omics-skills

agent-browser

Browser automation via agent-browser CLI for web navigation, form filling, screenshots, scraping, login flows, and UI testing.

Critically review, score, compare, and rank one or more AI scientist outputs for biology, bioinformatics, computational life science, or adjacent research tasks. Trigger when the user asks to evaluate notebooks, code, figures, analyses, manuscripts, software, or final reports produced by AI scientists; compare multiple AI scientists on the same task; judge publication readiness; or audit rigor, reproducibility, novelty, and task completion. Do not use this skill to perform the original research task itself unless the user is explicitly asking for a reviewer-style audit of already produced outputs.

arxiv-search

Search arXiv preprints through the official arXiv API and turn arXiv IDs into local Markdown summaries. Use when you need CS, math, physics, or quantitative biology preprints, especially recent submissions that may not yet appear in peer-reviewed literature indexes.

beautiful-data-viz

Create publication-quality matplotlib/seaborn charts with readable axes, tight layout, curated palettes, and Tufte-style high-data-ink design.

bio-annotation

Functional annotation and taxonomy inference from sequence homology.

bio-assembly-qc

Assemble genomes/metagenomes and produce assembly QC artifacts.

bio-binning-qc

Perform metagenomic binning with QuickBin, refinement, and QC with completeness/contamination checks.

bio-fasta-database-curator

Curate, validate, and standardize FASTA/FAA sequence databases: standardize headers, merge databases, remove duplicates, convert GenBank to FASTA, and generate statistics. Use when preparing reference databases for HMM searches, MMseqs2, BLAST, and other bioinformatics workflows.

bio-foundation-housekeeping

Initialize a bioinformatics project scaffold with reproducible environments, schemas, and data cataloging. Use for new projects or repo setup.

bio-gene-calling

Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.

bio-logic

Evaluate scientific rigor, methods, biases, and evidence quality for claims, papers, and study designs.

bio-phylogenomics

Build marker gene alignments and phylogenetic trees.

Show all 36 bundled skills

Web & Frontend Listed

bio-prefect-dask-nextflow

Design and scaffold bioinformatics pipelines using Prefect+Dask for local/distributed execution or Nextflow for HPC schedulers.

bio-protein-clustering-pangenome

Cluster proteins into orthogroups and derive pangenome matrices.

bio-reads-qc-mapping

Ingest, QC, and map reads with reproducible outputs. Use for raw read processing and coverage stats.

bio-stats-ml-reporting

Aggregate results, train ML models, and produce reports with validated references.

bio-structure-annotation

Structure prediction and structure-based annotation.

bio-viromics

Detect, classify, and QC viral contigs.

bio-workflow-methods-docwriter

Generate reproducible Methods documentation from workflow run artifacts (Nextflow/Snakemake/CWL), including exact commands, versions, parameters, QC gates, and outputs.

biorxiv-search

Search bioRxiv preprints through the official bioRxiv API and locally filter titles, abstracts, and authors for keyword queries. Use when you need recent biology preprints, bioRxiv-native metadata, date-range scans, DOI lookups, or author shortlists that may not yet appear in peer-reviewed literature indexes.

API & Backend Listed

crossref-lookup

Query the Crossref REST API for DOI validation, title search, citation metadata, and bibliography audits. Use when you need DOI lookup, title-to-DOI matching, or reference metadata cleanup.

csag-extraction

Extract a CSAG (Conditional Scientific Argumentation Graph) from a manuscript using the canonical argumentation spine (Assertions, EvidenceItems, EvidenceLinks, InferenceSteps) while enforcing CSAG conditionality (no assertion without at least one Context). Also generates paper-grounded Q&A items using bundled QA templates.

exploratory-data-analysis

Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.

API & Backend Listed

get-api-docs

Fetch current API and SDK documentation with the chub CLI. Use when writing or reviewing code against fast-changing APIs, especially when the user asks for the latest or current docs.

handoff

Create a session handoff document for context continuity. Captures work completed, decisions, knowledge, and next steps in docs/handoffs/.

jgi-lakehouse

Queries JGI Lakehouse (Dremio) for genomics metadata from GOLD, IMG, Mycocosm, Phytozome. Downloads genome files from JGI filesystem using IMG taxon OIDs and links JGI taxon OIDs to read files through PMO/GOLD identifiers and JAMO. Use when working with JGI data, GOLD projects, IMG annotations, or downloading genomes.

Code & Development Listed

manuscript-review-council

Run a multi-agent scientific manuscript review with parallel specialist reviewers, disagreement checks, and an editor meta-review. Use when reviewing a manuscript, preprint, revision, or rebuttal in Codex or Claude Code.

notebooks

Author, execute, and deliver reproducible analysis notebooks in marimo (default) or Jupyter, with all cells run end-to-end and figures embedded. Also converts between marimo and Jupyter on request.

pdf-to-md

Convert any PDF (or DOCX/PPTX/XLSX/image) to clean Markdown. For scientific papers, produce the canonical paper-to-md bundle (Markdown plus section_audit.json and article.json) using the remote OCR API when an OCR key is available, or LiteParse v2 locally when it is not. For any non-paper PDF, defer to a fast, local, no-API-key LiteParse v2 conversion. Use when turning a PDF or manuscript into Markdown, extracting article structure, or preparing input for csag-extraction.

pickup

Read and resume from the latest session handoff. Queries memd first when project memory is configured and available, then falls back to docs/handoffs/ for filesystem handoffs. Summarizes both and auto-archives filesystem handoffs.

plotly-dashboard-skill

Build production-ready Plotly Dash dashboards with consistent theming, clear layouts, and performant callbacks.

polars-dovmed

Search the PMC Open Access literature with polars-dovmed. Author structured JSON queries directly, then use the hosted API when an API key is available or fall back to local dovmed scan over PMC, bioRxiv, or both parquet corpora.

Code & Development Listed

proposal-review

Structured, decision-ready review framework for AI/ML, computational biology, and bioscience proposals. Use when evaluating grant, project, or funding proposals.

DevOps & Infrastructure Listed

scientific-impact-assessment

Assess paper and journal impact using OpenAlex citation counts, optional Altmetric data, and curated journal impact-factor references. Use when comparing papers, journals, or literature shortlists by reach and influence.

scientific-writing

Draft, review, and iteratively revise scientific manuscripts with a provider-agnostic multi-agent workflow for Codex and Claude Code. Use for new manuscripts, section rewrites, rebuttals, response letters, manuscript QA, or sentence-level writing reviews when claims must stay grounded in supplied artifacts.

tracking-taxonomy-updates

Track and reconcile taxonomy updates across NCBI, GTDB, ICTV, and community eukaryote frameworks with versioned provenance.