omics-skills

ai-scientist-evaluator

Score completed AI-generated biology or bioinformatics work against its original task and required artifacts. Use when auditing or comparing AI scientist submissions for task completion, scientific validity, and reproducibility.

arxiv-search

Search arXiv through its official API and save local Markdown summaries. Use when finding recent CS, math, physics, or quantitative-biology preprints or resolving arXiv IDs.

beautiful-data-viz

Create publication-quality static charts with matplotlib or seaborn. Use when scientific figures need readable axes, accessible palettes, tight layouts, and high data-ink design.

bio-annotation

Annotate genes or proteins and infer taxonomy from sequence homology. Use when assigning functions, domains, or taxonomic labels to genomes, contigs, or protein sets.

bio-assembly-qc

Assemble genomes or metagenomes and assess assembly quality. Use when turning sequence reads into contigs and reporting completeness, continuity, and contamination evidence.

bio-binning-qc

Bin and refine metagenomic contigs, then assess MAG quality. Use when recovering genomes with QuickBin and checking completeness, contamination, and bin consistency.

bio-fasta-database-curator

Curate and validate FASTA or FAA databases. Use when standardizing headers, merging references, deduplicating sequences, converting GenBank files, or preparing BLAST, MMseqs2, and HMM inputs.

bio-foundation-housekeeping

Add schema-backed metadata validation, normalized Parquet tables, and a DuckDB catalog to a bioinformatics project. Use when an analysis needs LinkML/Pydantic records or a queryable data catalog.

bio-gene-calling

Predict coding sequences and screen assemblies for non-coding RNA features. Use when calling genes in prokaryotic, viral, or eukaryotic assemblies, or when a tRNA, rRNA, or other ncRNA census is needed before functional annotation.

bio-interdomain-hgt

Detect and polarize interdomain horizontal gene transfer with homology, context, and phylogenetic checks. Use when studying lateral gene transfer, virus-host gene exchange, endogenous viral elements, or donor direction.

bio-logic

Assess a scientific claim, study design, method, or interpretation against its evidence. Use when testing causal reasoning, finding methodological bias, weighing alternative explanations, or revising hypotheses.

bio-phylogenomics

Build and validate marker-gene alignments and phylogenetic trees. Use when inferring evolutionary relationships, choosing models, or checking tree support and contamination.

Show all 35 bundled skills

Web & Frontend Listed

bio-prefect-dask-nextflow

Design reproducible bioinformatics pipelines with Prefect plus Dask or Nextflow. Use when scaffolding local, distributed, or scheduler-backed workflows.

bio-protein-clustering-pangenome

Cluster proteins into orthogroups and build pangenome matrices. Use when comparing gene-family presence, absence, expansion, contraction, or core and accessory content across genomes.

bio-reads-qc-mapping

Ingest, quality-control, and map sequencing reads with reproducible outputs. Use when processing raw reads, removing contaminants, or calculating mapping and coverage statistics.

bio-stats-ml-reporting

Analyze biological results with statistics or machine learning and produce validated reports. Use when aggregating features, testing hypotheses, training models, or reporting performance.

bio-structure-annotation

Predict protein or complex structures and annotate proteins by structural similarity. Use when predicting a fold, judging prediction confidence, or finding structural homologs for proteins with weak sequence evidence.

bio-viromics

Detect, quality-control, and classify viral contigs. Use when identifying viruses in assemblies, checking viral completeness and contamination, or assigning viral taxonomy.

bio-workflow-methods-docwriter

Generate reproducible Methods from Nextflow, Snakemake, or CWL run artifacts. Use when documenting exact commands, versions, parameters, QC gates, provenance, and outputs.

API & Backend Listed

bioinformatics-project

Structure reproducible bioinformatics projects with canonical layouts, restartable drivers, pinned environments, provenance, and lab notebooks. Use when starting or reorganizing a genomics project or making a sequencing analysis rerunnable.

API & Backend Listed

biorxiv-search

Search bioRxiv through its official API and filter title, abstract, and author metadata. Use when finding recent biology preprints, scanning date ranges, resolving DOIs, or building author shortlists.

crossref-lookup

Query Crossref for DOI validation, title matching, citation metadata, and bibliography audits. Use when resolving references or cleaning citation records.

csag-extraction

Extract a Conditional Scientific Argumentation Graph and grounded Q&A from a manuscript. Use when representing assertions, contexts, evidence links, and inference steps in machine-readable form.

exploratory-data-analysis

Inspect scientific data and generate a Markdown structure-and-quality report. Use when triaging tabular, array, sequence, HDF5, JSON, or raster files before downstream analysis.

jgi-lakehouse

Query JGI Lakehouse metadata and retrieve JGI genome or read files. Use when linking GOLD, IMG, MycoCosm, Phytozome, PMO, or JAMO identifiers and datasets.

Code & Development Listed

manuscript-review-council

Produce a journal-style peer review of a scientific manuscript with specialist reports and an editor decision. Use when assessing publication readiness, or whether a revision or author response resolves scientific objections.

notebooks

Author, execute, validate, and convert reproducible marimo or Jupyter notebooks. Use when delivering an analysis notebook with all cells run and figures embedded.

pdf-to-md

Convert PDFs and office documents to clean Markdown, with structured bundles for scientific papers. Use when extracting article structure, preparing a manuscript for analysis, or creating CSAG input.

plotly-dashboard-skill

Build production-ready Plotly Dash dashboards. Use when scientific data needs an interactive, consistently themed layout with clear and performant callbacks.

polars-dovmed

Search PMC Open Access and bioRxiv corpora with polars-dovmed. Use when structured, reproducible literature queries should run through the hosted API or local parquet indexes.

Code & Development Listed

proposal-review

Evaluate a proposed AI/ML, computational-biology, or bioscience research project for a funding decision. Use when reviewing a grant, research proposal, or funding application against sponsor criteria, feasibility, budget, and risks.

public-db-lookup

Fetch bounded JSON records from UniProt, NCBI Entrez, NCBI Datasets, MGnify, InterPro, AlphaFold DB, STRING, or ENA over HTTP GET. Use when looking up an accession, taxon, entry, or structure record from a public database.

DevOps & Infrastructure Listed

scientific-impact-assessment

Assess research reach with OpenAlex citations, optional Altmetric data, and journal context. Use when comparing papers, journals, or literature shortlists by influence.

DevOps & Infrastructure Listed

scientific-writing

Draft or edit scientific prose while preserving its claims and evidence. Use when writing manuscript sections, proposal narratives, rebuttals, or response letters, or when checking sentence-level clarity and style.

tracking-taxonomy-updates

Track taxonomy changes and triage sequence assignments across NCBI, GTDB, ICTV, and eukaryotic frameworks. Use when comparing releases, resolving renamed taxa, or routing genomes, bins, and contigs by domain.