatics workflows. Prefect+Dask or Nextflow scaffolds with clear execution boundaries.
bio-workflow-methods-docwriter Turning workflow artifacts into a Methods section. Reproducible Methods text with commands, versions, parameters, QC gates, and outputs.
bio-logic Auditing scientific reasoning, study design, bias, or strength of evidence. A structured critique with uncertainty, alternative explanations, and follow-up checks.
jgi-lakehouse Querying JGI Lakehouse, GOLD, IMG, Mycocosm, or Phytozome data. SQL-backed metadata pulls and, when allowed, downloaded IMG genome files.

Literature, Metadata, and APIs

Skill Use when Main result
polars-dovmed Searching PMC Open Access and bioRxiv with structured literature queries. Source-backed literature summaries when users provide API access or local parquet corpora prepared with upstream polars-dovmed.
arxiv-search Searching recent or specific arXiv preprints. Local Markdown summaries from arXiv metadata and IDs.
biorxiv-search Searching bioRxiv preprints by keyword, date range, DOI, or author. Filtered preprint shortlists with bioRxiv-native metadata.
crossref-lookup Validating DOIs or matching titles to citation metadata. Crossref records, DOI matches, and bibliography cleanup evidence.
scientific-impact-assessment Comparing papers, journals, or literature shortlists by influence. OpenAlex citation counts, optional Altmetric context, and impact summaries.
get-api-docs Checking current API or SDK behavior before coding against a fast-moving interface. Fresh documentation snippets gathered through the chub CLI.

Writing, Review, and Evaluation

Skill Use when Main result
scientific-writing Drafting, revising, or reviewing manuscripts, response letters, and grounded scientific prose. A claim-safe draft or revision plan that stays tied to supplied evidence.
csag-extraction Converting manuscripts into structured Conditional Scientific Argumentation Graphs. Schema-valid claim/evidence/inference graphs with TextSpan grounding, validation reports, and paper-grounded Q&A items.
manuscript-review-council Running a multi-angle manuscript review. Parallel specialist reviews, disagreement checks, and an editor synthesis.
proposal-review Reviewing grant, project, or funding proposals. A decision-ready critique of strengths, risks, missing evidence, and fundability.
ai-scientist-evaluator Evaluating finished outputs from one or more AI scientists. A scored audit of rigor, reproducibility, novelty, task completion, and publication readiness.

Visualization and Notebooks

Skill Use when Main result
notebooks Building or converting reproducible marimo or Jupyter notebooks. A fully executed notebook with embedded figures and clear analysis flow.
beautiful-data-viz Producing publication-quality matplotlib or seaborn figures. High-data-ink static figures with readable axes, direct labels where feasible, tight layout, and appropriate palettes.
plotly-dashboard-skill Building interactive Plotly Dash dashboards. A production-ready dashboard layout with themed components and performant callbacks.

The source directory for every skill is available under skills/. When editing a skill, keep the SKILL.md frontmatter name equal to the directory name and rebuild the catalog afterward.